PATH=C:\PlatSDK\Bin\Win64\x86\AMD64;C:\PlatSDK\Bin;C:\PlatSDK\Bin\WinNT;C:\Perl64-5.12\site\bin;C:\Perl64-5.12\bin;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files (x86)\Perforce;C:\mysql\bin Start 2011-04-16T03:51:19 ActivePerl-1200 CPAN-1.9402 LIB=C:\PlatSDK\Lib\AMD64;C:\PlatSDK\Lib\AMD64\atlmfc INCLUDE=C:\PlatSDK\Include;C:\PlatSDK\Include\crt;C:\PlatSDK\Include\crt\sys;C:\PlatSDK\Include\mfc;C:\PlatSDK\Include\atl PATH=C:/CPANFL~1.12/var/libs/bin;C:\PlatSDK\Bin\Win64\x86\AMD64;C:\PlatSDK\Bin;C:\PlatSDK\Bin\WinNT;C:\Perl64-5.12\site\bin;C:\Perl64-5.12\bin;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~1\v1.0;C:\PROGRA~2\Perforce;C:\mysql\bin Going to read 'C:\cpanfly-5.12\var\cpan\Metadata' Database was generated on Fri, 15 Apr 2011 22:29:42 GMT Running make for C/CJ/CJFIELDS/BioPerl-1.6.900.tar.gz Fetching with LWP: http://cpan.nas.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.900.tar.gz Fetching with LWP: http://cpan.nas.activestate.com/authors/id/C/CJ/CJFIELDS/CHECKSUMS Checksum for C:\cpanfly-5.12\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.900.tar.gz ok BioPerl-1.6.900 BioPerl-1.6.900/Build.PL BioPerl-1.6.900/AUTHORS BioPerl-1.6.900/META.json BioPerl-1.6.900/DEPENDENCIES BioPerl-1.6.900/INSTALL.SKIP BioPerl-1.6.900/INSTALL BioPerl-1.6.900/LICENSE BioPerl-1.6.900/README BioPerl-1.6.900/Changes BioPerl-1.6.900/DEPRECATED BioPerl-1.6.900/BioPerl.pm BioPerl-1.6.900/BUGS BioPerl-1.6.900/INSTALL.WIN BioPerl-1.6.900/MANIFEST BioPerl-1.6.900/META.yml BioPerl-1.6.900/maintenance BioPerl-1.6.900/maintenance/check_NAME.pl BioPerl-1.6.900/maintenance/deprecated.pl BioPerl-1.6.900/maintenance/version.pl BioPerl-1.6.900/maintenance/modules.pl BioPerl-1.6.900/maintenance/perltidy.conf BioPerl-1.6.900/maintenance/pod.pl BioPerl-1.6.900/maintenance/README BioPerl-1.6.900/maintenance/module_usage.pl BioPerl-1.6.900/maintenance/ncbi_blast_switches.pl BioPerl-1.6.900/maintenance/dependencies.pl BioPerl-1.6.900/maintenance/authors.pl BioPerl-1.6.900/maintenance/symlink_script.pl BioPerl-1.6.900/maintenance/check_URLs.pl BioPerl-1.6.900/maintenance/cvs2cl_by_file.pl BioPerl-1.6.900/maintenance/find_mod_deps.pl BioPerl-1.6.900/maintenance/big_split BioPerl-1.6.900/maintenance/big_split/file_classification.csv BioPerl-1.6.900/maintenance/big_split/rbuels_notes.txt BioPerl-1.6.900/Bio BioPerl-1.6.900/Bio/AnalysisResultI.pm BioPerl-1.6.900/Bio/IdCollectionI.pm BioPerl-1.6.900/Bio/AnalysisParserI.pm BioPerl-1.6.900/Bio/Seq.pm BioPerl-1.6.900/Bio/AnnotationI.pm BioPerl-1.6.900/Bio/LocationI.pm BioPerl-1.6.900/Bio/PrimarySeq.pm BioPerl-1.6.900/Bio/FeatureHolderI.pm BioPerl-1.6.900/Bio/SearchDist.pm BioPerl-1.6.900/Bio/PhyloNetwork.pm BioPerl-1.6.900/Bio/IdentifiableI.pm BioPerl-1.6.900/Bio/DasI.pm BioPerl-1.6.900/Bio/SimpleAlign.pm BioPerl-1.6.900/Bio/UpdateableSeqI.pm BioPerl-1.6.900/Bio/PullParserI.pm BioPerl-1.6.900/Bio/AnnotationCollectionI.pm BioPerl-1.6.900/Bio/AlignIO.pm BioPerl-1.6.900/Bio/SeqIO.pm BioPerl-1.6.900/Bio/FeatureIO.pm BioPerl-1.6.900/Bio/SeqFeatureI.pm BioPerl-1.6.900/Bio/NexmlIO.pm BioPerl-1.6.900/Bio/Taxonomy.pm BioPerl-1.6.900/Bio/SeqI.pm BioPerl-1.6.900/Bio/PrimarySeqI.pm BioPerl-1.6.900/Bio/Taxon.pm BioPerl-1.6.900/Bio/Range.pm BioPerl-1.6.900/Bio/HandlerBaseI.pm BioPerl-1.6.900/Bio/WebAgent.pm BioPerl-1.6.900/Bio/SeqUtils.pm BioPerl-1.6.900/Bio/DescribableI.pm BioPerl-1.6.900/Bio/Perl.pm BioPerl-1.6.900/Bio/TreeIO.pm BioPerl-1.6.900/Bio/AnalysisI.pm BioPerl-1.6.900/Bio/ClusterI.pm BioPerl-1.6.900/Bio/Biblio.pm BioPerl-1.6.900/Bio/ParameterBaseI.pm BioPerl-1.6.900/Bio/RangeI.pm BioPerl-1.6.900/Bio/DBLinkContainerI.pm BioPerl-1.6.900/Bio/AnnotatableI.pm BioPerl-1.6.900/Bio/OntologyIO.pm BioPerl-1.6.900/Bio/Species.pm BioPerl-1.6.900/Bio/SimpleAnalysisI.pm BioPerl-1.6.900/Bio/SearchIO.pm BioPerl-1.6.900/Bio/MapIO.pm BioPerl-1.6.900/Bio/ClusterIO.pm BioPerl-1.6.900/Bio/SeqAnalysisParserI.pm BioPerl-1.6.900/Bio/LocatableSeq.pm BioPerl-1.6.900/Bio/SeqEvolution BioPerl-1.6.900/Bio/SeqEvolution/EvolutionI.pm BioPerl-1.6.900/Bio/SeqEvolution/Factory.pm BioPerl-1.6.900/Bio/SeqEvolution/DNAPoint.pm BioPerl-1.6.900/Bio/Align BioPerl-1.6.900/Bio/Align/DNAStatistics.pm BioPerl-1.6.900/Bio/Align/StatisticsI.pm BioPerl-1.6.900/Bio/Align/PairwiseStatistics.pm BioPerl-1.6.900/Bio/Align/Utilities.pm BioPerl-1.6.900/Bio/Align/Graphics.pm BioPerl-1.6.900/Bio/Align/AlignI.pm BioPerl-1.6.900/Bio/Align/ProteinStatistics.pm BioPerl-1.6.900/Bio/Factory BioPerl-1.6.900/Bio/Factory/TreeFactoryI.pm BioPerl-1.6.900/Bio/Factory/SequenceStreamI.pm BioPerl-1.6.900/Bio/Factory/ObjectFactory.pm BioPerl-1.6.900/Bio/Factory/FTLocationFactory.pm BioPerl-1.6.900/Bio/Factory/ApplicationFactoryI.pm BioPerl-1.6.900/Bio/Factory/ObjectBuilderI.pm BioPerl-1.6.900/Bio/Factory/SequenceFactoryI.pm BioPerl-1.6.900/Bio/Factory/SeqAnalysisParserFactoryI.pm BioPerl-1.6.900/Bio/Factory/AnalysisI.pm BioPerl-1.6.900/Bio/Factory/SequenceProcessorI.pm BioPerl-1.6.900/Bio/Factory/LocationFactoryI.pm BioPerl-1.6.900/Bio/Factory/MapFactoryI.pm BioPerl-1.6.900/Bio/Factory/SeqAnalysisParserFactory.pm BioPerl-1.6.900/Bio/Factory/DriverFactory.pm BioPerl-1.6.900/Bio/Factory/ObjectFactoryI.pm BioPerl-1.6.900/Bio/Matrix BioPerl-1.6.900/Bio/Matrix/Mlagan.pm BioPerl-1.6.900/Bio/Matrix/MatrixI.pm BioPerl-1.6.900/Bio/Matrix/Generic.pm BioPerl-1.6.900/Bio/Matrix/IO.pm BioPerl-1.6.900/Bio/Matrix/PhylipDist.pm BioPerl-1.6.900/Bio/Matrix/Scoring.pm BioPerl-1.6.900/Bio/Matrix/IO BioPerl-1.6.900/Bio/Matrix/IO/mlagan.pm BioPerl-1.6.900/Bio/Matrix/IO/phylip.pm BioPerl-1.6.900/Bio/Matrix/IO/scoring.pm BioPerl-1.6.900/Bio/Matrix/PSM BioPerl-1.6.900/Bio/Matrix/PSM/PsmHeaderI.pm BioPerl-1.6.900/Bio/Matrix/PSM/SiteMatrix.pm BioPerl-1.6.900/Bio/Matrix/PSM/InstanceSiteI.pm BioPerl-1.6.900/Bio/Matrix/PSM/PsmHeader.pm BioPerl-1.6.900/Bio/Matrix/PSM/SiteMatrixI.pm BioPerl-1.6.900/Bio/Matrix/PSM/PsmI.pm BioPerl-1.6.900/Bio/Matrix/PSM/ProtMatrix.pm BioPerl-1.6.900/Bio/Matrix/PSM/Psm.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO.pm BioPerl-1.6.900/Bio/Matrix/PSM/ProtPsm.pm BioPerl-1.6.900/Bio/Matrix/PSM/InstanceSite.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO BioPerl-1.6.900/Bio/Matrix/PSM/IO/meme.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO/psiblast.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO/masta.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO/mast.pm BioPerl-1.6.900/Bio/Matrix/PSM/IO/transfac.pm BioPerl-1.6.900/Bio/Location BioPerl-1.6.900/Bio/Location/FuzzyLocationI.pm BioPerl-1.6.900/Bio/Location/Split.pm BioPerl-1.6.900/Bio/Location/SplitLocationI.pm BioPerl-1.6.900/Bio/Location/CoordinatePolicyI.pm BioPerl-1.6.900/Bio/Location/Simple.pm BioPerl-1.6.900/Bio/Location/Atomic.pm BioPerl-1.6.900/Bio/Location/Fuzzy.pm BioPerl-1.6.900/Bio/Location/WidestCoordPolicy.pm BioPerl-1.6.900/Bio/Location/AvWithinCoordPolicy.pm BioPerl-1.6.900/Bio/Location/NarrowestCoordPolicy.pm BioPerl-1.6.900/Bio/Annotation BioPerl-1.6.900/Bio/Annotation/Reference.pm BioPerl-1.6.900/Bio/Annotation/Relation.pm BioPerl-1.6.900/Bio/Annotation/SimpleValue.pm BioPerl-1.6.900/Bio/Annotation/Collection.pm BioPerl-1.6.900/Bio/Annotation/Tree.pm BioPerl-1.6.900/Bio/Annotation/DBLink.pm BioPerl-1.6.900/Bio/Annotation/Comment.pm BioPerl-1.6.900/Bio/Annotation/TagTree.pm BioPerl-1.6.900/Bio/Annotation/OntologyTerm.pm BioPerl-1.6.900/Bio/Annotation/StructuredValue.pm BioPerl-1.6.900/Bio/Annotation/TypeManager.pm BioPerl-1.6.900/Bio/Annotation/Target.pm BioPerl-1.6.900/Bio/Annotation/AnnotationFactory.pm BioPerl-1.6.900/Bio/Tools BioPerl-1.6.900/Bio/Tools/SeqPattern.pm BioPerl-1.6.900/Bio/Tools/ipcress.pm BioPerl-1.6.900/Bio/Tools/RandomDistFunctions.pm BioPerl-1.6.900/Bio/Tools/IUPAC.pm BioPerl-1.6.900/Bio/Tools/Blat.pm BioPerl-1.6.900/Bio/Tools/Genewise.pm BioPerl-1.6.900/Bio/Tools/EUtilities.pm BioPerl-1.6.900/Bio/Tools/AlignFactory.pm BioPerl-1.6.900/Bio/Tools/FootPrinter.pm BioPerl-1.6.900/Bio/Tools/Fgenesh.pm BioPerl-1.6.900/Bio/Tools/Coil.pm BioPerl-1.6.900/Bio/Tools/QRNA.pm BioPerl-1.6.900/Bio/Tools/Est2Genome.pm BioPerl-1.6.900/Bio/Tools/tRNAscanSE.pm BioPerl-1.6.900/Bio/Tools/Prints.pm BioPerl-1.6.900/Bio/Tools/Genemark.pm BioPerl-1.6.900/Bio/Tools/GuessSeqFormat.pm BioPerl-1.6.900/Bio/Tools/Lucy.pm BioPerl-1.6.900/Bio/Tools/dpAlign.pm BioPerl-1.6.900/Bio/Tools/Hmmpfam.pm BioPerl-1.6.900/Bio/Tools/Sigcleave.pm BioPerl-1.6.900/Bio/Tools/MZEF.pm BioPerl-1.6.900/Bio/Tools/ERPIN.pm BioPerl-1.6.900/Bio/Tools/AnalysisResult.pm BioPerl-1.6.900/Bio/Tools/ESTScan.pm BioPerl-1.6.900/Bio/Tools/Primer3.pm BioPerl-1.6.900/Bio/Tools/ECnumber.pm BioPerl-1.6.900/Bio/Tools/RNAMotif.pm BioPerl-1.6.900/Bio/Tools/Protparam.pm BioPerl-1.6.900/Bio/Tools/pICalculator.pm BioPerl-1.6.900/Bio/Tools/Eponine.pm BioPerl-1.6.900/Bio/Tools/EPCR.pm BioPerl-1.6.900/Bio/Tools/Profile.pm BioPerl-1.6.900/Bio/Tools/Glimmer.pm BioPerl-1.6.900/Bio/Tools/Grail.pm BioPerl-1.6.900/Bio/Tools/Genomewise.pm BioPerl-1.6.900/Bio/Tools/Geneid.pm BioPerl-1.6.900/Bio/Tools/Seg.pm BioPerl-1.6.900/Bio/Tools/TandemRepeatsFinder.pm BioPerl-1.6.900/Bio/Tools/Genscan.pm BioPerl-1.6.900/Bio/Tools/OddCodes.pm BioPerl-1.6.900/Bio/Tools/isPcr.pm BioPerl-1.6.900/Bio/Tools/SiRNA.pm BioPerl-1.6.900/Bio/Tools/Match.pm BioPerl-1.6.900/Bio/Tools/Infernal.pm BioPerl-1.6.900/Bio/Tools/SeqWords.pm BioPerl-1.6.900/Bio/Tools/RepeatMasker.pm BioPerl-1.6.900/Bio/Tools/pSW.pm BioPerl-1.6.900/Bio/Tools/Signalp.pm BioPerl-1.6.900/Bio/Tools/Promoterwise.pm BioPerl-1.6.900/Bio/Tools/PrositeScan.pm BioPerl-1.6.900/Bio/Tools/CodonTable.pm BioPerl-1.6.900/Bio/Tools/Tmhmm.pm BioPerl-1.6.900/Bio/Tools/TargetP.pm BioPerl-1.6.900/Bio/Tools/SeqStats.pm BioPerl-1.6.900/Bio/Tools/Pseudowise.pm BioPerl-1.6.900/Bio/Tools/GFF.pm BioPerl-1.6.900/Bio/Tools/Gel.pm BioPerl-1.6.900/Bio/Tools/Primer BioPerl-1.6.900/Bio/Tools/Primer/Pair.pm BioPerl-1.6.900/Bio/Tools/Primer/AssessorI.pm BioPerl-1.6.900/Bio/Tools/Primer/Feature.pm BioPerl-1.6.900/Bio/Tools/Primer/Assessor BioPerl-1.6.900/Bio/Tools/Primer/Assessor/Base.pm BioPerl-1.6.900/Bio/Tools/Signalp BioPerl-1.6.900/Bio/Tools/Signalp/ExtendedSignalp.pm BioPerl-1.6.900/Bio/Tools/SiRNA BioPerl-1.6.900/Bio/Tools/SiRNA/Ruleset BioPerl-1.6.900/Bio/Tools/SiRNA/Ruleset/tuschl.pm BioPerl-1.6.900/Bio/Tools/SiRNA/Ruleset/saigo.pm BioPerl-1.6.900/Bio/Tools/Prediction BioPerl-1.6.900/Bio/Tools/Prediction/Exon.pm BioPerl-1.6.900/Bio/Tools/Prediction/Gene.pm BioPerl-1.6.900/Bio/Tools/Run BioPerl-1.6.900/Bio/Tools/Run/RemoteBlast.pm BioPerl-1.6.900/Bio/Tools/Run/StandAloneBlast.pm BioPerl-1.6.900/Bio/Tools/Run/hmmer3.pm BioPerl-1.6.900/Bio/Tools/Run/StandAloneNCBIBlast.pm BioPerl-1.6.900/Bio/Tools/Run/WrapperBase.pm BioPerl-1.6.900/Bio/Tools/Run/GenericParameters.pm BioPerl-1.6.900/Bio/Tools/Run/README BioPerl-1.6.900/Bio/Tools/Run/ParametersI.pm BioPerl-1.6.900/Bio/Tools/Run/StandAloneWUBlast.pm BioPerl-1.6.900/Bio/Tools/Run/WrapperBase BioPerl-1.6.900/Bio/Tools/Run/WrapperBase/CommandExts.pm BioPerl-1.6.900/Bio/Tools/Analysis BioPerl-1.6.900/Bio/Tools/Analysis/SimpleAnalysisBase.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein BioPerl-1.6.900/Bio/Tools/Analysis/Protein/Sopma.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/NetPhos.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/GOR4.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/HNN.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/Scansite.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/Mitoprot.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/Domcut.pm BioPerl-1.6.900/Bio/Tools/Analysis/Protein/ELM.pm BioPerl-1.6.900/Bio/Tools/Analysis/DNA BioPerl-1.6.900/Bio/Tools/Analysis/DNA/ESEfinder.pm BioPerl-1.6.900/Bio/Tools/Sim4 BioPerl-1.6.900/Bio/Tools/Sim4/Results.pm BioPerl-1.6.900/Bio/Tools/Sim4/Exon.pm BioPerl-1.6.900/Bio/Tools/HMMER BioPerl-1.6.900/Bio/Tools/HMMER/Results.pm BioPerl-1.6.900/Bio/Tools/HMMER/Set.pm BioPerl-1.6.900/Bio/Tools/HMMER/Domain.pm BioPerl-1.6.900/Bio/Tools/SeqPattern BioPerl-1.6.900/Bio/Tools/SeqPattern/Backtranslate.pm BioPerl-1.6.900/Bio/Tools/Alignment BioPerl-1.6.900/Bio/Tools/Alignment/Consed.pm BioPerl-1.6.900/Bio/Tools/Alignment/Trim.pm BioPerl-1.6.900/Bio/Tools/EMBOSS BioPerl-1.6.900/Bio/Tools/EMBOSS/Palindrome.pm BioPerl-1.6.900/Bio/Tools/EUtilities BioPerl-1.6.900/Bio/Tools/EUtilities/EUtilParameters.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Summary.pm BioPerl-1.6.900/Bio/Tools/EUtilities/HistoryI.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Info.pm BioPerl-1.6.900/Bio/Tools/EUtilities/History.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Link.pm BioPerl-1.6.900/Bio/Tools/EUtilities/EUtilDataI.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Query.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Query BioPerl-1.6.900/Bio/Tools/EUtilities/Query/GlobalQuery.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Summary BioPerl-1.6.900/Bio/Tools/EUtilities/Summary/ItemContainerI.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Summary/DocSum.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Summary/Item.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Link BioPerl-1.6.900/Bio/Tools/EUtilities/Link/UrlLink.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Link/LinkSet.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Info BioPerl-1.6.900/Bio/Tools/EUtilities/Info/FieldInfo.pm BioPerl-1.6.900/Bio/Tools/EUtilities/Info/LinkInfo.pm BioPerl-1.6.900/Bio/Tools/Spidey BioPerl-1.6.900/Bio/Tools/Spidey/Results.pm BioPerl-1.6.900/Bio/Tools/Spidey/Exon.pm BioPerl-1.6.900/Bio/Tools/Phylo BioPerl-1.6.900/Bio/Tools/Phylo/Gumby.pm BioPerl-1.6.900/Bio/Tools/Phylo/Molphy.pm BioPerl-1.6.900/Bio/Tools/Phylo/Gerp.pm BioPerl-1.6.900/Bio/Tools/Phylo/PAML.pm BioPerl-1.6.900/Bio/Tools/Phylo/Molphy BioPerl-1.6.900/Bio/Tools/Phylo/Molphy/Result.pm BioPerl-1.6.900/Bio/Tools/Phylo/Phylip BioPerl-1.6.900/Bio/Tools/Phylo/Phylip/ProtDist.pm BioPerl-1.6.900/Bio/Tools/Phylo/PAML BioPerl-1.6.900/Bio/Tools/Phylo/PAML/Codeml.pm BioPerl-1.6.900/Bio/Tools/Phylo/PAML/Result.pm BioPerl-1.6.900/Bio/Tools/Phylo/PAML/ModelResult.pm BioPerl-1.6.900/Bio/Cluster BioPerl-1.6.900/Bio/Cluster/ClusterFactory.pm BioPerl-1.6.900/Bio/Cluster/FamilyI.pm BioPerl-1.6.900/Bio/Cluster/SequenceFamily.pm BioPerl-1.6.900/Bio/Cluster/UniGene.pm BioPerl-1.6.900/Bio/Cluster/UniGeneI.pm BioPerl-1.6.900/Bio/Seq BioPerl-1.6.900/Bio/Seq/Quality.pm BioPerl-1.6.900/Bio/Seq/RichSeqI.pm BioPerl-1.6.900/Bio/Seq/SeqFactory.pm BioPerl-1.6.900/Bio/Seq/MetaI.pm BioPerl-1.6.900/Bio/Seq/QualI.pm BioPerl-1.6.900/Bio/Seq/EncodedSeq.pm BioPerl-1.6.900/Bio/Seq/Meta.pm BioPerl-1.6.900/Bio/Seq/RichSeq.pm BioPerl-1.6.900/Bio/Seq/LargePrimarySeq.pm BioPerl-1.6.900/Bio/Seq/SeqBuilder.pm BioPerl-1.6.900/Bio/Seq/LargeLocatableSeq.pm BioPerl-1.6.900/Bio/Seq/BaseSeqProcessor.pm BioPerl-1.6.900/Bio/Seq/SeqWithQuality.pm BioPerl-1.6.900/Bio/Seq/PrimedSeq.pm BioPerl-1.6.900/Bio/Seq/TraceI.pm BioPerl-1.6.900/Bio/Seq/PrimaryQual.pm BioPerl-1.6.900/Bio/Seq/LargeSeq.pm BioPerl-1.6.900/Bio/Seq/LargeSeqI.pm BioPerl-1.6.900/Bio/Seq/SeqFastaSpeedFactory.pm BioPerl-1.6.900/Bio/Seq/SequenceTrace.pm BioPerl-1.6.900/Bio/Seq/Meta BioPerl-1.6.900/Bio/Seq/Meta/Array.pm BioPerl-1.6.900/Bio/Index BioPerl-1.6.900/Bio/Index/SwissPfam.pm BioPerl-1.6.900/Bio/Index/Hmmer.pm BioPerl-1.6.900/Bio/Index/GenBank.pm BioPerl-1.6.900/Bio/Index/Blast.pm BioPerl-1.6.900/Bio/Index/AbstractSeq.pm BioPerl-1.6.900/Bio/Index/Fasta.pm BioPerl-1.6.900/Bio/Index/Qual.pm BioPerl-1.6.900/Bio/Index/Abstract.pm BioPerl-1.6.900/Bio/Index/Fastq.pm BioPerl-1.6.900/Bio/Index/EMBL.pm BioPerl-1.6.900/Bio/Index/Stockholm.pm BioPerl-1.6.900/Bio/Index/Swissprot.pm BioPerl-1.6.900/Bio/Index/BlastTable.pm BioPerl-1.6.900/Bio/CodonUsage BioPerl-1.6.900/Bio/CodonUsage/Table.pm BioPerl-1.6.900/Bio/CodonUsage/IO.pm BioPerl-1.6.900/Bio/Phenotype BioPerl-1.6.900/Bio/Phenotype/Correlate.pm BioPerl-1.6.900/Bio/Phenotype/Phenotype.pm BioPerl-1.6.900/Bio/Phenotype/PhenotypeI.pm BioPerl-1.6.900/Bio/Phenotype/Measure.pm BioPerl-1.6.900/Bio/Phenotype/MeSH BioPerl-1.6.900/Bio/Phenotype/MeSH/Term.pm BioPerl-1.6.900/Bio/Phenotype/MeSH/Twig.pm BioPerl-1.6.900/Bio/Phenotype/OMIM BioPerl-1.6.900/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm BioPerl-1.6.900/Bio/Phenotype/OMIM/OMIMparser.pm BioPerl-1.6.900/Bio/Phenotype/OMIM/MiniMIMentry.pm BioPerl-1.6.900/Bio/Phenotype/OMIM/OMIMentry.pm BioPerl-1.6.900/Bio/Root BioPerl-1.6.900/Bio/Root/Build.pm BioPerl-1.6.900/Bio/Root/Version.pm BioPerl-1.6.900/Bio/Root/RootI.pm BioPerl-1.6.900/Bio/Root/Utilities.pm BioPerl-1.6.900/Bio/Root/Exception.pm BioPerl-1.6.900/Bio/Root/Test.pm BioPerl-1.6.900/Bio/Root/Root.pm BioPerl-1.6.900/Bio/Root/IO.pm BioPerl-1.6.900/Bio/Root/HTTPget.pm BioPerl-1.6.900/Bio/Root/Storable.pm BioPerl-1.6.900/Bio/Root/Test BioPerl-1.6.900/Bio/Root/Test/Warn.pm BioPerl-1.6.900/Bio/DB BioPerl-1.6.900/Bio/DB/CUTG.pm BioPerl-1.6.900/Bio/DB/DBFetch.pm BioPerl-1.6.900/Bio/DB/LocationI.pm BioPerl-1.6.900/Bio/DB/EUtilities.pm BioPerl-1.6.900/Bio/DB/FileCache.pm BioPerl-1.6.900/Bio/DB/GenBank.pm BioPerl-1.6.900/Bio/DB/SwissProt.pm BioPerl-1.6.900/Bio/DB/Flat.pm BioPerl-1.6.900/Bio/DB/UpdateableSeqI.pm BioPerl-1.6.900/Bio/DB/InMemoryCache.pm BioPerl-1.6.900/Bio/DB/HIV.pm BioPerl-1.6.900/Bio/DB/BioFetch.pm BioPerl-1.6.900/Bio/DB/BiblioI.pm BioPerl-1.6.900/Bio/DB/Expression.pm BioPerl-1.6.900/Bio/DB/NCBIHelper.pm BioPerl-1.6.900/Bio/DB/GenericWebAgent.pm BioPerl-1.6.900/Bio/DB/WebDBSeqI.pm BioPerl-1.6.900/Bio/DB/SeqFeature.pm BioPerl-1.6.900/Bio/DB/Taxonomy.pm BioPerl-1.6.900/Bio/DB/SeqI.pm BioPerl-1.6.900/Bio/DB/GenPept.pm BioPerl-1.6.900/Bio/DB/Fasta.pm BioPerl-1.6.900/Bio/DB/SeqVersion.pm BioPerl-1.6.900/Bio/DB/Qual.pm BioPerl-1.6.900/Bio/DB/RandomAccessI.pm BioPerl-1.6.900/Bio/DB/MeSH.pm BioPerl-1.6.900/Bio/DB/TFBS.pm BioPerl-1.6.900/Bio/DB/EMBL.pm BioPerl-1.6.900/Bio/DB/Failover.pm BioPerl-1.6.900/Bio/DB/Universal.pm BioPerl-1.6.900/Bio/DB/EntrezGene.pm BioPerl-1.6.900/Bio/DB/SeqHound.pm BioPerl-1.6.900/Bio/DB/QueryI.pm BioPerl-1.6.900/Bio/DB/RefSeq.pm BioPerl-1.6.900/Bio/DB/Registry.pm BioPerl-1.6.900/Bio/DB/Ace.pm BioPerl-1.6.900/Bio/DB/GFF.pm BioPerl-1.6.900/Bio/DB/ReferenceI.pm BioPerl-1.6.900/Bio/DB/Flat BioPerl-1.6.900/Bio/DB/Flat/BDB.pm BioPerl-1.6.900/Bio/DB/Flat/BinarySearch.pm BioPerl-1.6.900/Bio/DB/Flat/BDB BioPerl-1.6.900/Bio/DB/Flat/BDB/embl.pm BioPerl-1.6.900/Bio/DB/Flat/BDB/genbank.pm BioPerl-1.6.900/Bio/DB/Flat/BDB/swiss.pm BioPerl-1.6.900/Bio/DB/Flat/BDB/fasta.pm BioPerl-1.6.900/Bio/DB/HIV BioPerl-1.6.900/Bio/DB/HIV/lanl-schema.xml BioPerl-1.6.900/Bio/DB/HIV/HIVQueryHelper.pm BioPerl-1.6.900/Bio/DB/HIV/HIVAnnotProcessor.pm BioPerl-1.6.900/Bio/DB/Query BioPerl-1.6.900/Bio/DB/Query/GenBank.pm BioPerl-1.6.900/Bio/DB/Query/WebQuery.pm BioPerl-1.6.900/Bio/DB/Query/HIVQuery.pm BioPerl-1.6.900/Bio/DB/Expression BioPerl-1.6.900/Bio/DB/Expression/geo.pm BioPerl-1.6.900/Bio/DB/GFF BioPerl-1.6.900/Bio/DB/GFF/Aggregator.pm BioPerl-1.6.900/Bio/DB/GFF/Featname.pm BioPerl-1.6.900/Bio/DB/GFF/Segment.pm BioPerl-1.6.900/Bio/DB/GFF/Typename.pm BioPerl-1.6.900/Bio/DB/GFF/RelSegment.pm BioPerl-1.6.900/Bio/DB/GFF/Homol.pm BioPerl-1.6.900/Bio/DB/GFF/Feature.pm BioPerl-1.6.900/Bio/DB/GFF/Util BioPerl-1.6.900/Bio/DB/GFF/Util/Binning.pm BioPerl-1.6.900/Bio/DB/GFF/Util/Rearrange.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator BioPerl-1.6.900/Bio/DB/GFF/Aggregator/coding.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/gene.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_acembly.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_refgene.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/match.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/processed_transcript.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_genscan.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/clone.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/none.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/alignment.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_softberry.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_unigene.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/orf.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/so_transcript.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/transcript.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm BioPerl-1.6.900/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor BioPerl-1.6.900/Bio/DB/GFF/Adaptor/berkeleydb.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/ace.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/biofetch_oracle.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/memory.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/biofetch.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/berkeleydb BioPerl-1.6.900/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/memory BioPerl-1.6.900/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/memory/iterator.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/oracleace.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/oracle.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/iterator.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/pg.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/mysql.pm BioPerl-1.6.900/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm BioPerl-1.6.900/Bio/DB/SeqFeature BioPerl-1.6.900/Bio/DB/SeqFeature/NormalizedFeature.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Segment.pm BioPerl-1.6.900/Bio/DB/SeqFeature/NormalizedFeatureI.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store.pm BioPerl-1.6.900/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store BioPerl-1.6.900/Bio/DB/SeqFeature/Store/berkeleydb.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/GFF3Loader.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/GFF2Loader.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/LoadHelper.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/berkeleydb3.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/Loader.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/bdb.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/memory.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/DBI BioPerl-1.6.900/Bio/DB/SeqFeature/Store/DBI/Pg.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/DBI/Iterator.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/DBI/SQLite.pm BioPerl-1.6.900/Bio/DB/SeqFeature/Store/DBI/mysql.pm BioPerl-1.6.900/Bio/DB/TFBS BioPerl-1.6.900/Bio/DB/TFBS/transfac_pro.pm BioPerl-1.6.900/Bio/DB/Taxonomy BioPerl-1.6.900/Bio/DB/Taxonomy/entrez.pm BioPerl-1.6.900/Bio/DB/Taxonomy/list.pm BioPerl-1.6.900/Bio/DB/Taxonomy/flatfile.pm BioPerl-1.6.900/Bio/DB/Biblio BioPerl-1.6.900/Bio/DB/Biblio/soap.pm BioPerl-1.6.900/Bio/DB/Biblio/eutils.pm BioPerl-1.6.900/Bio/DB/Biblio/biofetch.pm BioPerl-1.6.900/Bio/DB/SeqVersion BioPerl-1.6.900/Bio/DB/SeqVersion/gi.pm BioPerl-1.6.900/Bio/PopGen BioPerl-1.6.900/Bio/PopGen/Utilities.pm BioPerl-1.6.900/Bio/PopGen/Genotype.pm BioPerl-1.6.900/Bio/PopGen/PopStats.pm BioPerl-1.6.900/Bio/PopGen/PopulationI.pm BioPerl-1.6.900/Bio/PopGen/IndividualI.pm BioPerl-1.6.900/Bio/PopGen/Population.pm BioPerl-1.6.900/Bio/PopGen/MarkerI.pm BioPerl-1.6.900/Bio/PopGen/TagHaplotype.pm BioPerl-1.6.900/Bio/PopGen/HtSNP.pm BioPerl-1.6.900/Bio/PopGen/Statistics.pm BioPerl-1.6.900/Bio/PopGen/IO.pm BioPerl-1.6.900/Bio/PopGen/GenotypeI.pm BioPerl-1.6.900/Bio/PopGen/Marker.pm BioPerl-1.6.900/Bio/PopGen/Individual.pm BioPerl-1.6.900/Bio/PopGen/IO BioPerl-1.6.900/Bio/PopGen/IO/hapmap.pm BioPerl-1.6.900/Bio/PopGen/IO/prettybase.pm BioPerl-1.6.900/Bio/PopGen/IO/phase.pm BioPerl-1.6.900/Bio/PopGen/IO/csv.pm BioPerl-1.6.900/Bio/PopGen/Simulation BioPerl-1.6.900/Bio/PopGen/Simulation/GeneticDrift.pm BioPerl-1.6.900/Bio/PopGen/Simulation/Coalescent.pm BioPerl-1.6.900/Bio/LiveSeq BioPerl-1.6.900/Bio/LiveSeq/Chain.pm BioPerl-1.6.900/Bio/LiveSeq/Repeat_Unit.pm BioPerl-1.6.900/Bio/LiveSeq/ChainI.pm BioPerl-1.6.900/Bio/LiveSeq/Prim_Transcript.pm BioPerl-1.6.900/Bio/LiveSeq/SeqI.pm BioPerl-1.6.900/Bio/LiveSeq/Range.pm BioPerl-1.6.900/Bio/LiveSeq/Translation.pm BioPerl-1.6.900/Bio/LiveSeq/Mutation.pm BioPerl-1.6.900/Bio/LiveSeq/Repeat_Region.pm BioPerl-1.6.900/Bio/LiveSeq/Intron.pm BioPerl-1.6.900/Bio/LiveSeq/AARange.pm BioPerl-1.6.900/Bio/LiveSeq/DNA.pm BioPerl-1.6.900/Bio/LiveSeq/Exon.pm BioPerl-1.6.900/Bio/LiveSeq/Transcript.pm BioPerl-1.6.900/Bio/LiveSeq/Gene.pm BioPerl-1.6.900/Bio/LiveSeq/Mutator.pm BioPerl-1.6.900/Bio/LiveSeq/IO BioPerl-1.6.900/Bio/LiveSeq/IO/README BioPerl-1.6.900/Bio/LiveSeq/IO/Loader.pm BioPerl-1.6.900/Bio/LiveSeq/IO/BioPerl.pm BioPerl-1.6.900/Bio/SearchIO BioPerl-1.6.900/Bio/SearchIO/EventHandlerI.pm BioPerl-1.6.900/Bio/SearchIO/SearchWriterI.pm BioPerl-1.6.900/Bio/SearchIO/infernal.pm BioPerl-1.6.900/Bio/SearchIO/megablast.pm BioPerl-1.6.900/Bio/SearchIO/hmmer3.pm BioPerl-1.6.900/Bio/SearchIO/SearchResultEventBuilder.pm BioPerl-1.6.900/Bio/SearchIO/hmmer.pm BioPerl-1.6.900/Bio/SearchIO/axt.pm BioPerl-1.6.900/Bio/SearchIO/erpin.pm BioPerl-1.6.900/Bio/SearchIO/waba.pm BioPerl-1.6.900/Bio/SearchIO/rnamotif.pm BioPerl-1.6.900/Bio/SearchIO/exonerate.pm BioPerl-1.6.900/Bio/SearchIO/sim4.pm BioPerl-1.6.900/Bio/SearchIO/blasttable.pm BioPerl-1.6.900/Bio/SearchIO/psl.pm BioPerl-1.6.900/Bio/SearchIO/gmap_f9.pm BioPerl-1.6.900/Bio/SearchIO/FastHitEventBuilder.pm BioPerl-1.6.900/Bio/SearchIO/cross_match.pm BioPerl-1.6.900/Bio/SearchIO/blast.pm BioPerl-1.6.900/Bio/SearchIO/hmmer2.pm BioPerl-1.6.900/Bio/SearchIO/blastxml.pm BioPerl-1.6.900/Bio/SearchIO/hmmer_pull.pm BioPerl-1.6.900/Bio/SearchIO/IteratedSearchResultEventBuilder.pm BioPerl-1.6.900/Bio/SearchIO/fasta.pm BioPerl-1.6.900/Bio/SearchIO/wise.pm BioPerl-1.6.900/Bio/SearchIO/blast_pull.pm BioPerl-1.6.900/Bio/SearchIO/Writer BioPerl-1.6.900/Bio/SearchIO/Writer/GbrowseGFF.pm BioPerl-1.6.900/Bio/SearchIO/Writer/ResultTableWriter.pm BioPerl-1.6.900/Bio/SearchIO/Writer/HitTableWriter.pm BioPerl-1.6.900/Bio/SearchIO/Writer/TextResultWriter.pm BioPerl-1.6.900/Bio/SearchIO/Writer/HTMLResultWriter.pm BioPerl-1.6.900/Bio/SearchIO/Writer/BSMLResultWriter.pm BioPerl-1.6.900/Bio/SearchIO/Writer/HSPTableWriter.pm BioPerl-1.6.900/Bio/SearchIO/XML BioPerl-1.6.900/Bio/SearchIO/XML/BlastHandler.pm BioPerl-1.6.900/Bio/SearchIO/XML/PsiBlastHandler.pm BioPerl-1.6.900/Bio/Structure BioPerl-1.6.900/Bio/Structure/Residue.pm BioPerl-1.6.900/Bio/Structure/Chain.pm BioPerl-1.6.900/Bio/Structure/Entry.pm BioPerl-1.6.900/Bio/Structure/Atom.pm BioPerl-1.6.900/Bio/Structure/Model.pm BioPerl-1.6.900/Bio/Structure/IO.pm BioPerl-1.6.900/Bio/Structure/StructureI.pm BioPerl-1.6.900/Bio/Structure/IO BioPerl-1.6.900/Bio/Structure/IO/pdb.pm BioPerl-1.6.900/Bio/Structure/SecStr BioPerl-1.6.900/Bio/Structure/SecStr/STRIDE BioPerl-1.6.900/Bio/Structure/SecStr/STRIDE/Res.pm BioPerl-1.6.900/Bio/Structure/SecStr/DSSP BioPerl-1.6.900/Bio/Structure/SecStr/DSSP/Res.pm BioPerl-1.6.900/Bio/SeqFeature BioPerl-1.6.900/Bio/SeqFeature/Computation.pm BioPerl-1.6.900/Bio/SeqFeature/AnnotationAdaptor.pm BioPerl-1.6.900/Bio/SeqFeature/Annotated.pm BioPerl-1.6.900/Bio/SeqFeature/TypedSeqFeatureI.pm BioPerl-1.6.900/Bio/SeqFeature/Collection.pm BioPerl-1.6.900/Bio/SeqFeature/FeaturePair.pm BioPerl-1.6.900/Bio/SeqFeature/CollectionI.pm BioPerl-1.6.900/Bio/SeqFeature/Generic.pm BioPerl-1.6.900/Bio/SeqFeature/PositionProxy.pm BioPerl-1.6.900/Bio/SeqFeature/Primer.pm BioPerl-1.6.900/Bio/SeqFeature/Lite.pm BioPerl-1.6.900/Bio/SeqFeature/SimilarityPair.pm BioPerl-1.6.900/Bio/SeqFeature/Similarity.pm BioPerl-1.6.900/Bio/SeqFeature/SiRNA BioPerl-1.6.900/Bio/SeqFeature/SiRNA/Pair.pm BioPerl-1.6.900/Bio/SeqFeature/SiRNA/Oligo.pm BioPerl-1.6.900/Bio/SeqFeature/Tools BioPerl-1.6.900/Bio/SeqFeature/Tools/FeatureNamer.pm BioPerl-1.6.900/Bio/SeqFeature/Tools/IDHandler.pm BioPerl-1.6.900/Bio/SeqFeature/Tools/Unflattener.pm BioPerl-1.6.900/Bio/SeqFeature/Tools/TypeMapper.pm BioPerl-1.6.900/Bio/SeqFeature/Gene BioPerl-1.6.900/Bio/SeqFeature/Gene/GeneStructure.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/UTR.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/Poly_A_site.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/Intron.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/Exon.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/Transcript.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/Promoter.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/ExonI.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/NC_Feature.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/GeneStructureI.pm BioPerl-1.6.900/Bio/SeqFeature/Gene/TranscriptI.pm BioPerl-1.6.900/Bio/Event BioPerl-1.6.900/Bio/Event/EventHandlerI.pm BioPerl-1.6.900/Bio/Event/EventGeneratorI.pm BioPerl-1.6.900/Bio/Taxonomy BioPerl-1.6.900/Bio/Taxonomy/Tree.pm BioPerl-1.6.900/Bio/Taxonomy/Taxon.pm BioPerl-1.6.900/Bio/Taxonomy/Node.pm BioPerl-1.6.900/Bio/Taxonomy/FactoryI.pm BioPerl-1.6.900/Bio/Assembly BioPerl-1.6.900/Bio/Assembly/Singlet.pm BioPerl-1.6.900/Bio/Assembly/Scaffold.pm BioPerl-1.6.900/Bio/Assembly/ScaffoldI.pm BioPerl-1.6.900/Bio/Assembly/IO.pm BioPerl-1.6.900/Bio/Assembly/Contig.pm BioPerl-1.6.900/Bio/Assembly/ContigAnalysis.pm BioPerl-1.6.900/Bio/Assembly/IO BioPerl-1.6.900/Bio/Assembly/IO/bowtie.pm BioPerl-1.6.900/Bio/Assembly/IO/tigr.pm BioPerl-1.6.900/Bio/Assembly/IO/maq.pm BioPerl-1.6.900/Bio/Assembly/IO/ace.pm BioPerl-1.6.900/Bio/Assembly/IO/phrap.pm BioPerl-1.6.900/Bio/Assembly/IO/sam.pm BioPerl-1.6.900/Bio/Assembly/Tools BioPerl-1.6.900/Bio/Assembly/Tools/ContigSpectrum.pm BioPerl-1.6.900/Bio/Das BioPerl-1.6.900/Bio/Das/SegmentI.pm BioPerl-1.6.900/Bio/Das/FeatureTypeI.pm BioPerl-1.6.900/Bio/ClusterIO BioPerl-1.6.900/Bio/ClusterIO/dbsnp.pm BioPerl-1.6.900/Bio/ClusterIO/unigene.pm BioPerl-1.6.900/Bio/Tree BioPerl-1.6.900/Bio/Tree/Compatible.pm BioPerl-1.6.900/Bio/Tree/TreeI.pm BioPerl-1.6.900/Bio/Tree/DistanceFactory.pm BioPerl-1.6.900/Bio/Tree/Tree.pm BioPerl-1.6.900/Bio/Tree/NodeI.pm BioPerl-1.6.900/Bio/Tree/TreeFunctionsI.pm BioPerl-1.6.900/Bio/Tree/Statistics.pm BioPerl-1.6.900/Bio/Tree/AnnotatableNode.pm BioPerl-1.6.900/Bio/Tree/NodeNHX.pm BioPerl-1.6.900/Bio/Tree/AlleleNode.pm BioPerl-1.6.900/Bio/Tree/Node.pm BioPerl-1.6.900/Bio/Tree/RandomFactory.pm BioPerl-1.6.900/Bio/Tree/Draw BioPerl-1.6.900/Bio/Tree/Draw/Cladogram.pm BioPerl-1.6.900/Bio/Search BioPerl-1.6.900/Bio/Search/StatisticsI.pm BioPerl-1.6.900/Bio/Search/GenericDatabase.pm BioPerl-1.6.900/Bio/Search/GenericStatistics.pm BioPerl-1.6.900/Bio/Search/SearchUtils.pm BioPerl-1.6.900/Bio/Search/Processor.pm BioPerl-1.6.900/Bio/Search/DatabaseI.pm BioPerl-1.6.900/Bio/Search/BlastStatistics.pm BioPerl-1.6.900/Bio/Search/BlastUtils.pm BioPerl-1.6.900/Bio/Search/Tiling BioPerl-1.6.900/Bio/Search/Tiling/MapTileUtils.pm BioPerl-1.6.900/Bio/Search/Tiling/TilingI.pm BioPerl-1.6.900/Bio/Search/Tiling/MapTiling.pm BioPerl-1.6.900/Bio/Search/Result BioPerl-1.6.900/Bio/Search/Result/CrossMatchResult.pm BioPerl-1.6.900/Bio/Search/Result/BlastPullResult.pm BioPerl-1.6.900/Bio/Search/Result/HmmpfamResult.pm BioPerl-1.6.900/Bio/Search/Result/ResultI.pm BioPerl-1.6.900/Bio/Search/Result/PullResultI.pm BioPerl-1.6.900/Bio/Search/Result/ResultFactory.pm BioPerl-1.6.900/Bio/Search/Result/GenericResult.pm BioPerl-1.6.900/Bio/Search/Result/WABAResult.pm BioPerl-1.6.900/Bio/Search/Result/hmmer3Result.pm BioPerl-1.6.900/Bio/Search/Result/HMMERResult.pm BioPerl-1.6.900/Bio/Search/Result/BlastResult.pm BioPerl-1.6.900/Bio/Search/Hit BioPerl-1.6.900/Bio/Search/Hit/HmmpfamHit.pm BioPerl-1.6.900/Bio/Search/Hit/GenericHit.pm BioPerl-1.6.900/Bio/Search/Hit/HitFactory.pm BioPerl-1.6.900/Bio/Search/Hit/PsiBlastHit.pm BioPerl-1.6.900/Bio/Search/Hit/PullHitI.pm BioPerl-1.6.900/Bio/Search/Hit/HMMERHit.pm BioPerl-1.6.900/Bio/Search/Hit/HitI.pm BioPerl-1.6.900/Bio/Search/Hit/BlastPullHit.pm BioPerl-1.6.900/Bio/Search/Hit/Fasta.pm BioPerl-1.6.900/Bio/Search/Hit/hmmer3Hit.pm BioPerl-1.6.900/Bio/Search/Hit/ModelHit.pm BioPerl-1.6.900/Bio/Search/Hit/BlastHit.pm BioPerl-1.6.900/Bio/Search/Iteration BioPerl-1.6.900/Bio/Search/Iteration/GenericIteration.pm BioPerl-1.6.900/Bio/Search/Iteration/IterationI.pm BioPerl-1.6.900/Bio/Search/HSP BioPerl-1.6.900/Bio/Search/HSP/BlastPullHSP.pm BioPerl-1.6.900/Bio/Search/HSP/PsiBlastHSP.pm BioPerl-1.6.900/Bio/Search/HSP/hmmer3HSP.pm BioPerl-1.6.900/Bio/Search/HSP/ModelHSP.pm BioPerl-1.6.900/Bio/Search/HSP/FastaHSP.pm BioPerl-1.6.900/Bio/Search/HSP/HmmpfamHSP.pm BioPerl-1.6.900/Bio/Search/HSP/PSLHSP.pm BioPerl-1.6.900/Bio/Search/HSP/BlastHSP.pm BioPerl-1.6.900/Bio/Search/HSP/HSPFactory.pm BioPerl-1.6.900/Bio/Search/HSP/GenericHSP.pm BioPerl-1.6.900/Bio/Search/HSP/HSPI.pm BioPerl-1.6.900/Bio/Search/HSP/WABAHSP.pm BioPerl-1.6.900/Bio/Search/HSP/PullHSPI.pm BioPerl-1.6.900/Bio/Search/HSP/HMMERHSP.pm BioPerl-1.6.900/Bio/OntologyIO BioPerl-1.6.900/Bio/OntologyIO/simplehierarchy.pm BioPerl-1.6.900/Bio/OntologyIO/obo.pm BioPerl-1.6.900/Bio/OntologyIO/goflat.pm BioPerl-1.6.900/Bio/OntologyIO/soflat.pm BioPerl-1.6.900/Bio/OntologyIO/InterProParser.pm BioPerl-1.6.900/Bio/OntologyIO/dagflat.pm BioPerl-1.6.900/Bio/OntologyIO/Handlers BioPerl-1.6.900/Bio/OntologyIO/Handlers/BaseSAXHandler.pm BioPerl-1.6.900/Bio/OntologyIO/Handlers/InterProHandler.pm BioPerl-1.6.900/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm BioPerl-1.6.900/Bio/Biblio BioPerl-1.6.900/Bio/Biblio/Patent.pm BioPerl-1.6.900/Bio/Biblio/Ref.pm BioPerl-1.6.900/Bio/Biblio/MedlineJournal.pm BioPerl-1.6.900/Bio/Biblio/PubmedArticle.pm BioPerl-1.6.900/Bio/Biblio/Provider.pm BioPerl-1.6.900/Bio/Biblio/Article.pm BioPerl-1.6.900/Bio/Biblio/BookArticle.pm BioPerl-1.6.900/Bio/Biblio/BiblioBase.pm BioPerl-1.6.900/Bio/Biblio/PubmedJournalArticle.pm BioPerl-1.6.900/Bio/Biblio/Proceeding.pm BioPerl-1.6.900/Bio/Biblio/TechReport.pm BioPerl-1.6.900/Bio/Biblio/MedlineBookArticle.pm BioPerl-1.6.900/Bio/Biblio/WebResource.pm BioPerl-1.6.900/Bio/Biblio/MedlineJournalArticle.pm BioPerl-1.6.900/Bio/Biblio/Book.pm BioPerl-1.6.900/Bio/Biblio/Journal.pm BioPerl-1.6.900/Bio/Biblio/Organisation.pm BioPerl-1.6.900/Bio/Biblio/Service.pm BioPerl-1.6.900/Bio/Biblio/Person.pm BioPerl-1.6.900/Bio/Biblio/JournalArticle.pm BioPerl-1.6.900/Bio/Biblio/Thesis.pm BioPerl-1.6.900/Bio/Biblio/MedlineBook.pm BioPerl-1.6.900/Bio/Biblio/MedlineArticle.pm BioPerl-1.6.900/Bio/Biblio/IO.pm BioPerl-1.6.900/Bio/Biblio/PubmedBookArticle.pm BioPerl-1.6.900/Bio/Biblio/IO BioPerl-1.6.900/Bio/Biblio/IO/medlinexml.pm BioPerl-1.6.900/Bio/Biblio/IO/pubmed2ref.pm BioPerl-1.6.900/Bio/Biblio/IO/pubmedxml.pm BioPerl-1.6.900/Bio/Biblio/IO/medline2ref.pm BioPerl-1.6.900/Bio/Map BioPerl-1.6.900/Bio/Map/PositionHandlerI.pm BioPerl-1.6.900/Bio/Map/Clone.pm BioPerl-1.6.900/Bio/Map/OrderedPosition.pm BioPerl-1.6.900/Bio/Map/Relative.pm BioPerl-1.6.900/Bio/Map/CytoPosition.pm BioPerl-1.6.900/Bio/Map/Mappable.pm BioPerl-1.6.900/Bio/Map/EntityI.pm BioPerl-1.6.900/Bio/Map/OrderedPositionWithDistance.pm BioPerl-1.6.900/Bio/Map/CytoMap.pm BioPerl-1.6.900/Bio/Map/MappableI.pm BioPerl-1.6.900/Bio/Map/Position.pm BioPerl-1.6.900/Bio/Map/LinkagePosition.pm BioPerl-1.6.900/Bio/Map/GeneMap.pm BioPerl-1.6.900/Bio/Map/GeneRelative.pm BioPerl-1.6.900/Bio/Map/FPCMarker.pm BioPerl-1.6.900/Bio/Map/LinkageMap.pm BioPerl-1.6.900/Bio/Map/CytoMarker.pm BioPerl-1.6.900/Bio/Map/Physical.pm BioPerl-1.6.900/Bio/Map/MarkerI.pm BioPerl-1.6.900/Bio/Map/TranscriptionFactor.pm BioPerl-1.6.900/Bio/Map/PositionHandler.pm BioPerl-1.6.900/Bio/Map/Prediction.pm BioPerl-1.6.900/Bio/Map/PositionWithSequence.pm BioPerl-1.6.900/Bio/Map/Microsatellite.pm BioPerl-1.6.900/Bio/Map/PositionI.pm BioPerl-1.6.900/Bio/Map/GenePosition.pm BioPerl-1.6.900/Bio/Map/MapI.pm BioPerl-1.6.900/Bio/Map/Gene.pm BioPerl-1.6.900/Bio/Map/RelativeI.pm BioPerl-1.6.900/Bio/Map/SimpleMap.pm BioPerl-1.6.900/Bio/Map/Contig.pm BioPerl-1.6.900/Bio/Map/Marker.pm BioPerl-1.6.900/Bio/Nexml BioPerl-1.6.900/Bio/Nexml/Factory.pm BioPerl-1.6.900/Bio/Coordinate BioPerl-1.6.900/Bio/Coordinate/GeneMapper.pm BioPerl-1.6.900/Bio/Coordinate/Pair.pm BioPerl-1.6.900/Bio/Coordinate/Chain.pm BioPerl-1.6.900/Bio/Coordinate/ResultI.pm BioPerl-1.6.900/Bio/Coordinate/Collection.pm BioPerl-1.6.900/Bio/Coordinate/Graph.pm BioPerl-1.6.900/Bio/Coordinate/Utils.pm BioPerl-1.6.900/Bio/Coordinate/ExtrapolatingPair.pm BioPerl-1.6.900/Bio/Coordinate/Result.pm BioPerl-1.6.900/Bio/Coordinate/MapperI.pm BioPerl-1.6.900/Bio/Coordinate/Result BioPerl-1.6.900/Bio/Coordinate/Result/Match.pm BioPerl-1.6.900/Bio/Coordinate/Result/Gap.pm BioPerl-1.6.900/Bio/Symbol BioPerl-1.6.900/Bio/Symbol/Symbol.pm BioPerl-1.6.900/Bio/Symbol/README.Symbol BioPerl-1.6.900/Bio/Symbol/SymbolI.pm BioPerl-1.6.900/Bio/Symbol/Alphabet.pm BioPerl-1.6.900/Bio/Symbol/DNAAlphabet.pm BioPerl-1.6.900/Bio/Symbol/AlphabetI.pm BioPerl-1.6.900/Bio/Symbol/ProteinAlphabet.pm BioPerl-1.6.900/Bio/MolEvol BioPerl-1.6.900/Bio/MolEvol/CodonModel.pm BioPerl-1.6.900/Bio/Ontology BioPerl-1.6.900/Bio/Ontology/Path.pm BioPerl-1.6.900/Bio/Ontology/GOterm.pm BioPerl-1.6.900/Bio/Ontology/TermFactory.pm BioPerl-1.6.900/Bio/Ontology/DocumentRegistry.pm BioPerl-1.6.900/Bio/Ontology/RelationshipI.pm BioPerl-1.6.900/Bio/Ontology/OntologyStore.pm BioPerl-1.6.900/Bio/Ontology/RelationshipFactory.pm BioPerl-1.6.900/Bio/Ontology/InterProTerm.pm BioPerl-1.6.900/Bio/Ontology/OntologyI.pm BioPerl-1.6.900/Bio/Ontology/TermI.pm BioPerl-1.6.900/Bio/Ontology/Relationship.pm BioPerl-1.6.900/Bio/Ontology/PathI.pm BioPerl-1.6.900/Bio/Ontology/OntologyEngineI.pm BioPerl-1.6.900/Bio/Ontology/Term.pm BioPerl-1.6.900/Bio/Ontology/RelationshipType.pm BioPerl-1.6.900/Bio/Ontology/SimpleOntologyEngine.pm BioPerl-1.6.900/Bio/Ontology/OBOterm.pm BioPerl-1.6.900/Bio/Ontology/Ontology.pm BioPerl-1.6.900/Bio/Ontology/OBOEngine.pm BioPerl-1.6.900/Bio/Ontology/SimpleGOEngine BioPerl-1.6.900/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm BioPerl-1.6.900/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm BioPerl-1.6.900/Bio/PhyloNetwork BioPerl-1.6.900/Bio/PhyloNetwork/TreeFactoryMulti.pm BioPerl-1.6.900/Bio/PhyloNetwork/FactoryX.pm BioPerl-1.6.900/Bio/PhyloNetwork/TreeFactoryX.pm BioPerl-1.6.900/Bio/PhyloNetwork/Factory.pm BioPerl-1.6.900/Bio/PhyloNetwork/GraphViz.pm BioPerl-1.6.900/Bio/PhyloNetwork/muVector.pm BioPerl-1.6.900/Bio/PhyloNetwork/RandomFactory.pm BioPerl-1.6.900/Bio/PhyloNetwork/TreeFactory.pm BioPerl-1.6.900/Bio/AlignIO BioPerl-1.6.900/Bio/AlignIO/msf.pm BioPerl-1.6.900/Bio/AlignIO/largemultifasta.pm BioPerl-1.6.900/Bio/AlignIO/meme.pm BioPerl-1.6.900/Bio/AlignIO/stockholm.pm BioPerl-1.6.900/Bio/AlignIO/arp.pm BioPerl-1.6.900/Bio/AlignIO/mase.pm BioPerl-1.6.900/Bio/AlignIO/bl2seq.pm BioPerl-1.6.900/Bio/AlignIO/emboss.pm BioPerl-1.6.900/Bio/AlignIO/psi.pm BioPerl-1.6.900/Bio/AlignIO/xmfa.pm BioPerl-1.6.900/Bio/AlignIO/nexus.pm BioPerl-1.6.900/Bio/AlignIO/clustalw.pm BioPerl-1.6.900/Bio/AlignIO/mega.pm BioPerl-1.6.900/Bio/AlignIO/po.pm BioPerl-1.6.900/Bio/AlignIO/pfam.pm BioPerl-1.6.900/Bio/AlignIO/maf.pm BioPerl-1.6.900/Bio/AlignIO/prodom.pm BioPerl-1.6.900/Bio/AlignIO/nexml.pm BioPerl-1.6.900/Bio/AlignIO/proda.pm BioPerl-1.6.900/Bio/AlignIO/selex.pm BioPerl-1.6.900/Bio/AlignIO/phylip.pm BioPerl-1.6.900/Bio/AlignIO/fasta.pm BioPerl-1.6.900/Bio/AlignIO/metafasta.pm BioPerl-1.6.900/Bio/AlignIO/Handler BioPerl-1.6.900/Bio/AlignIO/Handler/GenericAlignHandler.pm BioPerl-1.6.900/Bio/FeatureIO BioPerl-1.6.900/Bio/FeatureIO/ptt.pm BioPerl-1.6.900/Bio/FeatureIO/gff.pm BioPerl-1.6.900/Bio/FeatureIO/bed.pm BioPerl-1.6.900/Bio/FeatureIO/gtf.pm BioPerl-1.6.900/Bio/FeatureIO/interpro.pm BioPerl-1.6.900/Bio/FeatureIO/vecscreen_simple.pm BioPerl-1.6.900/Bio/Restriction BioPerl-1.6.900/Bio/Restriction/Analysis.pm BioPerl-1.6.900/Bio/Restriction/EnzymeI.pm BioPerl-1.6.900/Bio/Restriction/Enzyme.pm BioPerl-1.6.900/Bio/Restriction/IO.pm BioPerl-1.6.900/Bio/Restriction/EnzymeCollection.pm BioPerl-1.6.900/Bio/Restriction/IO BioPerl-1.6.900/Bio/Restriction/IO/itype2.pm BioPerl-1.6.900/Bio/Restriction/IO/bairoch.pm BioPerl-1.6.900/Bio/Restriction/IO/prototype.pm BioPerl-1.6.900/Bio/Restriction/IO/withrefm.pm BioPerl-1.6.900/Bio/Restriction/IO/base.pm BioPerl-1.6.900/Bio/Restriction/Enzyme BioPerl-1.6.900/Bio/Restriction/Enzyme/MultiCut.pm BioPerl-1.6.900/Bio/Restriction/Enzyme/MultiSite.pm BioPerl-1.6.900/Bio/MapIO BioPerl-1.6.900/Bio/MapIO/mapmaker.pm BioPerl-1.6.900/Bio/MapIO/fpc.pm BioPerl-1.6.900/Bio/Draw BioPerl-1.6.900/Bio/Draw/Pictogram.pm BioPerl-1.6.900/Bio/Variation BioPerl-1.6.900/Bio/Variation/RNAChange.pm BioPerl-1.6.900/Bio/Variation/SNP.pm BioPerl-1.6.900/Bio/Variation/README BioPerl-1.6.900/Bio/Variation/VariantI.pm BioPerl-1.6.900/Bio/Variation/AAChange.pm BioPerl-1.6.900/Bio/Variation/AAReverseMutate.pm BioPerl-1.6.900/Bio/Variation/IO.pm BioPerl-1.6.900/Bio/Variation/SeqDiff.pm BioPerl-1.6.900/Bio/Variation/Allele.pm BioPerl-1.6.900/Bio/Variation/DNAMutation.pm BioPerl-1.6.900/Bio/Variation/IO BioPerl-1.6.900/Bio/Variation/IO/flat.pm BioPerl-1.6.900/Bio/Variation/IO/xml.pm BioPerl-1.6.900/Bio/TreeIO BioPerl-1.6.900/Bio/TreeIO/TreeEventBuilder.pm BioPerl-1.6.900/Bio/TreeIO/cluster.pm BioPerl-1.6.900/Bio/TreeIO/lintree.pm BioPerl-1.6.900/Bio/TreeIO/pag.pm BioPerl-1.6.900/Bio/TreeIO/nexus.pm BioPerl-1.6.900/Bio/TreeIO/NewickParser.pm BioPerl-1.6.900/Bio/TreeIO/nexml.pm BioPerl-1.6.900/Bio/TreeIO/phyloxml.pm BioPerl-1.6.900/Bio/TreeIO/svggraph.pm BioPerl-1.6.900/Bio/TreeIO/nhx.pm BioPerl-1.6.900/Bio/TreeIO/tabtree.pm BioPerl-1.6.900/Bio/TreeIO/newick.pm BioPerl-1.6.900/Bio/SeqIO BioPerl-1.6.900/Bio/SeqIO/seqxml.pm BioPerl-1.6.900/Bio/SeqIO/table.pm BioPerl-1.6.900/Bio/SeqIO/phd.pm BioPerl-1.6.900/Bio/SeqIO/gbxml.pm BioPerl-1.6.900/Bio/SeqIO/locuslink.pm BioPerl-1.6.900/Bio/SeqIO/chadoxml.pm BioPerl-1.6.900/Bio/SeqIO/lasergene.pm BioPerl-1.6.900/Bio/SeqIO/ztr.pm BioPerl-1.6.900/Bio/SeqIO/embl.pm BioPerl-1.6.900/Bio/SeqIO/tigrxml.pm BioPerl-1.6.900/Bio/SeqIO/pln.pm BioPerl-1.6.900/Bio/SeqIO/swissdriver.pm BioPerl-1.6.900/Bio/SeqIO/chaosxml.pm BioPerl-1.6.900/Bio/SeqIO/chaos.pm BioPerl-1.6.900/Bio/SeqIO/flybase_chadoxml.pm BioPerl-1.6.900/Bio/SeqIO/tigr.pm BioPerl-1.6.900/Bio/SeqIO/bsml.pm BioPerl-1.6.900/Bio/SeqIO/genbank.pm BioPerl-1.6.900/Bio/SeqIO/embldriver.pm BioPerl-1.6.900/Bio/SeqIO/entrezgene.pm BioPerl-1.6.900/Bio/SeqIO/ace.pm BioPerl-1.6.900/Bio/SeqIO/asciitree.pm BioPerl-1.6.900/Bio/SeqIO/bsml_sax.pm BioPerl-1.6.900/Bio/SeqIO/excel.pm BioPerl-1.6.900/Bio/SeqIO/raw.pm BioPerl-1.6.900/Bio/SeqIO/gcg.pm BioPerl-1.6.900/Bio/SeqIO/qual.pm BioPerl-1.6.900/Bio/SeqIO/kegg.pm BioPerl-1.6.900/Bio/SeqIO/nexml.pm BioPerl-1.6.900/Bio/SeqIO/mbsout.pm BioPerl-1.6.900/Bio/SeqIO/gbdriver.pm BioPerl-1.6.900/Bio/SeqIO/msout.pm BioPerl-1.6.900/Bio/SeqIO/strider.pm BioPerl-1.6.900/Bio/SeqIO/largefasta.pm BioPerl-1.6.900/Bio/SeqIO/FTHelper.pm BioPerl-1.6.900/Bio/SeqIO/game.pm BioPerl-1.6.900/Bio/SeqIO/swiss.pm BioPerl-1.6.900/Bio/SeqIO/ctf.pm BioPerl-1.6.900/Bio/SeqIO/interpro.pm BioPerl-1.6.900/Bio/SeqIO/MultiFile.pm BioPerl-1.6.900/Bio/SeqIO/fastq.pm BioPerl-1.6.900/Bio/SeqIO/pir.pm BioPerl-1.6.900/Bio/SeqIO/exp.pm BioPerl-1.6.900/Bio/SeqIO/tinyseq.pm BioPerl-1.6.900/Bio/SeqIO/alf.pm BioPerl-1.6.900/Bio/SeqIO/abi.pm BioPerl-1.6.900/Bio/SeqIO/scf.pm BioPerl-1.6.900/Bio/SeqIO/fasta.pm BioPerl-1.6.900/Bio/SeqIO/metafasta.pm BioPerl-1.6.900/Bio/SeqIO/agave.pm BioPerl-1.6.900/Bio/SeqIO/tab.pm BioPerl-1.6.900/Bio/SeqIO/game BioPerl-1.6.900/Bio/SeqIO/game/gameHandler.pm BioPerl-1.6.900/Bio/SeqIO/game/gameSubs.pm BioPerl-1.6.900/Bio/SeqIO/game/featHandler.pm BioPerl-1.6.900/Bio/SeqIO/game/gameWriter.pm BioPerl-1.6.900/Bio/SeqIO/game/seqHandler.pm BioPerl-1.6.900/Bio/SeqIO/tinyseq BioPerl-1.6.900/Bio/SeqIO/tinyseq/tinyseqHandler.pm BioPerl-1.6.900/Bio/SeqIO/Handler BioPerl-1.6.900/Bio/SeqIO/Handler/GenericRichSeqHandler.pm BioPerl-1.6.900/examples BioPerl-1.6.900/examples/longorf.pl BioPerl-1.6.900/examples/subsequence.cgi BioPerl-1.6.900/examples/generate_random_seq.pl BioPerl-1.6.900/examples/bioperl.pl BioPerl-1.6.900/examples/revcom_dir.pl BioPerl-1.6.900/examples/rev_and_trans.pl BioPerl-1.6.900/examples/make_primers.pl BioPerl-1.6.900/examples/db BioPerl-1.6.900/examples/db/dbfetch BioPerl-1.6.900/examples/db/getGenBank.pl BioPerl-1.6.900/examples/db/get_seqs.pl BioPerl-1.6.900/examples/db/est_tissue_query.pl BioPerl-1.6.900/examples/db/gb2features.pl BioPerl-1.6.900/examples/db/use_registry.pl BioPerl-1.6.900/examples/db/rfetch.pl BioPerl-1.6.900/examples/Bio-DB-GFF BioPerl-1.6.900/examples/Bio-DB-GFF/load_ucsc.pl BioPerl-1.6.900/examples/quality BioPerl-1.6.900/examples/quality/svgtrace.pl BioPerl-1.6.900/examples/searchio BioPerl-1.6.900/examples/searchio/hspwriter.pl BioPerl-1.6.900/examples/searchio/custom_writer.pl BioPerl-1.6.900/examples/searchio/waba2gff3.pl BioPerl-1.6.900/examples/searchio/waba2gff.pl BioPerl-1.6.900/examples/searchio/rawwriter.pl BioPerl-1.6.900/examples/searchio/hitwriter.pl BioPerl-1.6.900/examples/searchio/psiblast_features.pl BioPerl-1.6.900/examples/searchio/psiblast_iterations.pl BioPerl-1.6.900/examples/searchio/blast_example.pl BioPerl-1.6.900/examples/searchio/resultwriter.pl BioPerl-1.6.900/examples/searchio/htmlwriter.pl BioPerl-1.6.900/examples/tk BioPerl-1.6.900/examples/tk/hitdisplay.pl BioPerl-1.6.900/examples/tk/gsequence.pl BioPerl-1.6.900/examples/align BioPerl-1.6.900/examples/align/simplealign.pl BioPerl-1.6.900/examples/align/align_on_codons.pl BioPerl-1.6.900/examples/align/clustalw.pl BioPerl-1.6.900/examples/align/aligntutorial.pl BioPerl-1.6.900/examples/tools BioPerl-1.6.900/examples/tools/run_genscan.pl BioPerl-1.6.900/examples/tools/gb_to_gff.pl BioPerl-1.6.900/examples/tools/seq_pattern.pl BioPerl-1.6.900/examples/tools/run_primer3.pl BioPerl-1.6.900/examples/tools/gff2ps.pl BioPerl-1.6.900/examples/tools/reverse-translate.pl BioPerl-1.6.900/examples/tools/extract_genes.pl BioPerl-1.6.900/examples/tools/psw.pl BioPerl-1.6.900/examples/tools/standaloneblast.pl BioPerl-1.6.900/examples/tools/parse_codeml.pl BioPerl-1.6.900/examples/popgen BioPerl-1.6.900/examples/popgen/parse_calc_stats.pl BioPerl-1.6.900/examples/liveseq BioPerl-1.6.900/examples/liveseq/change_gene.pl BioPerl-1.6.900/examples/contributed BioPerl-1.6.900/examples/contributed/prosite2perl.pl BioPerl-1.6.900/examples/contributed/nmrpdb_parse.pl BioPerl-1.6.900/examples/contributed/rebase2list.pl BioPerl-1.6.900/examples/root BioPerl-1.6.900/examples/root/README BioPerl-1.6.900/examples/root/exceptions2.pl BioPerl-1.6.900/examples/root/exceptions3.pl BioPerl-1.6.900/examples/root/exceptions4.pl BioPerl-1.6.900/examples/root/exceptions1.pl BioPerl-1.6.900/examples/root/lib BioPerl-1.6.900/examples/root/lib/TestObject.pm BioPerl-1.6.900/examples/root/lib/TestInterface.pm BioPerl-1.6.900/examples/biblio BioPerl-1.6.900/examples/biblio/biblio_soap.pl BioPerl-1.6.900/examples/biblio/biblio-eutils-example.pl BioPerl-1.6.900/examples/biblio/biblio-soap-example.pl BioPerl-1.6.900/examples/structure BioPerl-1.6.900/examples/structure/structure-io.pl BioPerl-1.6.900/examples/tree BioPerl-1.6.900/examples/tree/paup2phylip.pl BioPerl-1.6.900/examples/cluster BioPerl-1.6.900/examples/cluster/dbsnp.pl BioPerl-1.6.900/examples/sirna BioPerl-1.6.900/examples/sirna/TAG BioPerl-1.6.900/examples/sirna/rnai_finder.cgi BioPerl-1.6.900/ide BioPerl-1.6.900/ide/bioperl.komodo BioPerl-1.6.900/ide/bioperl-mode BioPerl-1.6.900/ide/bioperl-mode/README BioPerl-1.6.900/ide/bioperl-mode/etc BioPerl-1.6.900/ide/bioperl-mode/etc/images BioPerl-1.6.900/ide/bioperl-mode/etc/images/bpmode-tool.xpm BioPerl-1.6.900/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm BioPerl-1.6.900/ide/bioperl-mode/site-lisp BioPerl-1.6.900/ide/bioperl-mode/site-lisp/bioperl-init.el BioPerl-1.6.900/ide/bioperl-mode/site-lisp/bioperl-skel.el BioPerl-1.6.900/ide/bioperl-mode/site-lisp/pod.el BioPerl-1.6.900/ide/bioperl-mode/site-lisp/bioperl-mode.el BioPerl-1.6.900/ide/bioperl-mode/dist BioPerl-1.6.900/ide/bioperl-mode/dist/SKIP BioPerl-1.6.900/ide/bioperl-mode/dist/bioperl-mode.tar BioPerl-1.6.900/ide/bioperl-mode/dist/bioperl-mode.tar.md5 BioPerl-1.6.900/ide/bioperl-mode/dist/package-me BioPerl-1.6.900/ide/bioperl-mode/dist/Changes BioPerl-1.6.900/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5 BioPerl-1.6.900/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar BioPerl-1.6.900/t BioPerl-1.6.900/t/TaxonTree.t BioPerl-1.6.900/t/Perl.t BioPerl-1.6.900/t/SeqEvolution.t BioPerl-1.6.900/t/PodSyntax.t BioPerl-1.6.900/t/nexml.t BioPerl-1.6.900/t/Species.t BioPerl-1.6.900/t/Alphabet.t BioPerl-1.6.900/t/SearchDist.t BioPerl-1.6.900/t/Symbol.t BioPerl-1.6.900/t/Align BioPerl-1.6.900/t/Align/TreeBuild.t BioPerl-1.6.900/t/Align/AlignUtil.t BioPerl-1.6.900/t/Align/Graphics.t BioPerl-1.6.900/t/Align/SimpleAlign.t BioPerl-1.6.900/t/Align/Utilities.t BioPerl-1.6.900/t/Align/AlignStats.t BioPerl-1.6.900/t/Matrix BioPerl-1.6.900/t/Matrix/SiteMatrix.t BioPerl-1.6.900/t/Matrix/ProtPsm.t BioPerl-1.6.900/t/Matrix/ProtMatrix.t BioPerl-1.6.900/t/Matrix/Matrix.t BioPerl-1.6.900/t/Matrix/InstanceSite.t BioPerl-1.6.900/t/Matrix/IO BioPerl-1.6.900/t/Matrix/IO/masta.t BioPerl-1.6.900/t/Matrix/IO/psm.t BioPerl-1.6.900/t/Annotation BioPerl-1.6.900/t/Annotation/AnnotationAdaptor.t BioPerl-1.6.900/t/Annotation/Annotation.t BioPerl-1.6.900/t/LocalDB BioPerl-1.6.900/t/LocalDB/DBFasta.t BioPerl-1.6.900/t/LocalDB/SeqFeature.t BioPerl-1.6.900/t/LocalDB/DBQual.t BioPerl-1.6.900/t/LocalDB/transfac_pro.t BioPerl-1.6.900/t/LocalDB/Flat.t BioPerl-1.6.900/t/LocalDB/BioDBGFF.t BioPerl-1.6.900/t/LocalDB/Registry.t BioPerl-1.6.900/t/LocalDB/Index BioPerl-1.6.900/t/LocalDB/Index/BlastTable.t BioPerl-1.6.900/t/LocalDB/Index/Index.t BioPerl-1.6.900/t/LocalDB/Index/Blast.t BioPerl-1.6.900/t/Tools BioPerl-1.6.900/t/Tools/Genpred.t BioPerl-1.6.900/t/Tools/Tmhmm.t BioPerl-1.6.900/t/Tools/tRNAscanSE.t BioPerl-1.6.900/t/Tools/IUPAC.t BioPerl-1.6.900/t/Tools/RepeatMasker.t BioPerl-1.6.900/t/Tools/ePCR.t BioPerl-1.6.900/t/Tools/QRNA.t BioPerl-1.6.900/t/Tools/Genewise.t BioPerl-1.6.900/t/Tools/RandDistFunctions.t BioPerl-1.6.900/t/Tools/GFF.t BioPerl-1.6.900/t/Tools/GuessSeqFormat.t BioPerl-1.6.900/t/Tools/Lucy.t BioPerl-1.6.900/t/Tools/Sigcleave.t BioPerl-1.6.900/t/Tools/FootPrinter.t BioPerl-1.6.900/t/Tools/SiRNA.t BioPerl-1.6.900/t/Tools/Genomewise.t BioPerl-1.6.900/t/Tools/Seg.t BioPerl-1.6.900/t/Tools/Match.t BioPerl-1.6.900/t/Tools/pICalculator.t BioPerl-1.6.900/t/Tools/Sim4.t BioPerl-1.6.900/t/Tools/Est2Genome.t BioPerl-1.6.900/t/Tools/TandemRepeatsFinder.t BioPerl-1.6.900/t/Tools/Signalp.t BioPerl-1.6.900/t/Tools/rnamotif.t BioPerl-1.6.900/t/Tools/Promoterwise.t BioPerl-1.6.900/t/Tools/Hmmer.t BioPerl-1.6.900/t/Tools/Primer3.t BioPerl-1.6.900/t/Tools/TargetP.t BioPerl-1.6.900/t/Tools/Pseudowise.t BioPerl-1.6.900/t/Tools/Geneid.t BioPerl-1.6.900/t/Tools/Signalp BioPerl-1.6.900/t/Tools/Signalp/ExtendedSignalp.t BioPerl-1.6.900/t/Tools/Run BioPerl-1.6.900/t/Tools/Run/WBCommandExts.t BioPerl-1.6.900/t/Tools/Run/StandAloneBlast.t BioPerl-1.6.900/t/Tools/Run/RemoteBlast_rpsblast.t BioPerl-1.6.900/t/Tools/Run/Dummy.pm BioPerl-1.6.900/t/Tools/Run/WrapperBase.t BioPerl-1.6.900/t/Tools/Run/RemoteBlast.t BioPerl-1.6.900/t/Tools/Run/Dummy BioPerl-1.6.900/t/Tools/Run/Dummy/Config.pm BioPerl-1.6.900/t/Tools/Analysis BioPerl-1.6.900/t/Tools/Analysis/Protein BioPerl-1.6.900/t/Tools/Analysis/Protein/NetPhos.t BioPerl-1.6.900/t/Tools/Analysis/Protein/Domcut.t BioPerl-1.6.900/t/Tools/Analysis/Protein/ELM.t BioPerl-1.6.900/t/Tools/Analysis/Protein/GOR4.t BioPerl-1.6.900/t/Tools/Analysis/Protein/HNN.t BioPerl-1.6.900/t/Tools/Analysis/Protein/Mitoprot.t BioPerl-1.6.900/t/Tools/Analysis/Protein/Sopma.t BioPerl-1.6.900/t/Tools/Analysis/Protein/Scansite.t BioPerl-1.6.900/t/Tools/Analysis/DNA BioPerl-1.6.900/t/Tools/Analysis/DNA/ESEfinder.t BioPerl-1.6.900/t/Tools/Alignment BioPerl-1.6.900/t/Tools/Alignment/Consed.t BioPerl-1.6.900/t/Tools/EMBOSS BioPerl-1.6.900/t/Tools/EMBOSS/Palindrome.t BioPerl-1.6.900/t/Tools/EUtilities BioPerl-1.6.900/t/Tools/EUtilities/epost.t BioPerl-1.6.900/t/Tools/EUtilities/elink_neighbor.t BioPerl-1.6.900/t/Tools/EUtilities/egquery.t BioPerl-1.6.900/t/Tools/EUtilities/elink_neighbor_history.t BioPerl-1.6.900/t/Tools/EUtilities/elink_acheck.t BioPerl-1.6.900/t/Tools/EUtilities/einfo.t BioPerl-1.6.900/t/Tools/EUtilities/elink_lcheck.t BioPerl-1.6.900/t/Tools/EUtilities/esearch.t BioPerl-1.6.900/t/Tools/EUtilities/elink_llinks.t BioPerl-1.6.900/t/Tools/EUtilities/elink_scores.t BioPerl-1.6.900/t/Tools/EUtilities/elink_ncheck.t BioPerl-1.6.900/t/Tools/EUtilities/esummary.t BioPerl-1.6.900/t/Tools/EUtilities/EUtilParameters.t BioPerl-1.6.900/t/Tools/EUtilities/espell.t BioPerl-1.6.900/t/Tools/Spidey BioPerl-1.6.900/t/Tools/Spidey/Spidey.t BioPerl-1.6.900/t/Tools/Phylo BioPerl-1.6.900/t/Tools/Phylo/Molphy.t BioPerl-1.6.900/t/Tools/Phylo/PAML.t BioPerl-1.6.900/t/Tools/Phylo/Gerp.t BioPerl-1.6.900/t/Tools/Phylo/Phylip BioPerl-1.6.900/t/Tools/Phylo/Phylip/ProtDist.t BioPerl-1.6.900/t/Seq BioPerl-1.6.900/t/Seq/EncodedSeq.t BioPerl-1.6.900/t/Seq/LargeLocatableSeq.t BioPerl-1.6.900/t/Seq/PrimarySeq.t BioPerl-1.6.900/t/Seq/PrimaryQual.t BioPerl-1.6.900/t/Seq/WithQuality.t BioPerl-1.6.900/t/Seq/MetaSeq.t BioPerl-1.6.900/t/Seq/Quality.t BioPerl-1.6.900/t/Seq/Seq.t BioPerl-1.6.900/t/Seq/LargePSeq.t BioPerl-1.6.900/t/Seq/LocatableSeq.t BioPerl-1.6.900/t/Seq/DBLink.t BioPerl-1.6.900/t/Seq/PrimedSeq.t BioPerl-1.6.900/t/lib BioPerl-1.6.900/t/lib/Error.pm BioPerl-1.6.900/t/lib/Test BioPerl-1.6.900/t/lib/Test/Simple.pm BioPerl-1.6.900/t/lib/Test/Exception.pm BioPerl-1.6.900/t/lib/Test/Tutorial.pod BioPerl-1.6.900/t/lib/Test/More.pm BioPerl-1.6.900/t/lib/Test/Builder.pm BioPerl-1.6.900/t/lib/Test/Harness.pm BioPerl-1.6.900/t/lib/Test/Warn.pm BioPerl-1.6.900/t/lib/Test/Builder BioPerl-1.6.900/t/lib/Test/Builder/Module.pm BioPerl-1.6.900/t/lib/Test/Builder/Tester.pm BioPerl-1.6.900/t/lib/Test/Builder/Tester BioPerl-1.6.900/t/lib/Test/Builder/Tester/Color.pm BioPerl-1.6.900/t/lib/Test/Harness BioPerl-1.6.900/t/lib/Test/Harness/Results.pm BioPerl-1.6.900/t/lib/Test/Harness/Point.pm BioPerl-1.6.900/t/lib/Test/Harness/Iterator.pm BioPerl-1.6.900/t/lib/Test/Harness/TAP.pod BioPerl-1.6.900/t/lib/Test/Harness/Assert.pm BioPerl-1.6.900/t/lib/Test/Harness/Util.pm BioPerl-1.6.900/t/lib/Test/Harness/Straps.pm BioPerl-1.6.900/t/lib/Array BioPerl-1.6.900/t/lib/Array/Compare.pm BioPerl-1.6.900/t/lib/Sub BioPerl-1.6.900/t/lib/Sub/Uplevel.pm BioPerl-1.6.900/t/lib/Tree BioPerl-1.6.900/t/lib/Tree/DAG_Node.pm BioPerl-1.6.900/t/Phenotype BioPerl-1.6.900/t/Phenotype/Measure.t BioPerl-1.6.900/t/Phenotype/OMIMentryAllelicVariant.t BioPerl-1.6.900/t/Phenotype/MeSH.t BioPerl-1.6.900/t/Phenotype/Phenotype.t BioPerl-1.6.900/t/Phenotype/OMIMentry.t BioPerl-1.6.900/t/Phenotype/OMIMparser.t BioPerl-1.6.900/t/Phenotype/Correlate.t BioPerl-1.6.900/t/Phenotype/MiniMIMentry.t BioPerl-1.6.900/t/Root BioPerl-1.6.900/t/Root/RootI.t BioPerl-1.6.900/t/Root/Exception.t BioPerl-1.6.900/t/Root/RootIO.t BioPerl-1.6.900/t/Root/Tempfile.t BioPerl-1.6.900/t/Root/Utilities.t BioPerl-1.6.900/t/Root/Storable.t BioPerl-1.6.900/t/Root/HTTPget.t BioPerl-1.6.900/t/PopGen BioPerl-1.6.900/t/PopGen/PopGen.t BioPerl-1.6.900/t/PopGen/PopGenSims.t BioPerl-1.6.900/t/PopGen/Coalescent.t BioPerl-1.6.900/t/PopGen/HtSNP.t BioPerl-1.6.900/t/PopGen/TagHaplotype.t BioPerl-1.6.900/t/PopGen/MK.t BioPerl-1.6.900/t/LiveSeq BioPerl-1.6.900/t/LiveSeq/Chain.t BioPerl-1.6.900/t/LiveSeq/LiveSeq.t BioPerl-1.6.900/t/LiveSeq/Mutator.t BioPerl-1.6.900/t/LiveSeq/Mutation.t BioPerl-1.6.900/t/SearchIO BioPerl-1.6.900/t/SearchIO/blastxml.t BioPerl-1.6.900/t/SearchIO/blasttable.t BioPerl-1.6.900/t/SearchIO/Tiling.t BioPerl-1.6.900/t/SearchIO/exonerate.t BioPerl-1.6.900/t/SearchIO/hmmer.t BioPerl-1.6.900/t/SearchIO/hmmer_pull.t BioPerl-1.6.900/t/SearchIO/wise.t BioPerl-1.6.900/t/SearchIO/infernal.t BioPerl-1.6.900/t/SearchIO/blast_pull.t BioPerl-1.6.900/t/SearchIO/blast.t BioPerl-1.6.900/t/SearchIO/SimilarityPair.t BioPerl-1.6.900/t/SearchIO/sim4.t BioPerl-1.6.900/t/SearchIO/rnamotif.t BioPerl-1.6.900/t/SearchIO/cross_match.t BioPerl-1.6.900/t/SearchIO/fasta.t BioPerl-1.6.900/t/SearchIO/waba.t BioPerl-1.6.900/t/SearchIO/axt.t BioPerl-1.6.900/t/SearchIO/CigarString.t BioPerl-1.6.900/t/SearchIO/erpin.t BioPerl-1.6.900/t/SearchIO/SearchIO.t BioPerl-1.6.900/t/SearchIO/psl.t BioPerl-1.6.900/t/SearchIO/gmap_f9.t BioPerl-1.6.900/t/SearchIO/megablast.t BioPerl-1.6.900/t/SearchIO/Writer BioPerl-1.6.900/t/SearchIO/Writer/TextWriter.t BioPerl-1.6.900/t/SearchIO/Writer/GbrowseGFF.t BioPerl-1.6.900/t/SearchIO/Writer/HitTableWriter.t BioPerl-1.6.900/t/SearchIO/Writer/HSPTableWriter.t BioPerl-1.6.900/t/SearchIO/Writer/HTMLWriter.t BioPerl-1.6.900/t/Structure BioPerl-1.6.900/t/Structure/Structure.t BioPerl-1.6.900/t/Structure/IO.t BioPerl-1.6.900/t/SeqFeature BioPerl-1.6.900/t/SeqFeature/LocationFactory.t BioPerl-1.6.900/t/SeqFeature/Unflattener.t BioPerl-1.6.900/t/SeqFeature/SeqAnalysisParser.t BioPerl-1.6.900/t/SeqFeature/SeqFeature.t BioPerl-1.6.900/t/SeqFeature/FeatureIO.t BioPerl-1.6.900/t/SeqFeature/RangeI.t BioPerl-1.6.900/t/SeqFeature/SeqFeaturePrimer.t BioPerl-1.6.900/t/SeqFeature/Location.t BioPerl-1.6.900/t/SeqFeature/Range.t BioPerl-1.6.900/t/SeqFeature/Unflattener2.t BioPerl-1.6.900/t/SeqFeature/Primer.t BioPerl-1.6.900/t/SeqFeature/SeqFeatCollection.t BioPerl-1.6.900/t/SeqFeature/Clone.t BioPerl-1.6.900/t/SeqFeature/SeqFeatAnnotated.t BioPerl-1.6.900/t/SeqTools BioPerl-1.6.900/t/SeqTools/OddCodes.t BioPerl-1.6.900/t/SeqTools/GuessSeqFormat.t BioPerl-1.6.900/t/SeqTools/SeqStats.t BioPerl-1.6.900/t/SeqTools/SeqUtils.t BioPerl-1.6.900/t/SeqTools/CodonTable.t BioPerl-1.6.900/t/SeqTools/ECnumber.t BioPerl-1.6.900/t/SeqTools/Backtranslate.t BioPerl-1.6.900/t/SeqTools/SeqPattern.t BioPerl-1.6.900/t/SeqTools/SeqWords.t BioPerl-1.6.900/t/Assembly BioPerl-1.6.900/t/Assembly/core.t BioPerl-1.6.900/t/Assembly/ContigSpectrum.t BioPerl-1.6.900/t/Assembly/IO BioPerl-1.6.900/t/Assembly/IO/bowtie.t BioPerl-1.6.900/t/Assembly/IO/sam.t BioPerl-1.6.900/t/ClusterIO BioPerl-1.6.900/t/ClusterIO/ClusterIO.t BioPerl-1.6.900/t/ClusterIO/unigene.t BioPerl-1.6.900/t/ClusterIO/SequenceFamily.t BioPerl-1.6.900/t/Tree BioPerl-1.6.900/t/Tree/Compatible.t BioPerl-1.6.900/t/Tree/RandomTreeFactory.t BioPerl-1.6.900/t/Tree/Node.t BioPerl-1.6.900/t/Tree/TreeStatistics.t BioPerl-1.6.900/t/Tree/Tree.t BioPerl-1.6.900/t/Tree/TreeIO.t BioPerl-1.6.900/t/Tree/PhyloNetwork BioPerl-1.6.900/t/Tree/PhyloNetwork/Factory.t BioPerl-1.6.900/t/Tree/PhyloNetwork/GraphViz.t BioPerl-1.6.900/t/Tree/PhyloNetwork/RandomFactory.t BioPerl-1.6.900/t/Tree/PhyloNetwork/TreeFactory.t BioPerl-1.6.900/t/Tree/PhyloNetwork/PhyloNetwork.t BioPerl-1.6.900/t/Tree/PhyloNetwork/MuVector.t BioPerl-1.6.900/t/Tree/TreeIO BioPerl-1.6.900/t/Tree/TreeIO/nexus.t BioPerl-1.6.900/t/Tree/TreeIO/nexml.t BioPerl-1.6.900/t/Tree/TreeIO/phyloxml.t BioPerl-1.6.900/t/Tree/TreeIO/newick.t BioPerl-1.6.900/t/Tree/TreeIO/nhx.t BioPerl-1.6.900/t/Tree/TreeIO/tabtree.t BioPerl-1.6.900/t/Tree/TreeIO/svggraph.t BioPerl-1.6.900/t/Tree/TreeIO/lintree.t BioPerl-1.6.900/t/Biblio BioPerl-1.6.900/t/Biblio/Biblio.t BioPerl-1.6.900/t/Biblio/eutils.t BioPerl-1.6.900/t/Biblio/biofetch.t BioPerl-1.6.900/t/Biblio/References.t BioPerl-1.6.900/t/Map BioPerl-1.6.900/t/Map/Map.t BioPerl-1.6.900/t/Map/Cyto.t BioPerl-1.6.900/t/Map/Physical.t BioPerl-1.6.900/t/Map/Linkage.t BioPerl-1.6.900/t/Map/MapIO.t BioPerl-1.6.900/t/Map/MicrosatelliteMarker.t BioPerl-1.6.900/t/Coordinate BioPerl-1.6.900/t/Coordinate/CoordinateMapper.t BioPerl-1.6.900/t/Coordinate/GeneCoordinateMapper.t BioPerl-1.6.900/t/Coordinate/CoordinateGraph.t BioPerl-1.6.900/t/RemoteDB BioPerl-1.6.900/t/RemoteDB/Taxonomy.t BioPerl-1.6.900/t/RemoteDB/RefSeq.t BioPerl-1.6.900/t/RemoteDB/EUtilities.t BioPerl-1.6.900/t/RemoteDB/MeSH.t BioPerl-1.6.900/t/RemoteDB/EMBL.t BioPerl-1.6.900/t/RemoteDB/SeqRead_fail.t BioPerl-1.6.900/t/RemoteDB/EntrezGene.t BioPerl-1.6.900/t/RemoteDB/GenPept.t BioPerl-1.6.900/t/RemoteDB/SeqVersion.t BioPerl-1.6.900/t/RemoteDB/SeqHound.t BioPerl-1.6.900/t/RemoteDB/BioFetch.t BioPerl-1.6.900/t/RemoteDB/GenBank.t BioPerl-1.6.900/t/RemoteDB/CUTG.t BioPerl-1.6.900/t/RemoteDB/SwissProt.t BioPerl-1.6.900/t/RemoteDB/HIV BioPerl-1.6.900/t/RemoteDB/HIV/HIVQuery.t BioPerl-1.6.900/t/RemoteDB/HIV/HIVAnnotProcessor.t BioPerl-1.6.900/t/RemoteDB/HIV/HIVQueryHelper.t BioPerl-1.6.900/t/RemoteDB/HIV/HIV.t BioPerl-1.6.900/t/RemoteDB/Query BioPerl-1.6.900/t/RemoteDB/Query/GenBank.t BioPerl-1.6.900/t/Ontology BioPerl-1.6.900/t/Ontology/Term.t BioPerl-1.6.900/t/Ontology/GraphAdaptor.t BioPerl-1.6.900/t/Ontology/GOterm.t BioPerl-1.6.900/t/Ontology/OntologyEngine.t BioPerl-1.6.900/t/Ontology/Ontology.t BioPerl-1.6.900/t/Ontology/RelationshipType.t BioPerl-1.6.900/t/Ontology/Relationship.t BioPerl-1.6.900/t/Ontology/OntologyStore.t BioPerl-1.6.900/t/Ontology/IO BioPerl-1.6.900/t/Ontology/IO/go.t BioPerl-1.6.900/t/Ontology/IO/obo.t BioPerl-1.6.900/t/Ontology/IO/interpro.t BioPerl-1.6.900/t/AlignIO BioPerl-1.6.900/t/AlignIO/clustalw.t BioPerl-1.6.900/t/AlignIO/psi.t BioPerl-1.6.900/t/AlignIO/msf.t BioPerl-1.6.900/t/AlignIO/xmfa.t BioPerl-1.6.900/t/AlignIO/mase.t BioPerl-1.6.900/t/AlignIO/po.t BioPerl-1.6.900/t/AlignIO/phylip.t BioPerl-1.6.900/t/AlignIO/selex.t BioPerl-1.6.900/t/AlignIO/bl2seq.t BioPerl-1.6.900/t/AlignIO/nexus.t BioPerl-1.6.900/t/AlignIO/nexml.t BioPerl-1.6.900/t/AlignIO/stockholm.t BioPerl-1.6.900/t/AlignIO/largemultifasta.t BioPerl-1.6.900/t/AlignIO/mega.t BioPerl-1.6.900/t/AlignIO/prodom.t BioPerl-1.6.900/t/AlignIO/metafasta.t BioPerl-1.6.900/t/AlignIO/pfam.t BioPerl-1.6.900/t/AlignIO/emboss.t BioPerl-1.6.900/t/AlignIO/maf.t BioPerl-1.6.900/t/AlignIO/fasta.t BioPerl-1.6.900/t/AlignIO/meme.t BioPerl-1.6.900/t/AlignIO/arp.t BioPerl-1.6.900/t/AlignIO/AlignIO.t BioPerl-1.6.900/t/data BioPerl-1.6.900/t/data/HUMBETGLOA.grailexp BioPerl-1.6.900/t/data/HUMBETGLOA.mzef BioPerl-1.6.900/t/data/intrablock-comment.nex BioPerl-1.6.900/t/data/lysozyme6.simple.protml BioPerl-1.6.900/t/data/targetp.out BioPerl-1.6.900/t/data/popgen_saureus.multidat BioPerl-1.6.900/t/data/testfuzzy.genbank BioPerl-1.6.900/t/data/bug3086.embl BioPerl-1.6.900/t/data/characters.nexml.old.xml BioPerl-1.6.900/t/data/polymorphism.xml BioPerl-1.6.900/t/data/glimmer3-fragment.predict BioPerl-1.6.900/t/data/seqfile.pir BioPerl-1.6.900/t/data/megablast_output.paracel_btk BioPerl-1.6.900/t/data/test.gcg BioPerl-1.6.900/t/data/Primate_mtDNA.nex BioPerl-1.6.900/t/data/tricky.wublast BioPerl-1.6.900/t/data/reference_ace.ace BioPerl-1.6.900/t/data/sim4.rev BioPerl-1.6.900/t/data/AHCYL1.kegg BioPerl-1.6.900/t/data/seqdatabase.ini BioPerl-1.6.900/t/data/HUMBETGLOA.gff BioPerl-1.6.900/t/data/headerless.psl BioPerl-1.6.900/t/data/03_bootstraps.xml BioPerl-1.6.900/t/data/multi_2.fa BioPerl-1.6.900/t/data/codeml315.mlc BioPerl-1.6.900/t/data/tandem_repeats_finder.dat BioPerl-1.6.900/t/data/LOAD_Ccd1.dnd BioPerl-1.6.900/t/data/genomic-seq.epcr BioPerl-1.6.900/t/data/BAB68554.gb BioPerl-1.6.900/t/data/MmCT BioPerl-1.6.900/t/data/tree_nonewline.nexus BioPerl-1.6.900/t/data/tandem_repeats_finder_no_desc.dat BioPerl-1.6.900/t/data/EG352462.gbxml BioPerl-1.6.900/t/data/bug2399.tblastn BioPerl-1.6.900/t/data/testaln.msf BioPerl-1.6.900/t/data/longnames.aln BioPerl-1.6.900/t/data/cds-266.fas BioPerl-1.6.900/t/data/glimmer3-fragment.detail BioPerl-1.6.900/t/data/traittree.nexus BioPerl-1.6.900/t/data/codeml_nssites.mlc BioPerl-1.6.900/t/data/short.blx BioPerl-1.6.900/t/data/U71225.gb BioPerl-1.6.900/t/data/pfam_tests.stk BioPerl-1.6.900/t/data/testaln.fasta BioPerl-1.6.900/t/data/hmmsearch.out BioPerl-1.6.900/t/data/HUMBETGLOA.FASTA BioPerl-1.6.900/t/data/hybrid2.gff3 BioPerl-1.6.900/t/data/LittleChrY.dbsnp.xml BioPerl-1.6.900/t/data/aaml_pairwise.mlc BioPerl-1.6.900/t/data/rebase.itype2 BioPerl-1.6.900/t/data/U71225.gb.win BioPerl-1.6.900/t/data/01_basic.xml BioPerl-1.6.900/t/data/pictogram.fa BioPerl-1.6.900/t/data/c200-vs-yeast.BLASTN.m8 BioPerl-1.6.900/t/data/test.ztr BioPerl-1.6.900/t/data/repeatmasker.fa.out BioPerl-1.6.900/t/data/ecoli_domains.rps.xml BioPerl-1.6.900/t/data/rfam_tests.stk BioPerl-1.6.900/t/data/hybrid1.gff3 BioPerl-1.6.900/t/data/Glimmer2.out BioPerl-1.6.900/t/data/sv40_small.xml BioPerl-1.6.900/t/data/signalp.short BioPerl-1.6.900/t/data/multiline-intrablock-comment.nex BioPerl-1.6.900/t/data/no_hsps.blastp BioPerl-1.6.900/t/data/1.bed BioPerl-1.6.900/t/data/test.ref.fas BioPerl-1.6.900/t/data/SPAN_Family8a.nex BioPerl-1.6.900/t/data/503384.MEGABLAST.2 BioPerl-1.6.900/t/data/sofa.ontology BioPerl-1.6.900/t/data/bl2seq.blastn.rev BioPerl-1.6.900/t/data/mpath.ontology.test BioPerl-1.6.900/t/data/pre_rel9.swiss BioPerl-1.6.900/t/data/Mcjanrna_rdbII.gbk BioPerl-1.6.900/t/data/exonerate.whitespace_before_query.works BioPerl-1.6.900/t/data/footprinter.out BioPerl-1.6.900/t/data/testaln.mase BioPerl-1.6.900/t/data/test.pir BioPerl-1.6.900/t/data/ecoli_domains.rpsblast BioPerl-1.6.900/t/data/genemark.out BioPerl-1.6.900/t/data/gf-s71.needle BioPerl-1.6.900/t/data/27-contig_Newbler.ace BioPerl-1.6.900/t/data/ar.embl BioPerl-1.6.900/t/data/503384.MEGABLAST.0 BioPerl-1.6.900/t/data/char-matrix-spaces.nex BioPerl-1.6.900/t/data/branchSite.mlc BioPerl-1.6.900/t/data/cysprot.fa BioPerl-1.6.900/t/data/bug2942.blastx BioPerl-1.6.900/t/data/meme.dat BioPerl-1.6.900/t/data/little.largemultifasta BioPerl-1.6.900/t/data/hs_owlmonkey.fas BioPerl-1.6.900/t/data/AF165282.gb BioPerl-1.6.900/t/data/unigene.data BioPerl-1.6.900/t/data/primer3_infile.txt BioPerl-1.6.900/t/data/ecoli-trna-qrna.out BioPerl-1.6.900/t/data/GO.defs.test BioPerl-1.6.900/t/data/AE003528_ecoli.bls BioPerl-1.6.900/t/data/test.mase BioPerl-1.6.900/t/data/mutations.xml BioPerl-1.6.900/t/data/worm_fam_2785.cdna BioPerl-1.6.900/t/data/NC_001284.gbk BioPerl-1.6.900/t/data/trna.strict.rnamotif BioPerl-1.6.900/t/data/ATF14F8.gbk BioPerl-1.6.900/t/data/dnaEbsub_ecoli.wutblastx BioPerl-1.6.900/t/data/expected.blast.out BioPerl-1.6.900/t/data/sparsealn.needle BioPerl-1.6.900/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml BioPerl-1.6.900/t/data/genomic-seq.mzef BioPerl-1.6.900/t/data/HUMBETGLOA.tblastx BioPerl-1.6.900/t/data/radical-whitespace_02.nex BioPerl-1.6.900/t/data/dna2.fa BioPerl-1.6.900/t/data/NT_021877.gbk BioPerl-1.6.900/t/data/AE003644_Adh-genomic.gb BioPerl-1.6.900/t/data/stress_test_pubmed.xml BioPerl-1.6.900/t/data/U83300.bsml BioPerl-1.6.900/t/data/testdata.crossmatch BioPerl-1.6.900/t/data/bug2391.megablast BioPerl-1.6.900/t/data/nucmatrix.txt BioPerl-1.6.900/t/data/baseml.pairwise BioPerl-1.6.900/t/data/plague_yeast.bls.xml BioPerl-1.6.900/t/data/L77119.hmmer BioPerl-1.6.900/t/data/brassica_ATH.WUBLASTN BioPerl-1.6.900/t/data/signalp.hmm.short BioPerl-1.6.900/t/data/codeml_nan.mlc BioPerl-1.6.900/t/data/test.genbank BioPerl-1.6.900/t/data/signalp.negative.out BioPerl-1.6.900/t/data/interpro_sample.xml BioPerl-1.6.900/t/data/signalp.nn.short BioPerl-1.6.900/t/data/testaln2.fasta BioPerl-1.6.900/t/data/testaln2.arp BioPerl-1.6.900/t/data/seg.out BioPerl-1.6.900/t/data/swiss.dat BioPerl-1.6.900/t/data/quoted-strings1.nex BioPerl-1.6.900/t/data/AY763288.gb BioPerl-1.6.900/t/data/P33897 BioPerl-1.6.900/t/data/GO.defs.test2 BioPerl-1.6.900/t/data/PX1CG.gb BioPerl-1.6.900/t/data/multiseq.bls BioPerl-1.6.900/t/data/codeml43_nssites.mlc BioPerl-1.6.900/t/data/Rab1.chaos-xml BioPerl-1.6.900/t/data/blast_plus.blastp BioPerl-1.6.900/t/data/atp1.matrix BioPerl-1.6.900/t/data/hsinsulin.blastcl3.blastn BioPerl-1.6.900/t/data/roa1.swiss BioPerl-1.6.900/t/data/exonerate.output.dontwork BioPerl-1.6.900/t/data/tblastn.out BioPerl-1.6.900/t/data/long-names.nex BioPerl-1.6.900/t/data/crab.njb BioPerl-1.6.900/t/data/SwissProt.dat BioPerl-1.6.900/t/data/cysprot1.FASTA BioPerl-1.6.900/t/data/humts1.pal BioPerl-1.6.900/t/data/CG2865.fasaln BioPerl-1.6.900/t/data/ZABJ4EA7014.CH878695.1.blast.txt BioPerl-1.6.900/t/data/codeml43.mlc BioPerl-1.6.900/t/data/mini-align.aln BioPerl-1.6.900/t/data/char-interleave.nex BioPerl-1.6.900/t/data/testaln.fastq BioPerl-1.6.900/t/data/test.tseq BioPerl-1.6.900/t/data/interpro.xml BioPerl-1.6.900/t/data/ay149291.gb BioPerl-1.6.900/t/data/mutations.old.dat BioPerl-1.6.900/t/data/tmhmm.out BioPerl-1.6.900/t/data/hg16_chroms.gff BioPerl-1.6.900/t/data/protpars.phy BioPerl-1.6.900/t/data/spidey.test1 BioPerl-1.6.900/t/data/AF305198.gb BioPerl-1.6.900/t/data/1A3I.pdb BioPerl-1.6.900/t/data/radical-whitespace.nex BioPerl-1.6.900/t/data/Genscan.FastA BioPerl-1.6.900/t/data/GlimmerM.out BioPerl-1.6.900/t/data/02_dogfish_no_taxrefs.xml BioPerl-1.6.900/t/data/BC000007.gbk BioPerl-1.6.900/t/data/psiblast.xml BioPerl-1.6.900/t/data/psi_xml.dat BioPerl-1.6.900/t/data/tmp.fst BioPerl-1.6.900/t/data/Q8GBD3.swiss BioPerl-1.6.900/t/data/nhx-bacteria.nhx BioPerl-1.6.900/t/data/test1.blasttab3 BioPerl-1.6.900/t/data/test.gcgfasta BioPerl-1.6.900/t/data/ecolitst.fa BioPerl-1.6.900/t/data/ssp160.embl.1 BioPerl-1.6.900/t/data/barns-combined.nex BioPerl-1.6.900/t/data/lucy.qual BioPerl-1.6.900/t/data/test.pfam BioPerl-1.6.900/t/data/blast_no_hit_desc.txt BioPerl-1.6.900/t/data/hs_fugu.newick BioPerl-1.6.900/t/data/AAC12660.fa BioPerl-1.6.900/t/data/spaces.nex BioPerl-1.6.900/t/data/entrezgene.dat BioPerl-1.6.900/t/data/phipsi.out BioPerl-1.6.900/t/data/cysprot1a.msf BioPerl-1.6.900/t/data/hmmpfam_fake.out BioPerl-1.6.900/t/data/bl2seq.tblastx.out BioPerl-1.6.900/t/data/pseudowise.out BioPerl-1.6.900/t/data/SPAN_Family7n.nex BioPerl-1.6.900/t/data/ctgdemo.fpc BioPerl-1.6.900/t/data/c200-vs-yeast.BLASTN BioPerl-1.6.900/t/data/sbay_c127.fas BioPerl-1.6.900/t/data/no_cds_example.gb BioPerl-1.6.900/t/data/cysprot.needle BioPerl-1.6.900/t/data/polymorphism.dat BioPerl-1.6.900/t/data/testaln.prodom BioPerl-1.6.900/t/data/lysozyme6.protml BioPerl-1.6.900/t/data/testaln.phylip BioPerl-1.6.900/t/data/test.swiss BioPerl-1.6.900/t/data/frac_problems2.blast BioPerl-1.6.900/t/data/test.fasta BioPerl-1.6.900/t/data/singlet_w_CT.ace BioPerl-1.6.900/t/data/hs_est.est2genome BioPerl-1.6.900/t/data/test2.infernal BioPerl-1.6.900/t/data/test.embl BioPerl-1.6.900/t/data/cysprot.tblastn BioPerl-1.6.900/t/data/test.phd BioPerl-1.6.900/t/data/test.lasergene BioPerl-1.6.900/t/data/test.abi BioPerl-1.6.900/t/data/lucy.stderr BioPerl-1.6.900/t/data/frac_problems3.blast BioPerl-1.6.900/t/data/rebase.withrefm BioPerl-1.6.900/t/data/test.interpro BioPerl-1.6.900/t/data/example.phase BioPerl-1.6.900/t/data/bug2982.embl BioPerl-1.6.900/t/data/trees.nexml.xml BioPerl-1.6.900/t/data/myco_sites.gff BioPerl-1.6.900/t/data/ECAPAH02.embl BioPerl-1.6.900/t/data/rel9.swiss BioPerl-1.6.900/t/data/test.metafasta BioPerl-1.6.900/t/data/test.bam BioPerl-1.6.900/t/data/signalp.hmm.summary BioPerl-1.6.900/t/data/cysprot1.fa BioPerl-1.6.900/t/data/tol-2010-02-18.nhx BioPerl-1.6.900/t/data/dnaEbsub_ecoli.wublastx BioPerl-1.6.900/t/data/contigspectrumtest.tigr BioPerl-1.6.900/t/data/testfile.erpin BioPerl-1.6.900/t/data/acefile.singlets BioPerl-1.6.900/t/data/biorecipe.nhx BioPerl-1.6.900/t/data/04_labeled_ancestors.xml BioPerl-1.6.900/t/data/seqs.fas BioPerl-1.6.900/t/data/testdbaccnums.out BioPerl-1.6.900/t/data/02_mackerel_no_taxrefs.xml BioPerl-1.6.900/t/data/interpro_relationship.xml BioPerl-1.6.900/t/data/genemark-fragment.out BioPerl-1.6.900/t/data/no_semicolon.newick BioPerl-1.6.900/t/data/adh.mb_tree.nexus BioPerl-1.6.900/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml BioPerl-1.6.900/t/data/5X_1895.FASTXY BioPerl-1.6.900/t/data/frac_problems.blast BioPerl-1.6.900/t/data/in.fasta BioPerl-1.6.900/t/data/cysprot1a.fa BioPerl-1.6.900/t/data/tab1part.mif BioPerl-1.6.900/t/data/qualfile.qual BioPerl-1.6.900/t/data/test_badlf.gcg BioPerl-1.6.900/t/data/seqxml.xml BioPerl-1.6.900/t/data/singleNSsite.mlc BioPerl-1.6.900/t/data/lucy.seq BioPerl-1.6.900/t/data/sequencefamily.dat BioPerl-1.6.900/t/data/test.waba BioPerl-1.6.900/t/data/1A11.pdb BioPerl-1.6.900/t/data/genewise.out BioPerl-1.6.900/t/data/2008.blasttable BioPerl-1.6.900/t/data/no-genes.genscan BioPerl-1.6.900/t/data/multifa.seq BioPerl-1.6.900/t/data/PAM250 BioPerl-1.6.900/t/data/match.output BioPerl-1.6.900/t/data/BN000066-tpa.embl BioPerl-1.6.900/t/data/popgen_saureus.dat BioPerl-1.6.900/t/data/phylipdist.out BioPerl-1.6.900/t/data/example.vcf BioPerl-1.6.900/t/data/BK000016-tpa.gbk BioPerl-1.6.900/t/data/ribosome-slippage.gb BioPerl-1.6.900/t/data/dmel_2Lchunk.gb BioPerl-1.6.900/t/data/genomic-seq.fasta BioPerl-1.6.900/t/data/sim4.for.rev BioPerl-1.6.900/t/data/traits.tab BioPerl-1.6.900/t/data/blat.psLayout3 BioPerl-1.6.900/t/data/bl2seq.bug940.out BioPerl-1.6.900/t/data/dcr1_sp.WUBLASTP BioPerl-1.6.900/t/data/testaln.aln BioPerl-1.6.900/t/data/test.locuslink BioPerl-1.6.900/t/data/longnames.dnd BioPerl-1.6.900/t/data/bug1986.blastp BioPerl-1.6.900/t/data/test.raw BioPerl-1.6.900/t/data/multi.blast.m8 BioPerl-1.6.900/t/data/regulation_test.obo BioPerl-1.6.900/t/data/blast.report BioPerl-1.6.900/t/data/chad100.scf BioPerl-1.6.900/t/data/contig-by-hand.wublastp BioPerl-1.6.900/t/data/sample_dataset.tigr BioPerl-1.6.900/t/data/bug2862.pmr BioPerl-1.6.900/t/data/ecolitst.wublastp BioPerl-1.6.900/t/data/humor.maf BioPerl-1.6.900/t/data/crypto.sim4-3 BioPerl-1.6.900/t/data/cys1_dicdi.water BioPerl-1.6.900/t/data/test.game BioPerl-1.6.900/t/data/mini-AE001405.gb BioPerl-1.6.900/t/data/testaln.nexus BioPerl-1.6.900/t/data/cysprot1b.fa BioPerl-1.6.900/t/data/crypto.sim4-4 BioPerl-1.6.900/t/data/factor7.embl BioPerl-1.6.900/t/data/omim_genemap_test_nolinebreak BioPerl-1.6.900/t/data/Glimmer3.predict BioPerl-1.6.900/t/data/testaln.arp BioPerl-1.6.900/t/data/test.cns.fastq BioPerl-1.6.900/t/data/test.gcgblast BioPerl-1.6.900/t/data/blosum62.bla BioPerl-1.6.900/t/data/mus.bls.xml BioPerl-1.6.900/t/data/tandem_repeats_finder.noresults BioPerl-1.6.900/t/data/calm.swiss BioPerl-1.6.900/t/data/mixedmast.dat BioPerl-1.6.900/t/data/HUMBETGLOA.fa BioPerl-1.6.900/t/data/bl2seq.blastn BioPerl-1.6.900/t/data/MSGEFTUA.gb BioPerl-1.6.900/t/data/blastp2215.blast BioPerl-1.6.900/t/data/codeml4.mlc BioPerl-1.6.900/t/data/dnaE-bsub.fa BioPerl-1.6.900/t/data/NC_006511-short.gbk BioPerl-1.6.900/t/data/BEL16-LTR_AG.embl BioPerl-1.6.900/t/data/characters+trees.nexml.xml BioPerl-1.6.900/t/data/mutations.old.xml BioPerl-1.6.900/t/data/sbay_c545-yeast.BLASTZ.PSL BioPerl-1.6.900/t/data/test.meme2 BioPerl-1.6.900/t/data/bug2937.fasta BioPerl-1.6.900/t/data/P39765.gb BioPerl-1.6.900/t/data/trees.nexml.old.xml BioPerl-1.6.900/t/data/test.nhx BioPerl-1.6.900/t/data/phylipdist-36.out BioPerl-1.6.900/t/data/newblast.xml BioPerl-1.6.900/t/data/mutations.dat BioPerl-1.6.900/t/data/noninterleaved.phy BioPerl-1.6.900/t/data/protpars_longid.phy BioPerl-1.6.900/t/data/test.bowtie BioPerl-1.6.900/t/data/test.nh BioPerl-1.6.900/t/data/8HVP.pdb BioPerl-1.6.900/t/data/phyloxml_examples.xml BioPerl-1.6.900/t/data/test.infernal BioPerl-1.6.900/t/data/neighbor.dist BioPerl-1.6.900/t/data/test.txt BioPerl-1.6.900/t/data/signalp.summary BioPerl-1.6.900/t/data/ENr111.mfa.example.elems BioPerl-1.6.900/t/data/omim_genemap_test BioPerl-1.6.900/t/data/primedseq.fa BioPerl-1.6.900/t/data/ay007676.gb BioPerl-1.6.900/t/data/AB077698.gb BioPerl-1.6.900/t/data/new_blastn.txt BioPerl-1.6.900/t/data/revcomp_mrna.gb BioPerl-1.6.900/t/data/popstats.prettybase BioPerl-1.6.900/t/data/ay116458.gb BioPerl-1.6.900/t/data/AF032047.gbk BioPerl-1.6.900/t/data/bug2982.gb BioPerl-1.6.900/t/data/puzzle.tre BioPerl-1.6.900/t/data/tab3part.mif BioPerl-1.6.900/t/data/P35527.gb BioPerl-1.6.900/t/data/D10483.gbk BioPerl-1.6.900/t/data/codeml.mlc BioPerl-1.6.900/t/data/promoterwise.out BioPerl-1.6.900/t/data/test_singlets.maq BioPerl-1.6.900/t/data/biofpc.cor BioPerl-1.6.900/t/data/urease.tre.nexus BioPerl-1.6.900/t/data/BOSS_DROME.FASTP_v35_04 BioPerl-1.6.900/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml BioPerl-1.6.900/t/data/qrna-relloc.out BioPerl-1.6.900/t/data/test_clear_range.fastq BioPerl-1.6.900/t/data/cysprot.msf BioPerl-1.6.900/t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml BioPerl-1.6.900/t/data/basic-bush.nex BioPerl-1.6.900/t/data/transfac.dat BioPerl-1.6.900/t/data/testaln.xmfa BioPerl-1.6.900/t/data/X98338_Adh-mRNA.gb BioPerl-1.6.900/t/data/amino.fa BioPerl-1.6.900/t/data/bl2seq.blastx.out BioPerl-1.6.900/t/data/basic-ladder.nex BioPerl-1.6.900/t/data/a_thaliana.blastn BioPerl-1.6.900/t/data/vecscreen_simple.test_output BioPerl-1.6.900/t/data/cysprot_vs_gadfly.FASTA BioPerl-1.6.900/t/data/purine_v081.infernal BioPerl-1.6.900/t/data/bug2901.fa BioPerl-1.6.900/t/data/05_ancestral_states.xml BioPerl-1.6.900/t/data/DQ018368.gb BioPerl-1.6.900/t/data/exsignalp.out BioPerl-1.6.900/t/data/multi.phd BioPerl-1.6.900/t/data/empty.bl2seq BioPerl-1.6.900/t/data/bug2246.blast BioPerl-1.6.900/t/data/cysprot1b.newick BioPerl-1.6.900/t/data/M0.mlc BioPerl-1.6.900/t/data/1BPT.pdb BioPerl-1.6.900/t/data/gmap_f9.txt BioPerl-1.6.900/t/data/example.hap BioPerl-1.6.900/t/data/test.interpro-go.xml BioPerl-1.6.900/t/data/aaml.mlc BioPerl-1.6.900/t/data/test 2.txt BioPerl-1.6.900/t/data/bug2869.tree BioPerl-1.6.900/t/data/mapmaker.out BioPerl-1.6.900/t/data/crab.dat.cn BioPerl-1.6.900/t/data/Treebase-chlamy-dna.nex BioPerl-1.6.900/t/data/psiblastreport.out BioPerl-1.6.900/t/data/ex1.nucl.nhx BioPerl-1.6.900/t/data/dnaE-bsub-prot.fa BioPerl-1.6.900/t/data/test.tab BioPerl-1.6.900/t/data/alnfile.fasta BioPerl-1.6.900/t/data/hmmscan_sec_struct.out BioPerl-1.6.900/t/data/hs_owlmonkey.fasta BioPerl-1.6.900/t/data/test.exp BioPerl-1.6.900/t/data/test.tigrxml BioPerl-1.6.900/t/data/Fang_2003.xml BioPerl-1.6.900/t/data/directives.gff3 BioPerl-1.6.900/t/data/hs_owlmonkey.aln BioPerl-1.6.900/t/data/bug1986.blast2 BioPerl-1.6.900/t/data/bug3021.gmap BioPerl-1.6.900/t/data/geneid_1.0.out BioPerl-1.6.900/t/data/CG11099.fasaln BioPerl-1.6.900/t/data/omim_text_test BioPerl-1.6.900/t/data/1ZZ19XR301R-Alignment.tblastn BioPerl-1.6.900/t/data/test.fastq BioPerl-1.6.900/t/data/testaln.psi BioPerl-1.6.900/t/data/O_sat.wgs BioPerl-1.6.900/t/data/cysprot.water BioPerl-1.6.900/t/data/multifa.seq.qual BioPerl-1.6.900/t/data/pep-266.aln BioPerl-1.6.900/t/data/rpsblast.bls BioPerl-1.6.900/t/data/test_data.axt BioPerl-1.6.900/t/data/roa1.genbank BioPerl-1.6.900/t/data/yn00.mlc BioPerl-1.6.900/t/data/wellcome_tol.nhx BioPerl-1.6.900/t/data/compLD_missingtest.prettybase BioPerl-1.6.900/t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml BioPerl-1.6.900/t/data/compLD_test.prettybase BioPerl-1.6.900/t/data/test1.wublastp BioPerl-1.6.900/t/data/primer3_output.txt BioPerl-1.6.900/t/data/exonerate.output.works BioPerl-1.6.900/t/data/03_bootstraps_in_tag.xml BioPerl-1.6.900/t/data/yeast.tRNAscanSE BioPerl-1.6.900/t/data/cysprot1b.msf BioPerl-1.6.900/t/data/fgenesh.out BioPerl-1.6.900/t/data/bootstrap.tre BioPerl-1.6.900/t/data/roa1_v2.dat BioPerl-1.6.900/t/data/knownGene.gff3 BioPerl-1.6.900/t/data/crypto.sim4-0 BioPerl-1.6.900/t/data/T7.aln BioPerl-1.6.900/t/data/AnnIX-v003.gbk BioPerl-1.6.900/t/data/Kingdoms_DNA.nex BioPerl-1.6.900/t/data/tab2part.mif BioPerl-1.6.900/t/data/swisspfam.data BioPerl-1.6.900/t/data/bug2120.phd BioPerl-1.6.900/t/data/NC_006346.gb BioPerl-1.6.900/t/data/polymorphism.old.xml BioPerl-1.6.900/t/data/bug2473.fasta BioPerl-1.6.900/t/data/Glimmer3.detail BioPerl-1.6.900/t/data/D12555.gbk BioPerl-1.6.900/t/data/sprintf.rnamotif BioPerl-1.6.900/t/data/U58726.gb BioPerl-1.6.900/t/data/interpro_short.xml BioPerl-1.6.900/t/data/test.embl2sq BioPerl-1.6.900/t/data/biofpc.fpc BioPerl-1.6.900/t/data/testaln.metafasta BioPerl-1.6.900/t/data/test.genbank.noseq BioPerl-1.6.900/t/data/hemoglobinA.meg BioPerl-1.6.900/t/data/echofilter.wublastn BioPerl-1.6.900/t/data/dnaEbsub_ecoli.wutblastn BioPerl-1.6.900/t/data/dna1.fa BioPerl-1.6.900/t/data/NM_002254.gb BioPerl-1.6.900/t/data/roa1.dat BioPerl-1.6.900/t/data/interpro_ebi.xml BioPerl-1.6.900/t/data/roa1.gbxml BioPerl-1.6.900/t/data/characters.nexml.xml BioPerl-1.6.900/t/data/gmap_f9-reverse-strand.txt BioPerl-1.6.900/t/data/test.ctf BioPerl-1.6.900/t/data/test.tsv BioPerl-1.6.900/t/data/multi_blast.bls BioPerl-1.6.900/t/data/BLOSUM50 BioPerl-1.6.900/t/data/AY095303S1.gbk BioPerl-1.6.900/t/data/acefile.ace.1 BioPerl-1.6.900/t/data/masta.dat BioPerl-1.6.900/t/data/genomewise.out BioPerl-1.6.900/t/data/GlimmerHMM.out BioPerl-1.6.900/t/data/SPAN_Family4nl.nex BioPerl-1.6.900/t/data/ecolitst.noseqs.wublastp BioPerl-1.6.900/t/data/hmmscan.out BioPerl-1.6.900/t/data/U71225.gb.unix BioPerl-1.6.900/t/data/alleles.fas BioPerl-1.6.900/t/data/genewise_output.paracel_btk BioPerl-1.6.900/t/data/insulin.water BioPerl-1.6.900/t/data/mast.dat BioPerl-1.6.900/t/data/test.ace BioPerl-1.6.900/t/data/test.xls BioPerl-1.6.900/t/data/Bird_Ovomucoids.nex BioPerl-1.6.900/t/data/hmmsearch3.out BioPerl-1.6.900/t/data/UnaSmithHIV-both.nex BioPerl-1.6.900/t/data/semicolon.newick BioPerl-1.6.900/t/data/lucy.info BioPerl-1.6.900/t/data/primer3_outfile.txt BioPerl-1.6.900/t/data/multi_1.fa BioPerl-1.6.900/t/data/multi.blast.m9 BioPerl-1.6.900/t/data/hmmpfam.out BioPerl-1.6.900/t/data/test.meme BioPerl-1.6.900/t/data/version3.scf BioPerl-1.6.900/t/data/bug2453.maf BioPerl-1.6.900/t/data/NC_008536.gb BioPerl-1.6.900/t/data/testaln.pfam BioPerl-1.6.900/t/data/sim4.for.for BioPerl-1.6.900/t/data/component.ontology.test2 BioPerl-1.6.900/t/data/so.obo BioPerl-1.6.900/t/data/multiseq_tags.phd BioPerl-1.6.900/t/data/test2.raw BioPerl-1.6.900/t/data/component.ontology.test BioPerl-1.6.900/t/data/signalp.positive.out BioPerl-1.6.900/t/data/no_FH.embl BioPerl-1.6.900/t/data/spidey.noalignment BioPerl-1.6.900/t/data/quoted-strings2.nex BioPerl-1.6.900/t/data/testaln.stockholm BioPerl-1.6.900/t/data/hmmscan_multi_domain.out BioPerl-1.6.900/t/data/bl2seq.out BioPerl-1.6.900/t/data/hmmpfam_cs.out BioPerl-1.6.900/t/data/cysprot1b.hmmsearch BioPerl-1.6.900/t/data/sp_subset.obo BioPerl-1.6.900/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml BioPerl-1.6.900/t/data/ecolitst.bls BioPerl-1.6.900/t/data/gmap_f9-multiple_results.txt BioPerl-1.6.900/t/data/stress_test_medline.xml BioPerl-1.6.900/t/data/testdat.exonerate BioPerl-1.6.900/t/data/HUMBETGLOA.grail BioPerl-1.6.900/t/data/prints.out BioPerl-1.6.900/t/data/M12730.gb BioPerl-1.6.900/t/data/dq519393.gb BioPerl-1.6.900/t/data/assembly_with_singlets.ace BioPerl-1.6.900/t/data/genomic-seq.genscan BioPerl-1.6.900/t/data/mapmaker.txt BioPerl-1.6.900/t/data/13-pilE-F.scf BioPerl-1.6.900/t/data/withrefm.906 BioPerl-1.6.900/t/data/test.pln BioPerl-1.6.900/t/data/baseml.usertree BioPerl-1.6.900/t/data/signalp.nn.summary BioPerl-1.6.900/t/data/crab.nj BioPerl-1.6.900/t/data/nei_gojobori_test.aln BioPerl-1.6.900/t/data/version2.scf BioPerl-1.6.900/t/data/test_singlets.cns.fastq BioPerl-1.6.900/t/data/test.ptt BioPerl-1.6.900/t/data/test.maq BioPerl-1.6.900/t/data/phi.out BioPerl-1.6.900/t/data/catalase-webblast.BLASTP BioPerl-1.6.900/t/data/cds_sample.embl BioPerl-1.6.900/t/data/testaln.list BioPerl-1.6.900/t/data/testaln.po BioPerl-1.6.900/t/data/testaln.selex BioPerl-1.6.900/t/data/map_hem BioPerl-1.6.900/t/data/map_hem/HEM13.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM1.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM1-HEM12.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM13-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM15.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM1-HEM3.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM2-HEM13.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM3.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM3-HEM12.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM12-HEM13.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM4-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM4-HEM12.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM4.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM4.fa BioPerl-1.6.900/t/data/map_hem/HEM3-HEM12.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM4.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM3-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM1.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM2-HEM12.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM4-HEM12.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM13-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM4-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM12.fa BioPerl-1.6.900/t/data/map_hem/HEM3-HEM4.fa BioPerl-1.6.900/t/data/map_hem/HEM14-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM4-HEM13.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM2-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM3-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM12.fa.revcom BioPerl-1.6.900/t/data/map_hem/HEM2-HEM3.fa BioPerl-1.6.900/t/data/map_hem/yeast.nc.1.freq BioPerl-1.6.900/t/data/map_hem/HEM2.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM1-HEM3.fa BioPerl-1.6.900/t/data/map_hem/HEM3-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM2.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM3-HEM13.fa BioPerl-1.6.900/t/data/map_hem/HEM4.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM2-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM12.fa BioPerl-1.6.900/t/data/map_hem/HEM4-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM4-HEM13.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM2.fa.revcom BioPerl-1.6.900/t/data/map_hem/HEM2-HEM13.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM12-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM12-HEM13.fa BioPerl-1.6.900/t/data/map_hem/HEM3-HEM4.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM2.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM13-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM3.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM14.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM13.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM1-HEM13.fa BioPerl-1.6.900/t/data/map_hem/HEM2-HEM4.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM14-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM12-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM12.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM12.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM3-HEM14.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM4.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM15.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM12-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM1-HEM13.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM3.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM3-HEM13.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM1-HEM15.fa BioPerl-1.6.900/t/data/map_hem/HEM12-HEM14.fa BioPerl-1.6.900/t/data/map_hem/HEM2.ups.fa_.revcom BioPerl-1.6.900/t/data/map_hem/HEM4-HEM15.meme.txt BioPerl-1.6.900/t/data/map_hem/HEM14.ups.fa_ BioPerl-1.6.900/t/data/map_hem/HEM13-HEM15.meme.txt BioPerl-1.6.900/t/data/eutils BioPerl-1.6.900/t/data/eutils/elink_neighbor_corr.xml BioPerl-1.6.900/t/data/eutils/egquery.xml BioPerl-1.6.900/t/data/eutils/elink_llinks.xml BioPerl-1.6.900/t/data/eutils/epost.xml BioPerl-1.6.900/t/data/eutils/elink_ncheck_corr.xml BioPerl-1.6.900/t/data/eutils/elink_ncheck.xml BioPerl-1.6.900/t/data/eutils/elink_nhist_corr.xml BioPerl-1.6.900/t/data/eutils/elink_nhist.xml BioPerl-1.6.900/t/data/eutils/espell.xml BioPerl-1.6.900/t/data/eutils/esummary1.xml BioPerl-1.6.900/t/data/eutils/elink_neighbor.xml BioPerl-1.6.900/t/data/eutils/esearch1.xml BioPerl-1.6.900/t/data/eutils/elink_scores.xml BioPerl-1.6.900/t/data/eutils/einfo_dbs.xml BioPerl-1.6.900/t/data/eutils/elink_acheck.xml BioPerl-1.6.900/t/data/eutils/elink_multidb.xml BioPerl-1.6.900/t/data/eutils/elink_lcheck_corr.xml BioPerl-1.6.900/t/data/eutils/elink_multidb_corr.xml BioPerl-1.6.900/t/data/eutils/esearch2.xml BioPerl-1.6.900/t/data/eutils/esummary2.xml BioPerl-1.6.900/t/data/eutils/elink_llinks_corr.xml BioPerl-1.6.900/t/data/eutils/elink_acheck_corr.xml BioPerl-1.6.900/t/data/eutils/elink_lcheck.xml BioPerl-1.6.900/t/data/eutils/elink_dball.xml BioPerl-1.6.900/t/data/eutils/einfo.xml BioPerl-1.6.900/t/data/seqfeaturedb BioPerl-1.6.900/t/data/seqfeaturedb/test.gff3 BioPerl-1.6.900/t/data/consed_project BioPerl-1.6.900/t/data/consed_project/phd_dir BioPerl-1.6.900/t/data/consed_project/phd_dir/ML4922R.phd.1 BioPerl-1.6.900/t/data/consed_project/phd_dir/ML4947F.phd.1 BioPerl-1.6.900/t/data/consed_project/phd_dir/ML4924R.phd.1 BioPerl-1.6.900/t/data/consed_project/phd_dir/ML4924F.phd.1 BioPerl-1.6.900/t/data/consed_project/edit_dir BioPerl-1.6.900/t/data/consed_project/edit_dir/test_projectNewChromats.fof BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.qual BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.log BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.phrap.out BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1 BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.problems BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.newtags BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2 BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.screen.out BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project_to_alu.cross BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.log BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.view BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.fasta.screen BioPerl-1.6.900/t/data/consed_project/edit_dir/test_project.contigs BioPerl-1.6.900/t/data/bad_dbfa BioPerl-1.6.900/t/data/bad_dbfa/bug3172.fa BioPerl-1.6.900/t/data/fastq BioPerl-1.6.900/t/data/fastq/test2_solexa.fastq BioPerl-1.6.900/t/data/fastq/error_short_qual.fastq BioPerl-1.6.900/t/data/fastq/error_qual_del.fastq BioPerl-1.6.900/t/data/fastq/bug2335.fastq BioPerl-1.6.900/t/data/fastq/solexa_faked.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_at_qual.fastq BioPerl-1.6.900/t/data/fastq/example.fasta BioPerl-1.6.900/t/data/fastq/error_spaces.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_in_qual.fastq BioPerl-1.6.900/t/data/fastq/error_tabs.fastq BioPerl-1.6.900/t/data/fastq/illumina_faked.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_at_seq.fastq BioPerl-1.6.900/t/data/fastq/example.qual BioPerl-1.6.900/t/data/fastq/error_qual_tab.fastq BioPerl-1.6.900/t/data/fastq/wrapping_issues.fastq BioPerl-1.6.900/t/data/fastq/error_double_seq.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_in_plus.fastq BioPerl-1.6.900/t/data/fastq/tricky.fastq BioPerl-1.6.900/t/data/fastq/error_double_qual.fastq BioPerl-1.6.900/t/data/fastq/sanger_faked.fastq BioPerl-1.6.900/t/data/fastq/error_diff_ids.fastq BioPerl-1.6.900/t/data/fastq/sanger_93.fastq BioPerl-1.6.900/t/data/fastq/error_long_qual.fastq BioPerl-1.6.900/t/data/fastq/error_qual_space.fastq BioPerl-1.6.900/t/data/fastq/solexa_example.fastq BioPerl-1.6.900/t/data/fastq/error_qual_escape.fastq BioPerl-1.6.900/t/data/fastq/example.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_at_plus.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_in_title.fastq BioPerl-1.6.900/t/data/fastq/test1_sanger.fastq BioPerl-1.6.900/t/data/fastq/evil_wrapping.fastq BioPerl-1.6.900/t/data/fastq/error_qual_null.fastq BioPerl-1.6.900/t/data/fastq/error_no_qual.fastq BioPerl-1.6.900/t/data/fastq/test3_illumina.fastq BioPerl-1.6.900/t/data/fastq/error_qual_unit_sep.fastq BioPerl-1.6.900/t/data/fastq/error_trunc_in_seq.fastq BioPerl-1.6.900/t/data/fastq/error_qual_vtab.fastq BioPerl-1.6.900/t/data/transfac_pro BioPerl-1.6.900/t/data/transfac_pro/readme.txt BioPerl-1.6.900/t/data/transfac_pro/matrix.dat BioPerl-1.6.900/t/data/transfac_pro/gene.dat BioPerl-1.6.900/t/data/transfac_pro/reference.dat BioPerl-1.6.900/t/data/transfac_pro/site.dat BioPerl-1.6.900/t/data/transfac_pro/factor.dat BioPerl-1.6.900/t/data/transfac_pro/fragment.dat BioPerl-1.6.900/t/data/dbfa BioPerl-1.6.900/t/data/dbfa/2.fa BioPerl-1.6.900/t/data/dbfa/5.fa BioPerl-1.6.900/t/data/dbfa/4.fa BioPerl-1.6.900/t/data/dbfa/7.fa BioPerl-1.6.900/t/data/dbfa/6.fa BioPerl-1.6.900/t/data/dbfa/1.fa BioPerl-1.6.900/t/data/dbfa/3.fa BioPerl-1.6.900/t/data/biodbgff BioPerl-1.6.900/t/data/biodbgff/test.gff BioPerl-1.6.900/t/data/biodbgff/test.gff3 BioPerl-1.6.900/t/data/msout BioPerl-1.6.900/t/data/msout/msout_infile4 BioPerl-1.6.900/t/data/msout/msout_infile1 BioPerl-1.6.900/t/data/msout/msout_infile3 BioPerl-1.6.900/t/data/msout/msout_infile2 BioPerl-1.6.900/t/data/codeml_lysozyme BioPerl-1.6.900/t/data/codeml_lysozyme/4fold.nuc BioPerl-1.6.900/t/data/codeml_lysozyme/mlc BioPerl-1.6.900/t/data/codeml_lysozyme/lnf BioPerl-1.6.900/t/data/codeml_lysozyme/2NG.tt BioPerl-1.6.900/t/data/codeml_lysozyme/2NG.dN BioPerl-1.6.900/t/data/codeml_lysozyme/lysozymeSmall.txt BioPerl-1.6.900/t/data/codeml_lysozyme/rst1 BioPerl-1.6.900/t/data/codeml_lysozyme/rst BioPerl-1.6.900/t/data/codeml_lysozyme/lysozymeSmall.ctl BioPerl-1.6.900/t/data/codeml_lysozyme/rub BioPerl-1.6.900/t/data/codeml_lysozyme/lysozymeSmall.trees BioPerl-1.6.900/t/data/codeml_lysozyme/2NG.dS BioPerl-1.6.900/t/data/dbqual BioPerl-1.6.900/t/data/dbqual/2.qual BioPerl-1.6.900/t/data/dbqual/1.qual BioPerl-1.6.900/t/data/dbqual/3.qual BioPerl-1.6.900/t/data/mbsout BioPerl-1.6.900/t/data/mbsout/mbsout_infile3 BioPerl-1.6.900/t/data/mbsout/mbsout_infile2 BioPerl-1.6.900/t/data/mbsout/mbsout_infile1 BioPerl-1.6.900/t/data/taxdump BioPerl-1.6.900/t/data/taxdump/nodes.dmp BioPerl-1.6.900/t/data/taxdump/names.dmp BioPerl-1.6.900/t/data/registry BioPerl-1.6.900/t/data/registry/flat BioPerl-1.6.900/t/data/registry/flat/seqdatabase.ini BioPerl-1.6.900/t/data/registry/bdb BioPerl-1.6.900/t/data/registry/bdb/seqdatabase.ini BioPerl-1.6.900/t/Restriction BioPerl-1.6.900/t/Restriction/Analysis.t BioPerl-1.6.900/t/Restriction/Analysis-refac.t BioPerl-1.6.900/t/Restriction/Gel.t BioPerl-1.6.900/t/Restriction/IO.t BioPerl-1.6.900/t/Draw BioPerl-1.6.900/t/Draw/Pictogram.t BioPerl-1.6.900/t/Variation BioPerl-1.6.900/t/Variation/DNAMutation.t BioPerl-1.6.900/t/Variation/Variation_IO.t BioPerl-1.6.900/t/Variation/AAReverseMutate.t BioPerl-1.6.900/t/Variation/RNAChange.t BioPerl-1.6.900/t/Variation/SeqDiff.t BioPerl-1.6.900/t/Variation/SNP.t BioPerl-1.6.900/t/Variation/AAChange.t BioPerl-1.6.900/t/Variation/Allele.t BioPerl-1.6.900/t/SeqIO BioPerl-1.6.900/t/SeqIO/table.t BioPerl-1.6.900/t/SeqIO/gbxml.t BioPerl-1.6.900/t/SeqIO/Handler.t BioPerl-1.6.900/t/SeqIO/pln.t BioPerl-1.6.900/t/SeqIO/chadoxml.t BioPerl-1.6.900/t/SeqIO/mbsout.t BioPerl-1.6.900/t/SeqIO/qual.t BioPerl-1.6.900/t/SeqIO/raw.t BioPerl-1.6.900/t/SeqIO/largefasta.t BioPerl-1.6.900/t/SeqIO/bsml_sax.t BioPerl-1.6.900/t/SeqIO/ctf.t BioPerl-1.6.900/t/SeqIO/genbank.t BioPerl-1.6.900/t/SeqIO/phd.t BioPerl-1.6.900/t/SeqIO/nexml.t BioPerl-1.6.900/t/SeqIO/Multiple_fasta.t BioPerl-1.6.900/t/SeqIO/asciitree.t BioPerl-1.6.900/t/SeqIO/Splicedseq.t BioPerl-1.6.900/t/SeqIO/strider.t BioPerl-1.6.900/t/SeqIO/fastq.t BioPerl-1.6.900/t/SeqIO/game.t BioPerl-1.6.900/t/SeqIO/SeqIO.t BioPerl-1.6.900/t/SeqIO/scf.t BioPerl-1.6.900/t/SeqIO/lasergene.t BioPerl-1.6.900/t/SeqIO/flybase_chadoxml.t BioPerl-1.6.900/t/SeqIO/entrezgene.t BioPerl-1.6.900/t/SeqIO/metafasta.t BioPerl-1.6.900/t/SeqIO/ace.t BioPerl-1.6.900/t/SeqIO/alf.t BioPerl-1.6.900/t/SeqIO/MultiFile.t BioPerl-1.6.900/t/SeqIO/ztr.t BioPerl-1.6.900/t/SeqIO/exp.t BioPerl-1.6.900/t/SeqIO/pir.t BioPerl-1.6.900/t/SeqIO/agave.t BioPerl-1.6.900/t/SeqIO/locuslink.t BioPerl-1.6.900/t/SeqIO/seqxml.t BioPerl-1.6.900/t/SeqIO/embl.t BioPerl-1.6.900/t/SeqIO/chaos.t BioPerl-1.6.900/t/SeqIO/msout.t BioPerl-1.6.900/t/SeqIO/kegg.t BioPerl-1.6.900/t/SeqIO/chaosxml.t BioPerl-1.6.900/t/SeqIO/fasta.t BioPerl-1.6.900/t/SeqIO/interpro.t BioPerl-1.6.900/t/SeqIO/tab.t BioPerl-1.6.900/t/SeqIO/abi.t BioPerl-1.6.900/t/SeqIO/swiss.t BioPerl-1.6.900/t/SeqIO/SeqBuilder.t BioPerl-1.6.900/t/SeqIO/tinyseq.t BioPerl-1.6.900/t/SeqIO/bsml.t BioPerl-1.6.900/t/SeqIO/excel.t BioPerl-1.6.900/t/SeqIO/tigr.t BioPerl-1.6.900/t/SeqIO/tigrxml.t BioPerl-1.6.900/t/SeqIO/gcg.t BioPerl-1.6.900/scripts BioPerl-1.6.900/scripts/README BioPerl-1.6.900/scripts/DB-HIV BioPerl-1.6.900/scripts/DB-HIV/hivq.PLS BioPerl-1.6.900/scripts/taxa BioPerl-1.6.900/scripts/taxa/taxonomy2tree.PLS BioPerl-1.6.900/scripts/taxa/TAG BioPerl-1.6.900/scripts/taxa/local_taxonomydb_query.PLS BioPerl-1.6.900/scripts/taxa/classify_hits_kingdom.PLS BioPerl-1.6.900/scripts/taxa/query_entrez_taxa.PLS BioPerl-1.6.900/scripts/taxa/taxid4species.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF BioPerl-1.6.900/scripts/Bio-DB-GFF/meta_gff.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/process_sgd.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/genbank2gff.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/bulk_load_gff.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/process_gadfly.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/README BioPerl-1.6.900/scripts/Bio-DB-GFF/genbank2gff3.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/process_wormbase.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/generate_histogram.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/fast_load_gff.PLS BioPerl-1.6.900/scripts/Bio-DB-GFF/load_gff.PLS BioPerl-1.6.900/scripts/searchio BioPerl-1.6.900/scripts/searchio/TAG BioPerl-1.6.900/scripts/searchio/README BioPerl-1.6.900/scripts/searchio/hmmer_to_table.PLS BioPerl-1.6.900/scripts/searchio/parse_hmmsearch.PLS BioPerl-1.6.900/scripts/searchio/fastam9_to_table.PLS BioPerl-1.6.900/scripts/searchio/filter_search.PLS BioPerl-1.6.900/scripts/searchio/search2table.PLS BioPerl-1.6.900/scripts/das BioPerl-1.6.900/scripts/das/TAG BioPerl-1.6.900/scripts/das/README BioPerl-1.6.900/scripts/das/das_server.pl BioPerl-1.6.900/scripts/Bio-DB-EUtilities BioPerl-1.6.900/scripts/Bio-DB-EUtilities/einfo.PLS BioPerl-1.6.900/scripts/DB BioPerl-1.6.900/scripts/DB/biofetch_genbank_proxy.PLS BioPerl-1.6.900/scripts/DB/TAG BioPerl-1.6.900/scripts/DB/bioflat_index.PLS BioPerl-1.6.900/scripts/DB/flanks.PLS BioPerl-1.6.900/scripts/DB/biogetseq.PLS BioPerl-1.6.900/scripts/utilities BioPerl-1.6.900/scripts/utilities/search2BSML.PLS BioPerl-1.6.900/scripts/utilities/TAG BioPerl-1.6.900/scripts/utilities/search2alnblocks.PLS BioPerl-1.6.900/scripts/utilities/search2gff.PLS BioPerl-1.6.900/scripts/utilities/bp_mrtrans.PLS BioPerl-1.6.900/scripts/utilities/mutate.PLS BioPerl-1.6.900/scripts/utilities/mask_by_search.PLS BioPerl-1.6.900/scripts/utilities/bp_nrdb.PLS BioPerl-1.6.900/scripts/utilities/pairwise_kaks.PLS BioPerl-1.6.900/scripts/utilities/README BioPerl-1.6.900/scripts/utilities/bp_sreformat.PLS BioPerl-1.6.900/scripts/utilities/download_query_genbank.PLS BioPerl-1.6.900/scripts/utilities/bp_netinstall.PLS BioPerl-1.6.900/scripts/utilities/remote_blast.PLS BioPerl-1.6.900/scripts/utilities/dbsplit.PLS BioPerl-1.6.900/scripts/utilities/search2tribe.PLS BioPerl-1.6.900/scripts/utilities/revtrans-motif.PLS BioPerl-1.6.900/scripts/utilities/seq_length.PLS BioPerl-1.6.900/scripts/seqstats BioPerl-1.6.900/scripts/seqstats/TAG BioPerl-1.6.900/scripts/seqstats/chaos_plot.PLS BioPerl-1.6.900/scripts/seqstats/aacomp.PLS BioPerl-1.6.900/scripts/seqstats/oligo_count.PLS BioPerl-1.6.900/scripts/seqstats/gccalc.PLS BioPerl-1.6.900/scripts/index BioPerl-1.6.900/scripts/index/TAG BioPerl-1.6.900/scripts/index/bp_index.PLS BioPerl-1.6.900/scripts/index/bp_seqret.PLS BioPerl-1.6.900/scripts/index/bp_fetch.PLS BioPerl-1.6.900/scripts/popgen BioPerl-1.6.900/scripts/popgen/heterogeneity_test.PLS BioPerl-1.6.900/scripts/popgen/composite_LD.PLS BioPerl-1.6.900/scripts/seq BioPerl-1.6.900/scripts/seq/extract_feature_seq.PLS BioPerl-1.6.900/scripts/seq/make_mrna_protein.PLS BioPerl-1.6.900/scripts/seq/TAG BioPerl-1.6.900/scripts/seq/unflatten_seq.PLS BioPerl-1.6.900/scripts/seq/split_seq.PLS BioPerl-1.6.900/scripts/seq/seqretsplit.PLS BioPerl-1.6.900/scripts/seq/translate_seq.PLS BioPerl-1.6.900/scripts/seq/seqconvert.PLS BioPerl-1.6.900/scripts/biblio BioPerl-1.6.900/scripts/biblio/TAG BioPerl-1.6.900/scripts/biblio/biblio.PLS BioPerl-1.6.900/scripts/Bio-DB-SeqFeature-Store BioPerl-1.6.900/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS BioPerl-1.6.900/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS BioPerl-1.6.900/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS BioPerl-1.6.900/scripts/tree BioPerl-1.6.900/scripts/tree/blast2tree.PLS BioPerl-1.6.900/scripts/tree/TAG BioPerl-1.6.900/scripts/tree/tree2pag.PLS BioPerl-1.6.900/scripts/tree/nexus2nh.PLS BioPerl-1.6.900/models BioPerl-1.6.900/models/bio_map.dia BioPerl-1.6.900/models/population_proposal.txt BioPerl-1.6.900/models/popgen.dia BioPerl-1.6.900/models/coordinatemapper.dia BioPerl-1.6.900/models/README BioPerl-1.6.900/models/bioperl.dia BioPerl-1.6.900/models/map_proposal.txt BioPerl-1.6.900/models/biblio.dia BioPerl-1.6.900/models/maps_and_markers.dia BioPerl-1.6.900/models/bio_liveseq_variation.dia BioPerl-1.6.900/models/bio_restriction.dia BioPerl-1.6.900/doc BioPerl-1.6.900/doc/makedoc.PL BioPerl-1.6.900/doc/README BioPerl-1.6.900/doc/Deobfuscator BioPerl-1.6.900/doc/Deobfuscator/Build.PL BioPerl-1.6.900/doc/Deobfuscator/LICENSE BioPerl-1.6.900/doc/Deobfuscator/README BioPerl-1.6.900/doc/Deobfuscator/Changes BioPerl-1.6.900/doc/Deobfuscator/excluded_modules.txt BioPerl-1.6.900/doc/Deobfuscator/Makefile.PL BioPerl-1.6.900/doc/Deobfuscator/MANIFEST BioPerl-1.6.900/doc/Deobfuscator/META.yml BioPerl-1.6.900/doc/Deobfuscator/lib BioPerl-1.6.900/doc/Deobfuscator/lib/Deobfuscator.pm BioPerl-1.6.900/doc/Deobfuscator/t BioPerl-1.6.900/doc/Deobfuscator/t/pod.t BioPerl-1.6.900/doc/Deobfuscator/t/00.load.t BioPerl-1.6.900/doc/Deobfuscator/cgi-bin BioPerl-1.6.900/doc/Deobfuscator/cgi-bin/deob_detail.cgi BioPerl-1.6.900/doc/Deobfuscator/cgi-bin/deob_flowchart.png BioPerl-1.6.900/doc/Deobfuscator/cgi-bin/deob_help.html BioPerl-1.6.900/doc/Deobfuscator/cgi-bin/deob_interface.cgi BioPerl-1.6.900/doc/Deobfuscator/bin BioPerl-1.6.900/doc/Deobfuscator/bin/deob_index.pl CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.900.tar.gz >>> C:\Perl64-5.12\bin\perl.exe Build.PL could not find ParserDetails.ini in C:/cpanfly-5.12/var/megalib/XML/SAX Checking prerequisites... requires: ! DB_File is not installed recommends: * GraphViz is not installed Checking optional features... DB_File Tests.........disabled requires: ! DB_File is not installed EntrezGene............disabled requires: ! Bio::ASN1::EntrezGene is not installed Pg Tests..............disabled requires: ! DBD::Pg is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation ############################# WARNING ############################# Bio::ASN1::EntrezGene not found. This is an *optional* module; however, because it has a circular dependency with BioPerl we do not include it on our list of recommended modules. If you require EntrezGene functionality, you can install Bio::ASN1::EntrezGene after BioPerl has finished installing. ############################# WARNING ############################# Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl' version '1.006900' ---- Unsatisfied dependencies detected during ---- ---- CJFIELDS/BioPerl-1.6.900.tar.gz ---- DB_File [requires] Running Build test Delayed until after prerequisites Running test for module 'DB_File' ______________________ D i s t r o P r e f s ______________________ DB_File.yml[0] Running make for P/PM/PMQS/DB_File-1.822.tar.gz Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0 PMQS/DB_File-1.822.tar.gz [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0 Running Build for C/CJ/CJFIELDS/BioPerl-1.6.900.tar.gz Has already been unwrapped into directory C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.900.tar.gz Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.900.tar.gz' failed when processing 'PMQS/DB_File-1.822.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> C:\Perl64-5.12\bin\perl.exe ./Build Building BioPerl CJFIELDS/BioPerl-1.6.900.tar.gz C:\Perl64-5.12\bin\perl.exe ./Build -- OK Running Build test >>> C:\Perl64-5.12\bin\perl.exe ./Build test verbose=1 Copying scripts\utilities\search2alnblocks.PLS -> blib\script\search2alnblocks.PLS Changing sharpbang in blib\script\search2alnblocks.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\search2alnblocks.PLS.bak Copying scripts\DB\bioflat_index.PLS -> blib\script\bioflat_index.PLS Changing sharpbang in blib\script\bioflat_index.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bioflat_index.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.PLS Copying scripts\utilities\mask_by_search.PLS -> blib\script\mask_by_search.PLS Changing sharpbang in blib\script\mask_by_search.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\mask_by_search.PLS.bak Copying scripts\utilities\bp_mrtrans.PLS -> blib\script\bp_mrtrans.PLS Changing sharpbang in blib\script\bp_mrtrans.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_mrtrans.PLS.bak Copying scripts\utilities\bp_sreformat.PLS -> blib\script\bp_sreformat.PLS Changing sharpbang in blib\script\bp_sreformat.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_sreformat.PLS.bak Copying scripts\utilities\search2gff.PLS -> blib\script\search2gff.PLS Changing sharpbang in blib\script\search2gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\search2gff.PLS.bak Copying scripts\searchio\hmmer_to_table.PLS -> blib\script\hmmer_to_table.PLS Changing sharpbang in blib\script\hmmer_to_table.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\hmmer_to_table.PLS.bak Copying scripts\seq\seqconvert.PLS -> blib\script\seqconvert.PLS Changing sharpbang in blib\script\seqconvert.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\seqconvert.PLS.bak Copying scripts\DB\flanks.PLS -> blib\script\flanks.PLS Changing sharpbang in blib\script\flanks.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\flanks.PLS.bak Copying scripts\utilities\seq_length.PLS -> blib\script\seq_length.PLS Changing sharpbang in blib\script\seq_length.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\seq_length.PLS.bak Copying scripts\DB-HIV\hivq.PLS -> blib\script\hivq.PLS Changing sharpbang in blib\script\hivq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\hivq.PLS.bak Copying scripts\Bio-DB-GFF\genbank2gff.PLS -> blib\script\genbank2gff.PLS Changing sharpbang in blib\script\genbank2gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\genbank2gff.PLS.bak Copying scripts\Bio-DB-EUtilities\einfo.PLS -> blib\script\einfo.PLS Changing sharpbang in blib\script\einfo.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\einfo.PLS.bak Copying scripts\Bio-DB-GFF\process_gadfly.PLS -> blib\script\process_gadfly.PLS Changing sharpbang in blib\script\process_gadfly.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\process_gadfly.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.PLS Changing sharpbang in blib\script\bp_seqfeature_delete.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_seqfeature_delete.PLS.bak Copying scripts\seq\extract_feature_seq.PLS -> blib\script\extract_feature_seq.PLS Changing sharpbang in blib\script\extract_feature_seq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\extract_feature_seq.PLS.bak Copying scripts\seq\make_mrna_protein.PLS -> blib\script\make_mrna_protein.PLS Changing sharpbang in blib\script\make_mrna_protein.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\make_mrna_protein.PLS.bak Copying scripts\DB\biofetch_genbank_proxy.PLS -> blib\script\biofetch_genbank_proxy.PLS Changing sharpbang in blib\script\biofetch_genbank_proxy.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\biofetch_genbank_proxy.PLS.bak Copying scripts\tree\nexus2nh.PLS -> blib\script\nexus2nh.PLS Changing sharpbang in blib\script\nexus2nh.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\nexus2nh.PLS.bak Copying scripts\searchio\filter_search.PLS -> blib\script\filter_search.PLS Changing sharpbang in blib\script\filter_search.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\filter_search.PLS.bak Copying scripts\tree\tree2pag.PLS -> blib\script\tree2pag.PLS Changing sharpbang in blib\script\tree2pag.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\tree2pag.PLS.bak Copying scripts\taxa\local_taxonomydb_query.PLS -> blib\script\local_taxonomydb_query.PLS Changing sharpbang in blib\script\local_taxonomydb_query.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\local_taxonomydb_query.PLS.bak Copying scripts\utilities\search2BSML.PLS -> blib\script\search2BSML.PLS Changing sharpbang in blib\script\search2BSML.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\search2BSML.PLS.bak Copying scripts\Bio-DB-GFF\process_sgd.PLS -> blib\script\process_sgd.PLS Changing sharpbang in blib\script\process_sgd.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\process_sgd.PLS.bak Copying scripts\utilities\search2tribe.PLS -> blib\script\search2tribe.PLS Changing sharpbang in blib\script\search2tribe.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\search2tribe.PLS.bak Copying scripts\Bio-DB-GFF\generate_histogram.PLS -> blib\script\generate_histogram.PLS Changing sharpbang in blib\script\generate_histogram.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\generate_histogram.PLS.bak Copying scripts\taxa\query_entrez_taxa.PLS -> blib\script\query_entrez_taxa.PLS Changing sharpbang in blib\script\query_entrez_taxa.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\query_entrez_taxa.PLS.bak Copying scripts\utilities\dbsplit.PLS -> blib\script\dbsplit.PLS Changing sharpbang in blib\script\dbsplit.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\dbsplit.PLS.bak Copying scripts\tree\blast2tree.PLS -> blib\script\blast2tree.PLS Changing sharpbang in blib\script\blast2tree.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\blast2tree.PLS.bak Copying scripts\Bio-DB-GFF\load_gff.PLS -> blib\script\load_gff.PLS Changing sharpbang in blib\script\load_gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\load_gff.PLS.bak Copying scripts\das\das_server.pl -> blib\script\das_server.pl Changing sharpbang in blib\script\das_server.pl to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\das_server.pl.bak Copying scripts\utilities\mutate.PLS -> blib\script\mutate.PLS Changing sharpbang in blib\script\mutate.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\mutate.PLS.bak Copying scripts\seq\unflatten_seq.PLS -> blib\script\unflatten_seq.PLS Changing sharpbang in blib\script\unflatten_seq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\unflatten_seq.PLS.bak Copying scripts\seqstats\chaos_plot.PLS -> blib\script\chaos_plot.PLS Changing sharpbang in blib\script\chaos_plot.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\chaos_plot.PLS.bak Copying scripts\Bio-DB-GFF\bulk_load_gff.PLS -> blib\script\bulk_load_gff.PLS Changing sharpbang in blib\script\bulk_load_gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bulk_load_gff.PLS.bak Copying scripts\Bio-DB-GFF\fast_load_gff.PLS -> blib\script\fast_load_gff.PLS Changing sharpbang in blib\script\fast_load_gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\fast_load_gff.PLS.bak Copying scripts\utilities\revtrans-motif.PLS -> blib\script\revtrans-motif.PLS Changing sharpbang in blib\script\revtrans-motif.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\revtrans-motif.PLS.bak Copying scripts\searchio\search2table.PLS -> blib\script\search2table.PLS Changing sharpbang in blib\script\search2table.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\search2table.PLS.bak Copying scripts\index\bp_seqret.PLS -> blib\script\bp_seqret.PLS Changing sharpbang in blib\script\bp_seqret.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_seqret.PLS.bak Copying scripts\popgen\composite_LD.PLS -> blib\script\composite_LD.PLS Changing sharpbang in blib\script\composite_LD.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\composite_LD.PLS.bak Copying scripts\biblio\biblio.PLS -> blib\script\biblio.PLS Changing sharpbang in blib\script\biblio.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\biblio.PLS.bak Copying scripts\seq\split_seq.PLS -> blib\script\split_seq.PLS Changing sharpbang in blib\script\split_seq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\split_seq.PLS.bak Copying scripts\searchio\parse_hmmsearch.PLS -> blib\script\parse_hmmsearch.PLS Changing sharpbang in blib\script\parse_hmmsearch.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\parse_hmmsearch.PLS.bak Copying scripts\Bio-DB-GFF\process_wormbase.PLS -> blib\script\process_wormbase.PLS Changing sharpbang in blib\script\process_wormbase.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\process_wormbase.PLS.bak Copying scripts\utilities\download_query_genbank.PLS -> blib\script\download_query_genbank.PLS Changing sharpbang in blib\script\download_query_genbank.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\download_query_genbank.PLS.bak Copying scripts\seqstats\aacomp.PLS -> blib\script\aacomp.PLS Changing sharpbang in blib\script\aacomp.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\aacomp.PLS.bak Copying scripts\utilities\bp_nrdb.PLS -> blib\script\bp_nrdb.PLS Changing sharpbang in blib\script\bp_nrdb.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_nrdb.PLS.bak Copying scripts\popgen\heterogeneity_test.PLS -> blib\script\heterogeneity_test.PLS Changing sharpbang in blib\script\heterogeneity_test.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\heterogeneity_test.PLS.bak Copying scripts\index\bp_fetch.PLS -> blib\script\bp_fetch.PLS Changing sharpbang in blib\script\bp_fetch.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_fetch.PLS.bak Copying scripts\taxa\taxid4species.PLS -> blib\script\taxid4species.PLS Changing sharpbang in blib\script\taxid4species.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\taxid4species.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.PLS Changing sharpbang in blib\script\bp_seqfeature_load.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_seqfeature_load.PLS.bak Copying scripts\taxa\taxonomy2tree.PLS -> blib\script\taxonomy2tree.PLS Changing sharpbang in blib\script\taxonomy2tree.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\taxonomy2tree.PLS.bak Copying scripts\Bio-DB-GFF\genbank2gff3.PLS -> blib\script\genbank2gff3.PLS Changing sharpbang in blib\script\genbank2gff3.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\genbank2gff3.PLS.bak Copying scripts\Bio-DB-GFF\meta_gff.PLS -> blib\script\meta_gff.PLS Changing sharpbang in blib\script\meta_gff.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\meta_gff.PLS.bak Copying scripts\seqstats\oligo_count.PLS -> blib\script\oligo_count.PLS Changing sharpbang in blib\script\oligo_count.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\oligo_count.PLS.bak Copying scripts\seq\seqretsplit.PLS -> blib\script\seqretsplit.PLS Changing sharpbang in blib\script\seqretsplit.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\seqretsplit.PLS.bak Copying scripts\index\bp_index.PLS -> blib\script\bp_index.PLS Changing sharpbang in blib\script\bp_index.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_index.PLS.bak Copying scripts\utilities\bp_netinstall.PLS -> blib\script\bp_netinstall.PLS Changing sharpbang in blib\script\bp_netinstall.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\bp_netinstall.PLS.bak Copying scripts\seqstats\gccalc.PLS -> blib\script\gccalc.PLS Changing sharpbang in blib\script\gccalc.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\gccalc.PLS.bak Copying scripts\DB\biogetseq.PLS -> blib\script\biogetseq.PLS Changing sharpbang in blib\script\biogetseq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\biogetseq.PLS.bak Copying scripts\seq\translate_seq.PLS -> blib\script\translate_seq.PLS Changing sharpbang in blib\script\translate_seq.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\translate_seq.PLS.bak Copying scripts\searchio\fastam9_to_table.PLS -> blib\script\fastam9_to_table.PLS Changing sharpbang in blib\script\fastam9_to_table.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\fastam9_to_table.PLS.bak Copying scripts\taxa\classify_hits_kingdom.PLS -> blib\script\classify_hits_kingdom.PLS Changing sharpbang in blib\script\classify_hits_kingdom.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\classify_hits_kingdom.PLS.bak Copying scripts\utilities\remote_blast.PLS -> blib\script\remote_blast.PLS Changing sharpbang in blib\script\remote_blast.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\remote_blast.PLS.bak Copying scripts\utilities\pairwise_kaks.PLS -> blib\script\pairwise_kaks.PLS Changing sharpbang in blib\script\pairwise_kaks.PLS to C:\Perl64-5.12\bin\perl.exe Deleting blib\script\pairwise_kaks.PLS.bak t/Align/AlignStats.t ......................... 1..45 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::AlignIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - The object isa Bio::Align::AlignI ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - The object isa Bio::Align::AlignI ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::Matrix::PhylipDist ok 39 ok 40 ok 41 ok 42 - The object isa Bio::PrimarySeqI ok 43 ok 44 - Warn if seqs don't overlap ok 45 ok t/Align/AlignUtil.t .......................... 1..33 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok t/Align/Graphics.t ........................... 1..41 ok 1 - use Bio::Align::Graphics; ok 2 - require Bio::Align::Graphics; ok 3 - Bio::Align::Graphics->can(...) ok 4 - input is defined ok 5 - AlignIO object is defined ok 6 - The object isa Bio::AlignIO ok 7 - alignment is there and defined ok 8 - all starts are present ok 9 - all ends are present ok 10 - all colors are present ok 11 - first end is further than first start ok 12 - second end is further than second start ok 13 - third end is further than third start ok 14 - domain labels are present ok 15 - domain starts are present ok 16 - domain ends are present ok 17 - domain colors are present ok 18 - label - first end is further than first start ok 19 - label - second end is further than second start ok 20 - label - third end is further than third start ok 21 - first label start is within domain range ok 22 - second label start is within domain range ok 23 - third label start is within domain range ok 24 - first label end is within domain range ok 25 - second label end is within domain range ok 26 - third label end is within domain range ok 27 - individual labels work ok 28 - The object isa Bio::Align::Graphics ok 29 - new object is defined ok 30 - pad_bottom is right ok 31 - default pad_top is right ok 32 - start point loaded ok 33 - end point loaded ok 34 - color of domain loaded ok 35 - domain labels loaded ok 36 - label starts loaded ok 37 - label ends loaded ok 38 - label colors loaded ok 39 - labels loaded ok 40 - output file is png ok 41 - wrapping length is not zero ok t/Align/SimpleAlign.t ........................ 1..199 ok 1 - use Bio::SimpleAlign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::Location::Simple; ok 5 - use Bio::Location::Split; ok 6 - The object isa Bio::AlignIO ok 7 - pfam input test ok 8 - match_line ok 9 - The object isa Bio::Align::AlignI ok 10 - num_sequences ok 11 - num_sequences ok 12 - select_noncont ok 13 - select_noncont ok 14 - num_sequences ok 15 - select_noncont ok 16 - select_noncont ok 17 - each_seq ok 18 - get_nse ok 19 - id ok 20 - num_gaps ok 21 - each_alphabetically ok 22 - column_from_residue_number ok 23 - display_name get/set ok 24 - display_name get ok 25 - consensus_string ok 26 - consensus_string ok 27 - consensus_string ok 28 ok 29 - each_seq_with_id ok 30 - is_flush ok 31 - id get/set ok 32 - length ok 33 - num_residues ok 34 - num_sequences ok 35 - overall_percentage_identity ok 36 - overall_percentage_identity (align) ok 37 - overall_percentage_identity (short) ok 38 - overall_percentage_identity (long) ok 39 - average_percentage_identity ok 40 ok 41 - set_displayname_count ok 42 ok 43 - set_displayname_flat ok 44 ok 45 - set_displayname_normal ok 46 ok 47 ok 48 - uppercase, map_chars ok 49 - match_line ok 50 - remove_seqs ok 51 - remove_seqs ok 52 - add_seq ok 53 - add_seq ok 54 - get_seq_by_pos ok 55 - get_seq_by_pos ok 56 ok 57 ok 58 ok 59 - purge ok 60 - purge ok 61 - IO::String consensus_iupac ok 62 - IO::String write_aln normal ok 63 - IO::String write_aln slice ok 64 - IO::String write_aln slice ok 65 - IO::String write_aln slice ok 66 - IO::String write_aln slice ok 67 - IO::String write_aln slice ok 68 ok 69 - remove_columns by position ok 70 - remove_columns by position (wrong order) ok 71 - cigar_line ok 72 - cigar_line ok 73 - cigar_line ok 74 - cigar_line ok 75 - sort_alphabetically - before ok 76 ok 77 - sort_alphabetically - after ok 78 - remove_gaps ok 79 - remove_gaps all_gaps_only ok 80 - set_new_reference ok 81 - set_new_reference ok 82 - uniq_seq ok 83 - bug 2099 ok 84 - bug 2099 ok 85 - bug 2793 ok 86 - bug 2793 ok 87 - bug 2793 ok 88 - bug 2793 ok 89 - Bad sequence, bad! ok 90 - added 3 seqs ok 91 - first 2 features added ok 92 - 3rd feature added not ok 93 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 1. # Overriding value [0] with value 1 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 94 - slice 1 len ok 95 - correct masked seq ok 96 - correct masked seq ok 97 - correct masked seq not ok 98 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [2] with value 3 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 99 - slice 2 len ok 100 - correct masked seq ok 101 - correct masked seq ok 102 - correct masked seq not ok 103 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [1] with value 3 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 104 - slice 3 len ok 105 - correct masked seq ok 106 - correct masked seq ok 107 - correct masked seq not ok 108 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 6. # Overriding value [4] with value 6 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 109 - slice 4 len ok 110 - correct masked seq ok 111 - correct masked seq ok 112 - correct masked seq ok 113 - initial display id ok ok 114 - safe display id ok ok 115 - restored display id ok ok 116 - sort by list ok ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 - BIC:GGATCCATT[C/C]CTACT ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT ok 126 - BIC:GGATCCATT[C/G]CTACT ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A] ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] ok 129 - BIC:GGATCCATT[C/G]CTACT ok 130 - BIC:GGATCCATT{C.C}CTACT ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT ok 133 - BIC:GGATCCATT{C.G}CTACT ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A} ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} ok 136 - BIC:GGATCCATT{C.G}CTACT ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 - The object isa Bio::SimpleAlign ok 195 - consensus string looks ok ok 196 - looks like correct unmasked alignment (from clustalw) ok 197 - looks like correct masked alignment (from clustalw) ok 198 ok 199 - align after looks ok ok t/Align/TreeBuild.t .......................... 1..13 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::Align::Utilities; ok 4 - use Bio::AlignIO; ok 5 - use Bio::Tree::DistanceFactory; ok 6 - use Bio::TreeIO; ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI ok 9 - Tree object gotten back isa Bio::Tree::TreeI ok 10 - NJ calculated Branch length ok 11 - NJ calculated Branch length ok 12 - Make sure two nodes are sister ok 13 - 10 replicates formulated ok t/Align/Utilities.t .......................... 1..13 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::PrimarySeq; ok 4 - use Bio::LocatableSeq; ok 5 - use Bio::AlignIO; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96, line 86. Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128, line 86. Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153, line 86. Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174, line 86. Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199, line 86. Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229, line 86. Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265, line 86. Subroutine new redefined at Bio\Seq\Meta.pm line 225, line 64. Subroutine meta redefined at Bio\Seq\Meta.pm line 269, line 64. Subroutine meta_text redefined at Bio\Seq\Meta.pm line 284, line 64. Subroutine named_meta redefined at Bio\Seq\Meta.pm line 300, line 64. Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 347, line 64. Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 377, line 64. Subroutine submeta redefined at Bio\Seq\Meta.pm line 409, line 64. Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 425, line 64. Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 444, line 64. Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 503, line 64. Subroutine meta_names redefined at Bio\Seq\Meta.pm line 518, line 64. Subroutine meta_length redefined at Bio\Seq\Meta.pm line 540, line 64. Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 556, line 64. Subroutine force_flush redefined at Bio\Seq\Meta.pm line 577, line 64. Subroutine _do_flush redefined at Bio\Seq\Meta.pm line 604, line 64. Subroutine is_flush redefined at Bio\Seq\Meta.pm line 637, line 64. Subroutine revcom redefined at Bio\Seq\Meta.pm line 679, line 64. Subroutine trunc redefined at Bio\Seq\Meta.pm line 702, line 64. Subroutine to_string redefined at Bio\Seq\Meta.pm line 726, line 64. t/AlignIO/AlignIO.t .......................... 1..28 ok 1 - use Bio::AlignIO; ok 2 - input filehandle method test : metafasta ok 3 - input filehandle method test : po ok 4 - input filehandle method test : nexus ok 5 - input filehandle method test : clustalw ok 6 - input filehandle method test : prodom ok 7 - input filehandle method test : fasta ok 8 - input filehandle method test : arp ok 9 - input filehandle method test : xmfa ok 10 - input filehandle method test : mase ok 11 - input filehandle method test : psi ok 12 - input filehandle method test : phylip ok 13 - input filehandle method test : pfam ok 14 - input filehandle method test : selex ok 15 - input filehandle method test : stockholm ok 16 - input filehandle method test : msf ok 17 - filehandle output test : metafasta ok 18 - filehandle output test : po ok 19 - filehandle output test : nexus ok 20 - filehandle output test : clustalw ok 21 - filehandle output test : fasta ok 22 - filehandle output test : xmfa ok 23 - filehandle output test : psi ok 24 - filehandle output test : phylip ok 25 - filehandle output test : pfam ok 26 - filehandle output test : selex ok 27 - filehandle output test : stockholm ok 28 - filehandle output test : msf ok Subroutine next_aln redefined at Bio\AlignIO\arp.pm line 116. Subroutine write_aln redefined at Bio\AlignIO\arp.pm line 199. Subroutine _process_sequence redefined at Bio\AlignIO\arp.pm line 206. Subroutine _process_annotation redefined at Bio\AlignIO\arp.pm line 218. Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96, line 86. Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128, line 86. Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153, line 86. Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174, line 86. Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199, line 86. Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229, line 86. Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265, line 86. t/AlignIO/arp.t .............................. 1..48 ok 1 - use Bio::AlignIO::arp; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 - ARP get_nse() ok 5 ok 6 - ARP num_sequences() ok 7 - ARP id() ok 8 - ARP description() ok 9 - The object isa Bio::AnnotationCollectionI ok 10 - The object isa Bio::AnnotationI ok 11 ok 12 ok 13 ok 14 ok 15 - The object isa Bio::AlignIO ok 16 - The object isa Bio::Align::AlignI ok 17 - ARP get_nse() ok 18 - ARP num_sequences() ok 19 - ARP id() ok 20 - ARP description() ok 21 - The object isa Bio::AnnotationCollectionI ok 22 - The object isa Bio::AnnotationI ok 23 ok 24 ok 25 ok 26 ok 27 - The object isa Bio::Align::AlignI ok 28 - ARP get_nse() ok 29 - ARP num_sequences() ok 30 - ARP id() ok 31 - ARP description() ok 32 - The object isa Bio::AnnotationCollectionI ok 33 - The object isa Bio::AnnotationI ok 34 ok 35 ok 36 ok 37 ok 38 - The object isa Bio::Align::AlignI ok 39 - ARP get_nse() ok 40 - ARP num_sequences() ok 41 - ARP id() ok 42 - ARP description() ok 43 - The object isa Bio::AnnotationCollectionI ok 44 - The object isa Bio::AnnotationI ok 45 ok 46 ok 47 ok 48 ok Subroutine _initialize redefined at Bio\AlignIO\bl2seq.pm line 124. Subroutine next_aln redefined at Bio\AlignIO\bl2seq.pm line 142. Subroutine write_aln redefined at Bio\AlignIO\bl2seq.pm line 184. Subroutine report_type redefined at Bio\AlignIO\bl2seq.pm line 200. Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 64. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 64. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 64. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 64. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 64. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 64. t/AlignIO/bl2seq.t ........................... 1..3 ok 1 - use Bio::AlignIO::bl2seq; ok 2 - The object isa Bio::Align::AlignI ok 3 - BLAST bl2seq format test ok Subroutine _initialize redefined at Bio\AlignIO\clustalw.pm line 100. Subroutine next_aln redefined at Bio\AlignIO\clustalw.pm line 121. Subroutine write_aln redefined at Bio\AlignIO\clustalw.pm line 233. Subroutine percentages redefined at Bio\AlignIO\clustalw.pm line 332. Subroutine line_length redefined at Bio\AlignIO\clustalw.pm line 351. t/AlignIO/clustalw.t ......................... 1..6 ok 1 - use Bio::AlignIO::clustalw; ok 2 - The object isa Bio::Align::AlignI ok 3 - clustalw consensus_string test ok 4 - clustalw (.aln) output test ok 5 - The object isa Bio::Align::AlignI ok 6 - clustalw (.aln) input test ok Subroutine _initialize redefined at Bio\AlignIO\emboss.pm line 92. Subroutine next_aln redefined at Bio\AlignIO\emboss.pm line 109. Subroutine write_aln redefined at Bio\AlignIO\emboss.pm line 252. t/AlignIO/emboss.t ........................... 1..37 ok 1 - use Bio::AlignIO::emboss; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 - The object isa Bio::Align::AlignI ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Align::AlignI ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Align::AlignI ok 19 ok 20 ok 21 - The object isa Bio::Align::AlignI ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 - The object isa Bio::Align::AlignI ok 33 ok 34 ok 35 ok 36 ok 37 ok Subroutine next_aln redefined at Bio\AlignIO\fasta.pm line 80. Subroutine write_aln redefined at Bio\AlignIO\fasta.pm line 185. Subroutine _get_len redefined at Bio\AlignIO\fasta.pm line 228. Subroutine width redefined at Bio\AlignIO\fasta.pm line 247. t/AlignIO/fasta.t ............................ 1..10 ok 1 - use Bio::AlignIO::fasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for end ok 7 - fasta input test for description ok 8 - fasta output test ok 9 - filehandle input test ok 10 - filehandle output test ok Subroutine _initialize redefined at Bio\AlignIO\largemultifasta.pm line 81. Subroutine next_seq redefined at Bio\AlignIO\largemultifasta.pm line 102. Subroutine next_aln redefined at Bio\AlignIO\largemultifasta.pm line 143. Subroutine write_aln redefined at Bio\AlignIO\largemultifasta.pm line 176. t/AlignIO/largemultifasta.t .................. 1..7 ok 1 - use Bio::AlignIO::largemultifasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for description ok 7 - fasta output test ok Subroutine _initialize redefined at Bio\AlignIO\maf.pm line 102. Subroutine next_aln redefined at Bio\AlignIO\maf.pm line 121. Subroutine write_aln redefined at Bio\AlignIO\maf.pm line 187. t/AlignIO/maf.t .............................. 1..11 ok 1 - use Bio::AlignIO::maf; ok 2 - The object isa Bio::Align::AlignI ok 3 - maf input test ok 4 ok 5 - The object isa Bio::Align::AlignI ok 6 - maf input test ok 7 ok 8 - maf input test ok 9 ok 10 - maf input test ok 11 ok Subroutine next_aln redefined at Bio\AlignIO\mase.pm line 82. Subroutine write_aln redefined at Bio\AlignIO\mase.pm line 158. t/AlignIO/mase.t ............................. 1..3 ok 1 - use Bio::AlignIO::mase; ok 2 - The object isa Bio::Align::AlignI ok 3 - mase input test ok Subroutine next_aln redefined at Bio\AlignIO\mega.pm line 115. Subroutine write_aln redefined at Bio\AlignIO\mega.pm line 188. t/AlignIO/mega.t ............................. 1..6 ok 1 - use Bio::AlignIO::mega; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 - mega output test ok Subroutine next_aln redefined at Bio\AlignIO\meme.pm line 104. Subroutine write_aln redefined at Bio\AlignIO\meme.pm line 198. Subroutine _initialize redefined at Bio\AlignIO\meme.pm line 207. t/AlignIO/meme.t ............................. 1..14 ok 1 - use Bio::AlignIO::meme; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok 12 ok 13 ok 14 ok Subroutine _initialize redefined at Bio\AlignIO\metafasta.pm line 89. Subroutine next_aln redefined at Bio\AlignIO\metafasta.pm line 107. Subroutine write_aln redefined at Bio\AlignIO\metafasta.pm line 181. Subroutine width redefined at Bio\AlignIO\metafasta.pm line 225. t/AlignIO/metafasta.t ........................ 1..4 ok 1 - use Bio::AlignIO::metafasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - consensus_string on metafasta ok 4 - symbol_chars() using metafasta ok Subroutine next_aln redefined at Bio\AlignIO\msf.pm line 90. Subroutine write_aln redefined at Bio\AlignIO\msf.pm line 173. t/AlignIO/msf.t .............................. 1..4 ok 1 - use Bio::AlignIO::msf; ok 2 - The object isa Bio::Align::AlignI ok 3 - msf input test ok 4 - msf output test ok Subroutine _initialize redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 71. Subroutine next_aln redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 90. Subroutine rewind redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 110. Subroutine doc redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 125. Subroutine _parse redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 133. Subroutine write_aln redefined at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 165. -------------------------- EXCEPTION ---------------------------- Message: Wrong version number, can only handle 0.9: 0.8 An exception of type Bio::Phylo::Util::Exceptions::BadFormat was thrown. This kind of error happens when a bad parse or unparse format was specified. Refer to the Bio::Phylo::Util::Exceptions documentation for more information. ------------------------- STACK TRACE --------------------------- STACK: Bio::Phylo::Parsers::Nexml::_handle_nexml('XML::Twig=HASH(0x57682c0)', 'XML::Twig::Elt=HASH(0x5fe8968)', 'Bio::Phylo::Parsers::Nexml=HASH(0x548af70)') called at C:\cpanfly-5.12\var\megalib/Bio/Phylo/Parsers/Nexml.pm line 160 STACK: Bio::Phylo::Parsers::Nexml::__ANON__('XML::Twig=HASH(0x57682c0)', 'XML::Twig::Elt=HASH(0x5fe8968)') called at C:\cpanfly-5.12\var\megalib/XML/Twig.pm line 2085 STACK: XML::Twig::_twig_end('XML::Parser::Expat=HASH(0x5769090)', 'nex:nexml') called at C:/Perl64-5.12/lib/XML/Parser/Expat.pm line 469 STACK: (eval)('XML::Parser::Expat=HASH(0x5769090)', 'nex:nexml') called at C:/Perl64-5.12/lib/XML/Parser/Expat.pm line 469 STACK: XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x5769090)', 'IO::File=GLOB(0x5fe6cc0)') called at C:/Perl64-5.12/lib/XML/Parser.pm line 187 STACK: (eval)('XML::Parser::Expat=HASH(0x5769090)', 'IO::File=GLOB(0x5fe6cc0)') called at C:/Perl64-5.12/lib/XML/Parser.pm line 186 STACK: XML::Parser::parse('XML::Twig=HASH(0x57682c0)', 'IO::File=GLOB(0x5fe6cc0)') called at C:\cpanfly-5.12\var\megalib/XML/Twig.pm line 693 STACK: (eval)('XML::Twig=HASH(0x57682c0)', 'IO::File=GLOB(0x5fe6cc0)') called at C:\cpanfly-5.12\var\megalib/XML/Twig.pm line 693 STACK: XML::Twig::parse('XML::Twig=HASH(0x57682c0)', 'IO::File=GLOB(0x5fe6cc0)') called at C:\cpanfly-5.12\var\megalib/Bio/Phylo/Parsers/Nexml.pm line 211 STACK: Bio::Phylo::Parsers::Nexml::_from_both('Bio::Phylo::Parsers::Nexml=HASH(0x548af70)', '-file', 't\data\characters.nexml.xml', '-handle', 'IO::File=GLOB(0x5fe6cc0)', '-as_project', '1', '-format', 'nexml') called at C:\cpanfly-5.12\var\megalib/Bio/Phylo/IO.pm line 207 STACK: Bio::Phylo::IO::parse('-file', 't\data\characters.nexml.xml', '-format', 'nexml', '-as_project', '1') called at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 140 STACK: Bio::AlignIO::nexml::_parse('Bio::AlignIO::nexml=HASH(0x54885f0)') called at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib/Bio\AlignIO\nexml.pm line 92 STACK: Bio::AlignIO::nexml::next_aln('Bio::AlignIO::nexml=HASH(0x54885f0)') called at t/AlignIO/nexml.t line 16 ----------------------------------------------------------------- # Looks like you planned 35 tests but ran 2. # Looks like your test exited with 255 just after 2. t/AlignIO/nexml.t ............................ 1..35 ok 1 - use Bio::AlignIO::nexml; ok 2 - make stream Dubious, test returned 255 (wstat 65280, 0xff00) Failed 33/35 subtests Subroutine _initialize redefined at Bio\AlignIO\nexus.pm line 103. Subroutine next_aln redefined at Bio\AlignIO\nexus.pm line 142. Subroutine _read_taxlabels redefined at Bio\AlignIO\nexus.pm line 339. Subroutine write_aln redefined at Bio\AlignIO\nexus.pm line 367. Subroutine flag redefined at Bio\AlignIO\nexus.pm line 463. t/AlignIO/nexus.t ............................ 1..43 ok 1 - use Bio::AlignIO::nexus; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - nexus output test ok 6 - The object isa Bio::AlignIO ok 7 - The object isa Bio::Align::AlignI ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 - The object isa Bio::AlignIO ok 11 - The object isa Bio::Align::AlignI ok 12 - The object isa Bio::AlignIO ok 13 - The object isa Bio::Align::AlignI ok 14 - The object isa Bio::AlignIO ok 15 - The object isa Bio::Align::AlignI ok 16 - The object isa Bio::AlignIO ok 17 - The object isa Bio::Align::AlignI ok 18 - The object isa Bio::AlignIO ok 19 - The object isa Bio::Align::AlignI ok 20 - The object isa Bio::AlignIO ok 21 - The object isa Bio::Align::AlignI ok 22 - The object isa Bio::AlignIO ok 23 - The object isa Bio::Align::AlignI ok 24 - The object isa Bio::AlignIO ok 25 - The object isa Bio::Align::AlignI ok 26 - The object isa Bio::AlignIO ok 27 - The object isa Bio::Align::AlignI ok 28 - The object isa Bio::AlignIO ok 29 - The object isa Bio::Align::AlignI ok 30 - The object isa Bio::AlignIO ok 31 - The object isa Bio::Align::AlignI ok 32 - The object isa Bio::AlignIO ok 33 - The object isa Bio::Align::AlignI ok 34 - The object isa Bio::AlignIO ok 35 - The object isa Bio::Align::AlignI ok 36 - The object isa Bio::AlignIO ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::AlignIO ok 39 - The object isa Bio::Align::AlignI ok 40 - The object isa Bio::AlignIO ok 41 - The object isa Bio::Align::AlignI ok 42 - The object isa Bio::AlignIO ok 43 - The object isa Bio::Align::AlignI ok Subroutine next_aln redefined at Bio\AlignIO\pfam.pm line 81. Subroutine write_aln redefined at Bio\AlignIO\pfam.pm line 140. t/AlignIO/pfam.t ............................. 1..5 ok 1 - use Bio::AlignIO::pfam; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - pfam output test ok Subroutine _initialize redefined at Bio\AlignIO\phylip.pm line 134. Subroutine next_aln redefined at Bio\AlignIO\phylip.pm line 171. Subroutine write_aln redefined at Bio\AlignIO\phylip.pm line 323. Subroutine interleaved redefined at Bio\AlignIO\phylip.pm line 443. Subroutine flag_SI redefined at Bio\AlignIO\phylip.pm line 466. Subroutine idlength redefined at Bio\AlignIO\phylip.pm line 486. Subroutine line_length redefined at Bio\AlignIO\phylip.pm line 505. Subroutine tag_length redefined at Bio\AlignIO\phylip.pm line 526. Subroutine id_linebreak redefined at Bio\AlignIO\phylip.pm line 546. Subroutine wrap_sequential redefined at Bio\AlignIO\phylip.pm line 566. Subroutine longid redefined at Bio\AlignIO\phylip.pm line 585. t/AlignIO/phylip.t ........................... 1..16 ok 1 - use Bio::AlignIO::phylip; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - phylip output test ok 6 ok 7 ok 8 not ok 9 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 44. # got: undef # expected: '0' not ok 10 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 45. # got: '50' # expected: '47' ok 11 - The object isa Bio::Align::AlignI ok 12 ok 13 - The object isa Bio::AlignIO ok 14 - The object isa Bio::Align::AlignI ok 15 ok 16 ok Subroutine next_aln redefined at Bio\AlignIO\po.pm line 83. Subroutine write_aln redefined at Bio\AlignIO\po.pm line 228. t/AlignIO/po.t ............................... 1..11 ok 1 - use Bio::AlignIO::po; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - The object isa Bio::AlignIO ok 6 - The object isa Bio::Align::AlignI ok 7 - po output test ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok Subroutine next_aln redefined at Bio\AlignIO\prodom.pm line 81. Subroutine write_aln redefined at Bio\AlignIO\prodom.pm line 134. t/AlignIO/prodom.t ........................... 1..3 ok 1 - use Bio::AlignIO::prodom; ok 2 - The object isa Bio::Align::AlignI ok 3 - prodom input test ok Subroutine next_aln redefined at Bio\AlignIO\psi.pm line 107. Subroutine write_aln redefined at Bio\AlignIO\psi.pm line 147. t/AlignIO/psi.t .............................. 1..5 ok 1 - use Bio::AlignIO::psi; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok Subroutine next_aln redefined at Bio\AlignIO\selex.pm line 95. Subroutine write_aln redefined at Bio\AlignIO\selex.pm line 162. t/AlignIO/selex.t ............................ 1..4 ok 1 - use Bio::AlignIO::selex; ok 2 - The object isa Bio::Align::AlignI ok 3 - selex format test ok 4 - selex output test ok Subroutine _initialize redefined at Bio\AlignIO\stockholm.pm line 354. Subroutine next_aln redefined at Bio\AlignIO\stockholm.pm line 379. Subroutine write_aln redefined at Bio\AlignIO\stockholm.pm line 514. Subroutine line_length redefined at Bio\AlignIO\stockholm.pm line 660. Subroutine spaces redefined at Bio\AlignIO\stockholm.pm line 679. Subroutine alignhandler redefined at Bio\AlignIO\stockholm.pm line 695. Subroutine _print_seqs redefined at Bio\AlignIO\stockholm.pm line 707. Subroutine new redefined at Bio\Seq\Meta.pm line 225, line 64. Subroutine meta redefined at Bio\Seq\Meta.pm line 269, line 64. Subroutine meta_text redefined at Bio\Seq\Meta.pm line 284, line 64. Subroutine named_meta redefined at Bio\Seq\Meta.pm line 300, line 64. Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 347, line 64. Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 377, line 64. Subroutine submeta redefined at Bio\Seq\Meta.pm line 409, line 64. Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 425, line 64. Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 444, line 64. Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 503, line 64. Subroutine meta_names redefined at Bio\Seq\Meta.pm line 518, line 64. Subroutine meta_length redefined at Bio\Seq\Meta.pm line 540, line 64. Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 556, line 64. Subroutine force_flush redefined at Bio\Seq\Meta.pm line 577, line 64. Subroutine _do_flush redefined at Bio\Seq\Meta.pm line 604, line 64. Subroutine is_flush redefined at Bio\Seq\Meta.pm line 637, line 64. Subroutine revcom redefined at Bio\Seq\Meta.pm line 679, line 64. Subroutine trunc redefined at Bio\Seq\Meta.pm line 702, line 64. Subroutine to_string redefined at Bio\Seq\Meta.pm line 726, line 64. t/AlignIO/stockholm.t ........................ 1..84 ok 1 - use Bio::AlignIO::stockholm; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - The object isa Bio::Annotation::Comment ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - The object isa Bio::Align::AlignI ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 - Stockholm annotation isa Bio::Annotation::Reference ok 21 - Stockholm annotation ok 22 - Stockholm annotation ok 23 - Stockholm annotation ok 24 - Stockholm annotation ok 25 - The object isa Bio::Seq::MetaI ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - The object isa Bio::Align::AlignI ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 - The object isa Bio::Seq::MetaI ok 36 - Rfam meta data ok 37 - Rfam meta data ok 38 - The object isa Bio::AlignIO ok 39 ok 40 - The object isa Bio::Align::AlignI ok 41 ok 42 ok 43 ok 44 ok 45 - The object isa Bio::Annotation::SimpleValue ok 46 - Pfam annotation ok 47 ok 48 - The object isa Bio::Align::AlignI ok 49 ok 50 ok 51 ok 52 ok 53 - The object isa Bio::Align::AlignI ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 - The object isa Bio::Seq::MetaI ok 60 - Pfam aln meta data ok 61 - Pfam aln meta data ok 62 - Pfam aln meta data ok 63 - Pfam aln meta data ok 64 - Pfam aln meta data ok 65 - Pfam aln meta data ok 66 - Pfam seq meta data ok 67 - Pfam seq meta data ok 68 - Pfam seq meta data ok 69 - Pfam seq meta data ok 70 ok 71 - The object isa Bio::SeqFeatureI ok 72 - The object isa Bio::Seq::Meta ok 73 - The object isa Bio::AnnotationI ok 74 - The object isa Bio::Annotation::DBLink ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok Subroutine next_aln redefined at Bio\AlignIO\xmfa.pm line 87. Subroutine write_aln redefined at Bio\AlignIO\xmfa.pm line 141. Subroutine _get_len redefined at Bio\AlignIO\xmfa.pm line 194. Subroutine width redefined at Bio\AlignIO\xmfa.pm line 212. Subroutine _process_seq redefined at Bio\AlignIO\xmfa.pm line 221. t/AlignIO/xmfa.t ............................. 1..30 ok 1 - use Bio::AlignIO::xmfa; ok 2 - The object isa Bio::Align::AlignI ok 3 - xmfa input test ok 4 - xmfa input test for start ok 5 - xmfa input test for end ok 6 - xmfa strand test ok 7 - xmfa input test for id ok 8 - xmfa input test for id ok 9 - xmfa input test ok 10 - xmfa input test for start ok 11 - xmfa input test for end ok 12 - xmfa strand test ok 13 - xmfa input test for id ok 14 - xmfa input test for id ok 15 - xmfa input test ok 16 - xmfa input test for start ok 17 - xmfa input test for end ok 18 - xmfa strand test ok 19 - xmfa input test for id ok 20 - xmfa input test for id ok 21 - xmfa alignment score ok 22 - The object isa Bio::Align::AlignI ok 23 - xmfa input test ok 24 - xmfa strand ok 25 - xmfa input test for description ok 26 - xmfa input test for id ok 27 - xmfa input test for end ok 28 - xmfa input test for end ok 29 - xmfa alignment score ok 30 - xmfa output test ok t/Alphabet.t ................................. 1..100 ok 1 - use Bio::Symbol::Alphabet; ok 2 - use Bio::Symbol::Symbol; ok 3 - use Bio::Symbol::DNAAlphabet; ok 4 - use Bio::Symbol::ProteinAlphabet; ok 5 - The object isa Bio::Symbol::Alphabet ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Symbol::AlphabetI ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - The object isa Bio::Symbol::AlphabetI ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96. Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128. Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153. Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174. Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199. Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229. Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265. Subroutine new redefined at Bio\Annotation\OntologyTerm.pm line 128. Subroutine as_text redefined at Bio\Annotation\OntologyTerm.pm line 172. Subroutine display_text redefined at Bio\Annotation\OntologyTerm.pm line 197. Subroutine hash_tree redefined at Bio\Annotation\OntologyTerm.pm line 218. Subroutine tagname redefined at Bio\Annotation\OntologyTerm.pm line 246. Subroutine term redefined at Bio\Annotation\OntologyTerm.pm line 274. Subroutine identifier redefined at Bio\Annotation\OntologyTerm.pm line 297. Subroutine name redefined at Bio\Annotation\OntologyTerm.pm line 313. Subroutine definition redefined at Bio\Annotation\OntologyTerm.pm line 330. Subroutine ontology redefined at Bio\Annotation\OntologyTerm.pm line 348. Subroutine is_obsolete redefined at Bio\Annotation\OntologyTerm.pm line 364. Subroutine comment redefined at Bio\Annotation\OntologyTerm.pm line 380. Subroutine get_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 394. Subroutine add_synonym redefined at Bio\Annotation\OntologyTerm.pm line 410. Subroutine remove_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 425. Subroutine get_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 441. Subroutine get_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 457. Subroutine add_dblink redefined at Bio\Annotation\OntologyTerm.pm line 477. Subroutine add_dbxref redefined at Bio\Annotation\OntologyTerm.pm line 496. Subroutine remove_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 512. Subroutine remove_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 528. Subroutine get_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 546. Subroutine add_secondary_id redefined at Bio\Annotation\OntologyTerm.pm line 563. Subroutine remove_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 578. Subroutine new redefined at Bio\Annotation\Comment.pm line 64. Subroutine as_text redefined at Bio\Annotation\Comment.pm line 92. Subroutine display_text redefined at Bio\Annotation\Comment.pm line 117. Subroutine hash_tree redefined at Bio\Annotation\Comment.pm line 138. Subroutine tagname redefined at Bio\Annotation\Comment.pm line 166. Subroutine text redefined at Bio\Annotation\Comment.pm line 193. Subroutine type redefined at Bio\Annotation\Comment.pm line 231. Subroutine Bio::Annotation::Comment::value redefined at Bio\Annotation\Comment.pm line 215. Subroutine new redefined at Bio\Annotation\Target.pm line 67. Subroutine as_text redefined at Bio\Annotation\Target.pm line 104. Subroutine display_text redefined at Bio\Annotation\Target.pm line 134. Subroutine tagname redefined at Bio\Annotation\Target.pm line 163. Subroutine target_id redefined at Bio\Annotation\Target.pm line 198. Subroutine new redefined at Bio\Tree\Tree.pm line 131. Subroutine nodelete redefined at Bio\Tree\Tree.pm line 179. Subroutine get_nodes redefined at Bio\Tree\Tree.pm line 196. Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 230. Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 245. Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 269. Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 283. Subroutine id redefined at Bio\Tree\Tree.pm line 306. Subroutine score redefined at Bio\Tree\Tree.pm line 327. Subroutine as_text redefined at Bio\Tree\Tree.pm line 375. Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 411. Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 432. Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 452. Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 472. Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 488. Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 504. Subroutine has_tag redefined at Bio\Tree\Tree.pm line 520. Subroutine clone redefined at Bio\Tree\Tree.pm line 540. Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 558. Subroutine new redefined at Bio\Tree\Node.pm line 110. Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 163. Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 221. Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 259. Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 322. Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 357. Subroutine ancestor redefined at Bio\Tree\Node.pm line 396. Subroutine branch_length redefined at Bio\Tree\Node.pm line 437. Subroutine bootstrap redefined at Bio\Tree\Node.pm line 461. Subroutine description redefined at Bio\Tree\Node.pm line 482. Subroutine id redefined at Bio\Tree\Node.pm line 511. Subroutine internal_id redefined at Bio\Tree\Node.pm line 553. Subroutine _creation_id redefined at Bio\Tree\Node.pm line 567. Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 588. Subroutine height redefined at Bio\Tree\Node.pm line 606. Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 631. Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 652. Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 674. Subroutine remove_tag redefined at Bio\Tree\Node.pm line 695. Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 715. Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 731. Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 749. Subroutine has_tag redefined at Bio\Tree\Node.pm line 765. Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 770. Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 800. Subroutine new redefined at Bio\Annotation\Tree.pm line 73. Subroutine as_text redefined at Bio\Annotation\Tree.pm line 114. Subroutine display_text redefined at Bio\Annotation\Tree.pm line 141. Subroutine hash_tree redefined at Bio\Annotation\Tree.pm line 161. Subroutine tagname redefined at Bio\Annotation\Tree.pm line 185. Subroutine tree_id redefined at Bio\Annotation\Tree.pm line 206. Subroutine tree redefined at Bio\Annotation\Tree.pm line 223. Subroutine new redefined at Bio\Annotation\TagTree.pm line 139. Subroutine as_text redefined at Bio\Annotation\TagTree.pm line 178. Subroutine display_text redefined at Bio\Annotation\TagTree.pm line 202. Subroutine hash_tree redefined at Bio\Annotation\TagTree.pm line 223. Subroutine tagname redefined at Bio\Annotation\TagTree.pm line 243. Subroutine value redefined at Bio\Annotation\TagTree.pm line 265. Subroutine tagformat redefined at Bio\Annotation\TagTree.pm line 313. Subroutine node redefined at Bio\Annotation\TagTree.pm line 336. Subroutine element redefined at Bio\Annotation\TagTree.pm line 378. Subroutine data redefined at Bio\Annotation\TagTree.pm line 394. Subroutine children redefined at Bio\Annotation\TagTree.pm line 418. Subroutine subnodes redefined at Bio\Annotation\TagTree.pm line 436. Subroutine get redefined at Bio\Annotation\TagTree.pm line 453. Subroutine find redefined at Bio\Annotation\TagTree.pm line 470. Subroutine findnode redefined at Bio\Annotation\TagTree.pm line 487. Subroutine findval redefined at Bio\Annotation\TagTree.pm line 503. Subroutine addchild redefined at Bio\Annotation\TagTree.pm line 526. Subroutine add redefined at Bio\Annotation\TagTree.pm line 561. Subroutine set redefined at Bio\Annotation\TagTree.pm line 583. Subroutine unset redefined at Bio\Annotation\TagTree.pm line 604. Subroutine free redefined at Bio\Annotation\TagTree.pm line 619. Subroutine hash redefined at Bio\Annotation\TagTree.pm line 635. Subroutine pairs redefined at Bio\Annotation\TagTree.pm line 652. Subroutine qmatch redefined at Bio\Annotation\TagTree.pm line 668. Subroutine tnodes redefined at Bio\Annotation\TagTree.pm line 683. Subroutine ntnodes redefined at Bio\Annotation\TagTree.pm line 698. Subroutine get_all_values redefined at Bio\Annotation\TagTree.pm line 721. t/Annotation/Annotation.t .................... 1..159 ok 1 - use Bio::Annotation::Collection; ok 2 - use Bio::Annotation::DBLink; ok 3 - use Bio::Annotation::Comment; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Annotation::SimpleValue; ok 6 - use Bio::Annotation::Target; ok 7 - use Bio::Annotation::AnnotationFactory; ok 8 - use Bio::Annotation::StructuredValue; ok 9 - use Bio::Annotation::TagTree; ok 10 - use Bio::Annotation::Tree; ok 11 - use Bio::Seq; ok 12 - use Bio::SimpleAlign; ok 13 - use Bio::Cluster::UniGene; ok 14 - The object isa Bio::AnnotationI ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 - The object isa Bio::AnnotationI ok 22 ok 23 ok 24 ok 25 - The object isa Bio::AnnotationCollectionI ok 26 ok 27 ok 28 - The object isa Bio::AnnotationI ok 29 ok 30 - The object isa Bio::AnnotationI ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 - The object isa Bio::AnnotationI ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 - The object isa Bio::AnnotationCollectionI ok 69 ok 70 ok 71 ok 72 ok 73 - The object isa Bio::Annotation::StructuredValue ok 74 ok 75 ok 76 ok 77 ok 78 - use Bio::Annotation::OntologyTerm; ok 79 - The object isa Bio::Ontology::Term ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 - The object isa Bio::AnnotatableI ok 86 - isa SeqFeatureI isa Bio::SeqFeatureI ok 87 - isa AnnotatableI isa Bio::AnnotatableI ok 88 - isa SeqFeatureI isa Bio::SeqFeatureI ok 89 - isa AnnotatableI isa Bio::AnnotatableI ok 90 - The object isa Bio::AnnotatableI ok 91 - The object isa Bio::AnnotatableI ok 92 - The object isa Bio::Factory::ObjectFactoryI ok 93 - The object isa Bio::Annotation::SimpleValue ok 94 ok 95 - The object isa Bio::Annotation::OntologyTerm ok 96 - Bio::Annotation::Comment ok 97 - The object isa Bio::Annotation::Comment ok 98 ok 99 - Bio::Annotation::Comment ok 100 - The object isa Bio::Annotation::Comment ok 101 - Bio::Annotation::Comment ok 102 - The object isa Bio::Annotation::Comment ok 103 ok 104 - The object isa Bio::Annotation::Target ok 105 ok 106 ok 107 - The object isa Bio::AnnotationI ok 108 - tree_id() ok 109 - tagname() ok 110 - The object isa Bio::AnnotatableI ok 111 ok 112 - add tree to AlignI ok 113 - get seq from node id ok 114 ok 115 - The object isa Bio::Annotation::Tree ok 116 - The object isa Bio::AnnotationI ok 117 - default itext ok 118 - roundtrip ok 119 - itext ok 120 - spxr ok 121 - indent ok 122 - xml ok 123 - The object isa Data::Stag::StagI ok 124 ok 125 - child changes ok 126 - The object isa Data::Stag::StagI ok 127 ok 128 - child changes ok 129 - The object isa Data::Stag::StagI ok 130 ok 131 - child changes ok 132 - child changes in parent node ok 133 - no tags ok 134 - before Stag node ok 135 - after Stag node ok 136 - both stag nodes ok 137 - different instances ok 138 - before TagTree ok 139 - after TagTree ok 140 - both stag nodes ok 141 - different instances ok 142 - before TagTree ok 143 - after TagTree ok 144 - stag nodes ok 145 - same instance ok 146 - before TagTree ok 147 - after TagTree ok 148 - stag nodes ok 149 - different instance ok 150 - The object isa Bio::AnnotationI ok 151 - The object isa Data::Stag::StagI ok 152 - child changes ok 153 - The object isa Data::Stag::StagI ok 154 - child changes ok 155 - The object isa Data::Stag::StagI ok 156 - child changes ok 157 ok 158 ok 159 - The object isa Bio::Annotation::TagTree ok t/Annotation/AnnotationAdaptor.t ............. 1..23 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::SeqFeature::AnnotationAdaptor; ok 3 - use Bio::Annotation::DBLink; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::SimpleValue; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio/SeqFeature/Collection.pm line 146. BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146. Compilation failed in require at Bio/Assembly/Singlet.pm line 91. BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91. Compilation failed in require at Bio\Assembly\IO\tigr.pm line 237. BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 237. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296 STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138 STACK: t/Assembly/ContigSpectrum.t:12 ----------------------------------------------------------- # Failed test 'The thing isa Bio::Assembly::IO' # at t/Assembly/ContigSpectrum.t line 16. # The thing isn't defined Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 17. # Looks like you planned 236 tests but ran 3. # Looks like you failed 1 test of 3 run. # Looks like your test exited with 2 just after 3. t/Assembly/ContigSpectrum.t .................. 1..236 ok 1 - use Bio::Assembly::IO; ok 2 - use Bio::Assembly::Tools::ContigSpectrum; not ok 3 - The thing isa Bio::Assembly::IO Dubious, test returned 2 (wstat 512, 0x200) Failed 234/236 subtests t/Assembly/IO/bowtie.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed t/Assembly/IO/sam.t .......................... skipped: The optional module DB_File (or dependencies thereof) was not installed t/Assembly/core.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed t/Biblio/Biblio.t ............................ 1..24 ok 1 - use Bio::Biblio; ok 2 - use Bio::Biblio::IO; ok 3 ok 4 ok 5 - citation 1 ok 6 - citation 2 ok 7 - citation 3 ok 8 - in callback ok 9 - in callback ok 10 - in callback ok 11 - calling callback ok 12 - citation 1 ok 13 - citation 2 ok 14 - citation 1 ok 15 - citation 2 ok 16 ok 17 - citation 1 ok 18 - citation 2 ok 19 - citation 3 ok 20 - citation 4 ok 21 - filehandle test ok 22 - filehandle test ok 23 - filehandle test ok 24 - filehandle test ok t/Biblio/References.t ........................ 1..537 ok 1 - use Bio::Biblio::Article; ok 2 - use Bio::Biblio::Book; ok 3 - use Bio::Biblio::BookArticle; ok 4 - use Bio::Biblio::Journal; ok 5 - use Bio::Biblio::JournalArticle; ok 6 - use Bio::Biblio::MedlineArticle; ok 7 - use Bio::Biblio::MedlineBook; ok 8 - use Bio::Biblio::MedlineBookArticle; ok 9 - use Bio::Biblio::MedlineJournal; ok 10 - use Bio::Biblio::MedlineJournalArticle; ok 11 - use Bio::Biblio::Organisation; ok 12 - use Bio::Biblio::Patent; ok 13 - use Bio::Biblio::Person; ok 14 - use Bio::Biblio::Proceeding; ok 15 - use Bio::Biblio::Provider; ok 16 - use Bio::Biblio::Ref; ok 17 - use Bio::Biblio::Service; ok 18 - use Bio::Biblio::TechReport; ok 19 - use Bio::Biblio::Thesis; ok 20 - use Bio::Biblio::WebResource; ok 21 - use Bio::Biblio::PubmedArticle; ok 22 - use Bio::Biblio::PubmedBookArticle; ok 23 - use Bio::Biblio::PubmedJournalArticle; ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - set 'abstract' ok 48 - get 'abstract' ok 49 - set 'abstract_language' ok 50 - get 'abstract_language' ok 51 - set 'abstract_type' ok 52 - get 'abstract_type' ok 53 - set 'author_list_complete' ok 54 - get 'author_list_complete' ok 55 - set 'cross_references_list_complete' ok 56 - get 'cross_references_list_complete' ok 57 - set 'date' ok 58 - get 'date' ok 59 - set 'date_completed' ok 60 - get 'date_completed' ok 61 - set 'date_created' ok 62 - get 'date_created' ok 63 - set 'date_revised' ok 64 - get 'date_revised' ok 65 - set 'format' ok 66 - get 'format' ok 67 - set 'identifier' ok 68 - get 'identifier' ok 69 - set 'language' ok 70 - get 'language' ok 71 - set 'last_modified_date' ok 72 - get 'last_modified_date' ok 73 - set 'repository_subset' ok 74 - get 'repository_subset' ok 75 - set 'rights' ok 76 - get 'rights' ok 77 - set 'spatial_location' ok 78 - get 'spatial_location' ok 79 - set 'subject_headings_source' ok 80 - get 'subject_headings_source' ok 81 - set 'temporal_period' ok 82 - get 'temporal_period' ok 83 - set 'title' ok 84 - get 'title' ok 85 - set 'toc' ok 86 - get 'toc' ok 87 - set 'toc_type' ok 88 - get 'toc_type' ok 89 - set 'type' ok 90 - get 'type' ok 91 - set 'first_page' ok 92 - get 'first_page' ok 93 - set 'last_page' ok 94 - get 'last_page' ok 95 - set 'issue' ok 96 - get 'issue' ok 97 - set 'issue_supplement' ok 98 - get 'issue_supplement' ok 99 - set 'volume' ok 100 - get 'volume' ok 101 - set 'affiliation' ok 102 - get 'affiliation' ok 103 - set 'citation_owner' ok 104 - get 'citation_owner' ok 105 - set 'date_of_electronic_publication' ok 106 - get 'date_of_electronic_publication' ok 107 - set 'gene_symbols' ok 108 - get 'gene_symbols' ok 109 - set 'grant_list_complete' ok 110 - get 'grant_list_complete' ok 111 - set 'medline_date' ok 112 - get 'medline_date' ok 113 - set 'medline_id' ok 114 - get 'medline_id' ok 115 - set 'medline_page' ok 116 - get 'medline_page' ok 117 - set 'number_of_references' ok 118 - get 'number_of_references' ok 119 - set 'other_languages' ok 120 - get 'other_languages' ok 121 - set 'pmid' ok 122 - get 'pmid' ok 123 - set 'season' ok 124 - get 'season' ok 125 - set 'status' ok 126 - get 'status' ok 127 - set 'vernacular_title' ok 128 - get 'vernacular_title' ok 129 ok 130 - abstract ok 131 - abstract_language ok 132 - abstract_type ok 133 - author_list_complete ok 134 - cross_references_list_complete ok 135 - date ok 136 - date_completed ok 137 - date_created ok 138 - date_revised ok 139 - format ok 140 - identifier ok 141 - language ok 142 - last_modified_date ok 143 - repository_subset ok 144 - rights ok 145 - spatial_location ok 146 - subject_headings_source ok 147 - temporal_period ok 148 - title ok 149 - toc ok 150 - toc_type ok 151 - type ok 152 - first_page ok 153 - last_page ok 154 - issue ok 155 - issue_supplement ok 156 - volume ok 157 - affiliation ok 158 - citation_owner ok 159 - date_of_electronic_publication ok 160 - gene_symbols ok 161 - grant_list_complete ok 162 - medline_date ok 163 - medline_id ok 164 - medline_page ok 165 - number_of_references ok 166 - other_languages ok 167 - pmid ok 168 - season ok 169 - status ok 170 - vernacular_title ok 171 - get 'authors' ok 172 - get 'cross_references' ok 173 - get 'codes' ok 174 - get 'contributors' ok 175 - get 'keywords' ok 176 - get 'publisher' ok 177 - get 'subject_headings' ok 178 - get 'journal' ok 179 - get 'chemicals' ok 180 - get 'comment_ins' ok 181 - get 'comment_ons' ok 182 - get 'erratum_fors' ok 183 - get 'erratum_ins' ok 184 - get 'general_notes' ok 185 - get 'grants' ok 186 - get 'mesh_headings' ok 187 - get 'original_report_ins' ok 188 - get 'other_abstracts' ok 189 - get 'other_ids' ok 190 - get 'republished_froms' ok 191 - get 'republished_ins' ok 192 - get 'retraction_ins' ok 193 - get 'retraction_ofs' ok 194 - get 'summary_for_patients_ins' ok 195 - get 'update_ins' ok 196 - get 'update_ofs' ok 197 - get 'journal' ok 198 - add_author 1 ok 199 - add_author 2 ok 200 - get authors ok 201 - add_contributor 1 ok 202 - add_contributor 2 ok 203 - get contributors ok 204 - add_cross_reference 1 ok 205 - add_cross_reference 2 ok 206 - get cross_references ok 207 - get cross_references ok 208 - set 'abstract' ok 209 - get 'abstract' ok 210 - set 'abstract_language' ok 211 - get 'abstract_language' ok 212 - set 'abstract_type' ok 213 - get 'abstract_type' ok 214 - set 'author_list_complete' ok 215 - get 'author_list_complete' ok 216 - set 'cross_references_list_complete' ok 217 - get 'cross_references_list_complete' ok 218 - set 'date' ok 219 - get 'date' ok 220 - set 'date_completed' ok 221 - get 'date_completed' ok 222 - set 'date_created' ok 223 - get 'date_created' ok 224 - set 'date_revised' ok 225 - get 'date_revised' ok 226 - set 'format' ok 227 - get 'format' ok 228 - set 'identifier' ok 229 - get 'identifier' ok 230 - set 'language' ok 231 - get 'language' ok 232 - set 'last_modified_date' ok 233 - get 'last_modified_date' ok 234 - set 'repository_subset' ok 235 - get 'repository_subset' ok 236 - set 'rights' ok 237 - get 'rights' ok 238 - set 'spatial_location' ok 239 - get 'spatial_location' ok 240 - set 'subject_headings_source' ok 241 - get 'subject_headings_source' ok 242 - set 'temporal_period' ok 243 - get 'temporal_period' ok 244 - set 'title' ok 245 - get 'title' ok 246 - set 'toc' ok 247 - get 'toc' ok 248 - set 'toc_type' ok 249 - get 'toc_type' ok 250 - set 'type' ok 251 - get 'type' ok 252 - set 'first_page' ok 253 - get 'first_page' ok 254 - set 'last_page' ok 255 - get 'last_page' ok 256 - set 'affiliation' ok 257 - get 'affiliation' ok 258 - set 'citation_owner' ok 259 - get 'citation_owner' ok 260 - set 'date_of_electronic_publication' ok 261 - get 'date_of_electronic_publication' ok 262 - set 'gene_symbols' ok 263 - get 'gene_symbols' ok 264 - set 'grant_list_complete' ok 265 - get 'grant_list_complete' ok 266 - set 'medline_date' ok 267 - get 'medline_date' ok 268 - set 'medline_id' ok 269 - get 'medline_id' ok 270 - set 'medline_page' ok 271 - get 'medline_page' ok 272 - set 'number_of_references' ok 273 - get 'number_of_references' ok 274 - set 'other_languages' ok 275 - get 'other_languages' ok 276 - set 'pmid' ok 277 - get 'pmid' ok 278 - set 'season' ok 279 - get 'season' ok 280 - set 'status' ok 281 - get 'status' ok 282 - set 'vernacular_title' ok 283 - get 'vernacular_title' ok 284 ok 285 - abstract ok 286 - abstract_language ok 287 - abstract_type ok 288 - author_list_complete ok 289 - cross_references_list_complete ok 290 - date ok 291 - date_completed ok 292 - date_created ok 293 - date_revised ok 294 - format ok 295 - identifier ok 296 - language ok 297 - last_modified_date ok 298 - repository_subset ok 299 - rights ok 300 - spatial_location ok 301 - subject_headings_source ok 302 - temporal_period ok 303 - title ok 304 - toc ok 305 - toc_type ok 306 - type ok 307 - first_page ok 308 - last_page ok 309 - affiliation ok 310 - citation_owner ok 311 - date_of_electronic_publication ok 312 - gene_symbols ok 313 - grant_list_complete ok 314 - medline_date ok 315 - medline_id ok 316 - medline_page ok 317 - number_of_references ok 318 - other_languages ok 319 - pmid ok 320 - season ok 321 - status ok 322 - vernacular_title ok 323 - get 'authors' ok 324 - get 'cross_references' ok 325 - get 'codes' ok 326 - get 'contributors' ok 327 - get 'keywords' ok 328 - get 'publisher' ok 329 - get 'subject_headings' ok 330 - get 'book' ok 331 - get 'chemicals' ok 332 - get 'comment_ins' ok 333 - get 'comment_ons' ok 334 - get 'erratum_fors' ok 335 - get 'erratum_ins' ok 336 - get 'general_notes' ok 337 - get 'grants' ok 338 - get 'mesh_headings' ok 339 - get 'original_report_ins' ok 340 - get 'other_abstracts' ok 341 - get 'other_ids' ok 342 - get 'republished_froms' ok 343 - get 'republished_ins' ok 344 - get 'retraction_ins' ok 345 - get 'retraction_ofs' ok 346 - get 'summary_for_patients_ins' ok 347 - get 'update_ins' ok 348 - get 'update_ofs' ok 349 - get 'book' ok 350 - set 'abstract' ok 351 - get 'abstract' ok 352 - set 'abstract_language' ok 353 - get 'abstract_language' ok 354 - set 'abstract_type' ok 355 - get 'abstract_type' ok 356 - set 'author_list_complete' ok 357 - get 'author_list_complete' ok 358 - set 'cross_references_list_complete' ok 359 - get 'cross_references_list_complete' ok 360 - set 'date' ok 361 - get 'date' ok 362 - set 'date_completed' ok 363 - get 'date_completed' ok 364 - set 'date_created' ok 365 - get 'date_created' ok 366 - set 'date_revised' ok 367 - get 'date_revised' ok 368 - set 'format' ok 369 - get 'format' ok 370 - set 'identifier' ok 371 - get 'identifier' ok 372 - set 'language' ok 373 - get 'language' ok 374 - set 'last_modified_date' ok 375 - get 'last_modified_date' ok 376 - set 'repository_subset' ok 377 - get 'repository_subset' ok 378 - set 'rights' ok 379 - get 'rights' ok 380 - set 'spatial_location' ok 381 - get 'spatial_location' ok 382 - set 'subject_headings_source' ok 383 - get 'subject_headings_source' ok 384 - set 'temporal_period' ok 385 - get 'temporal_period' ok 386 - set 'title' ok 387 - get 'title' ok 388 - set 'toc' ok 389 - get 'toc' ok 390 - set 'toc_type' ok 391 - get 'toc_type' ok 392 - set 'type' ok 393 - get 'type' ok 394 - set 'edition' ok 395 - get 'edition' ok 396 - set 'isbn' ok 397 - get 'isbn' ok 398 - set 'series' ok 399 - get 'series' ok 400 - set 'volume' ok 401 - get 'volume' ok 402 ok 403 - abstract ok 404 - abstract_language ok 405 - abstract_type ok 406 - author_list_complete ok 407 - cross_references_list_complete ok 408 - date ok 409 - date_completed ok 410 - date_created ok 411 - date_revised ok 412 - format ok 413 - identifier ok 414 - language ok 415 - last_modified_date ok 416 - repository_subset ok 417 - rights ok 418 - spatial_location ok 419 - subject_headings_source ok 420 - temporal_period ok 421 - title ok 422 - toc ok 423 - toc_type ok 424 - type ok 425 - edition ok 426 - isbn ok 427 - series ok 428 - volume ok 429 - get 'authors' ok 430 - get 'cross_references' ok 431 - get 'codes' ok 432 - get 'contributors' ok 433 - get 'keywords' ok 434 - get 'publisher' ok 435 - get 'subject_headings' ok 436 - get 'editor' ok 437 - set 'abbreviation' ok 438 - get 'abbreviation' ok 439 - set 'issn' ok 440 - get 'issn' ok 441 - set 'name' ok 442 - get 'name' ok 443 - set 'coden' ok 444 - get 'coden' ok 445 - set 'country' ok 446 - get 'country' ok 447 - set 'medline_code' ok 448 - get 'medline_code' ok 449 - set 'medline_ta' ok 450 - get 'medline_ta' ok 451 - set 'nlm_unique_id' ok 452 - get 'nlm_unique_id' ok 453 ok 454 - abbreviation ok 455 - issn ok 456 - name ok 457 - coden ok 458 - country ok 459 - medline_code ok 460 - medline_ta ok 461 - nlm_unique_id ok 462 - set 'doc_number' ok 463 - get 'doc_number' ok 464 - set 'doc_office' ok 465 - get 'doc_office' ok 466 - set 'doc_type' ok 467 - get 'doc_type' ok 468 ok 469 - doc_number ok 470 - doc_office ok 471 - doc_type ok 472 - get 'applicants' ok 473 - set 'url' ok 474 - get 'url' ok 475 - set 'estimated_size' ok 476 - get 'estimated_size' ok 477 - set 'cost' ok 478 - get 'cost' ok 479 ok 480 - url ok 481 - estimated_size ok 482 - cost ok 483 - set 'type' ok 484 - get 'type' ok 485 - set 'affiliation' ok 486 - get 'affiliation' ok 487 - set 'email' ok 488 - get 'email' ok 489 - set 'firstname' ok 490 - get 'firstname' ok 491 - set 'forename' ok 492 - get 'forename' ok 493 - set 'initials' ok 494 - get 'initials' ok 495 - set 'lastname' ok 496 - get 'lastname' ok 497 - set 'middlename' ok 498 - get 'middlename' ok 499 - set 'postal_address' ok 500 - get 'postal_address' ok 501 - set 'suffix' ok 502 - get 'suffix' ok 503 ok 504 - type ok 505 - affiliation ok 506 - email ok 507 - firstname ok 508 - forename ok 509 - initials ok 510 - lastname ok 511 - middlename ok 512 - postal_address ok 513 - suffix ok 514 - set 'type' ok 515 - get 'type' ok 516 - set 'name' ok 517 - get 'name' ok 518 ok 519 - type ok 520 - name ok 521 - set 'type' ok 522 - get 'type' ok 523 - set 'name' ok 524 - get 'name' ok 525 ok 526 - type ok 527 - name ok 528 - set 'pubmed_status' ok 529 - get 'pubmed_status' ok 530 - set 'pubmed_provider_id' ok 531 - get 'pubmed_provider_id' ok 532 ok 533 - pubmed_status ok 534 - pubmed_provider_id ok 535 - get 'pubmed_history_list' ok 536 - get 'pubmed_article_id_list' ok 537 - get 'pubmed_url_list' ok t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested t/Biblio/eutils.t ............................ skipped: Network tests have not been requested t/ClusterIO/ClusterIO.t ...................... 1..12 ok 1 - use Bio::ClusterIO; ok 2 - use Bio::Cluster::ClusterFactory; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Cluster::UniGeneI ok 12 - The object isa Bio::Cluster::UniGeneI ok t/ClusterIO/SequenceFamily.t ................. 1..19 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Cluster::SequenceFamily; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok Subroutine new redefined at Bio\Cluster\UniGene.pm line 258. Subroutine unigene_id redefined at Bio\Cluster\UniGene.pm line 320. Subroutine title redefined at Bio\Cluster\UniGene.pm line 342. Subroutine gene redefined at Bio\Cluster\UniGene.pm line 363. Subroutine cytoband redefined at Bio\Cluster\UniGene.pm line 381. Subroutine mgi redefined at Bio\Cluster\UniGene.pm line 398. Subroutine locuslink redefined at Bio\Cluster\UniGene.pm line 426. Subroutine homol redefined at Bio\Cluster\UniGene.pm line 455. Subroutine restr_expr redefined at Bio\Cluster\UniGene.pm line 472. Subroutine gnm_terminus redefined at Bio\Cluster\UniGene.pm line 490. Subroutine scount redefined at Bio\Cluster\UniGene.pm line 506. Subroutine express redefined at Bio\Cluster\UniGene.pm line 528. Subroutine chromosome redefined at Bio\Cluster\UniGene.pm line 546. Subroutine sts redefined at Bio\Cluster\UniGene.pm line 564. Subroutine txmap redefined at Bio\Cluster\UniGene.pm line 582. Subroutine protsim redefined at Bio\Cluster\UniGene.pm line 600. Subroutine sequences redefined at Bio\Cluster\UniGene.pm line 623. Subroutine species redefined at Bio\Cluster\UniGene.pm line 643. Subroutine display_id redefined at Bio\Cluster\UniGene.pm line 675. Subroutine description redefined at Bio\Cluster\UniGene.pm line 692. Subroutine size redefined at Bio\Cluster\UniGene.pm line 710. Subroutine cluster_score redefined at Bio\Cluster\UniGene.pm line 742. Subroutine get_members redefined at Bio\Cluster\UniGene.pm line 765. Subroutine annotation redefined at Bio\Cluster\UniGene.pm line 814. Subroutine add_member redefined at Bio\Cluster\UniGene.pm line 846. Subroutine remove_members redefined at Bio\Cluster\UniGene.pm line 876. Subroutine next_locuslink redefined at Bio\Cluster\UniGene.pm line 905. Subroutine next_express redefined at Bio\Cluster\UniGene.pm line 931. Subroutine next_chromosome redefined at Bio\Cluster\UniGene.pm line 958. Subroutine next_protsim redefined at Bio\Cluster\UniGene.pm line 985. Subroutine next_sts redefined at Bio\Cluster\UniGene.pm line 1012. Subroutine next_txmap redefined at Bio\Cluster\UniGene.pm line 1039. Subroutine _next_element redefined at Bio\Cluster\UniGene.pm line 1052. Subroutine object_id redefined at Bio\Cluster\UniGene.pm line 1089. Subroutine version redefined at Bio\Cluster\UniGene.pm line 1111. Subroutine authority redefined at Bio\Cluster\UniGene.pm line 1133. Subroutine namespace redefined at Bio\Cluster\UniGene.pm line 1155. Subroutine display_name redefined at Bio\Cluster\UniGene.pm line 1183. Subroutine next_seq redefined at Bio\Cluster\UniGene.pm line 1234. Subroutine sequence_factory redefined at Bio\Cluster\UniGene.pm line 1292. Subroutine _annotation_value redefined at Bio\Cluster\UniGene.pm line 1320. Subroutine _annotation_value_ary redefined at Bio\Cluster\UniGene.pm line 1361. Subroutine _annotation_dblink redefined at Bio\Cluster\UniGene.pm line 1397. Subroutine _remove_dblink redefined at Bio\Cluster\UniGene.pm line 1432. Subroutine Bio::Cluster::UniGene::sequence redefined at Bio\Cluster\UniGene.pm line 1456. t/ClusterIO/unigene.t ........................ 1..73 ok 1 - use Bio::ClusterIO; ok 2 - new Bio::ClusterIO object defined ok 3 ok 4 - The object isa Bio::Cluster::UniGeneI ok 5 - The object isa Bio::ClusterI ok 6 - The object isa Bio::IdentifiableI ok 7 - The object isa Bio::DescribableI ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 - The object isa Bio::PrimarySeqI ok 49 ok 50 ok 51 - annotation object defined ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 - The object isa Bio::PrimarySeqI ok 67 ok 68 - next cluster ok 69 ok 70 ok 71 ok 72 ok 73 ok t/Coordinate/CoordinateGraph.t ............... 1..7 ok 1 - use Bio::Coordinate::Graph; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/Coordinate/CoordinateMapper.t .............. 1..175 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::Result::Match; ok 4 - use Bio::Coordinate::Result::Gap; ok 5 - use Bio::Coordinate::Chain; ok 6 - use Bio::Coordinate::Collection; ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Coordinate::Result ok 15 - The object isa Bio::Location::SplitLocationI ok 16 ok 17 ok 18 ok 19 - The object isa Bio::LocationI ok 20 - The object isa Bio::Coordinate::Result::Match ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Coordinate::Result::Gap ok 38 - The object isa Bio::LocationI ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 - The object isa Bio::Coordinate::Result::Match ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 - Match: |314696| Test: 314696| ok 139 ok 140 ok 141 ok 142 - Match: |341| Test: 341| ok 143 ok 144 ok 145 ok 146 - Match: |315843| Test: 315843| ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - Match: |627011| Test: 627011| ok 153 ok 154 ok 155 ok 156 - Match: |chr1| Test: chr1| ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok t/Coordinate/GeneCoordinateMapper.t .......... 1..116 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::ExtrapolatingPair; ok 4 - use Bio::Coordinate::GeneMapper; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Location::Simple ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 - The object isa Bio::Location::Simple ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok t/Draw/Pictogram.t ........................... 1..6 ok 1 - use Bio::Draw::Pictogram; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Matrix::PSM::IO; ok 4 - The object isa Bio::Draw::Pictogram ok 5 ok 6 ok t/LiveSeq/Chain.t ............................ 1..45 ok 1 - use Bio::LiveSeq::Chain; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok t/LiveSeq/LiveSeq.t .......................... 1..48 ok 1 - use Bio::LiveSeq::IO::BioPerl; ok 2 ok 3 ok 4 - Bio::LiveSeq::Gene ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok t/LiveSeq/Mutation.t ......................... 1..19 ok 1 - use Bio::LiveSeq::Mutation; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok t/LiveSeq/Mutator.t .......................... 1..24 ok 1 - use Bio::LiveSeq::Mutator; ok 2 - use Bio::LiveSeq::IO::BioPerl; ok 3 - use Bio::Variation::IO; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok t/LocalDB/BioDBGFF.t ......................... skipped: Not compatible with your Operating System t/LocalDB/DBFasta.t .......................... 1..17 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 - bug 3126 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - threw Regexp ((?-xism:FASTA header doesn't match)) ok t/LocalDB/DBQual.t ........................... 1..38 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 - The object isa Bio::Seq::PrimaryQual ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 - The object isa Bio::Seq::PrimaryQual ok 26 ok 27 ok 28 - The object isa Bio::Seq::PrimaryQual ok 29 ok 30 ok 31 ok 32 - The object isa Bio::Seq::PrimaryQual ok 33 ok 34 - The object isa Bio::Seq::PrimaryQual ok 35 ok 36 ok 37 ok 38 ok t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. t/LocalDB/Index/Blast.t ...................... 1..26 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::Blast; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok --------------------- WARNING --------------------- MSG: overwriting a current value stored for SP130_MOUSE --------------------------------------------------- --------------------- WARNING --------------------- MSG: overwriting a current value stored for SDS3_MOUSE --------------------------------------------------- --------------------- WARNING --------------------- MSG: overwriting a current value stored for IKZF1_MOUSE --------------------------------------------------- t/LocalDB/Index/BlastTable.t ................. 1..27 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::BlastTable; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok t/LocalDB/Index/Index.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed t/LocalDB/Registry.t ......................... 1..14 ok 1 - use Bio::DB::Registry; ok 2 - use Bio::DB::Flat; ok 3 ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok # Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;' # in t/LocalDB/SeqFeature.t at line 16. # Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'. # Error: Can't locate DB_File.pm in @INC (@INC contains: . .. ./t/lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 38. # BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 16. # Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. # Compilation failed in require at (eval 58) line 2. # BEGIN failed--compilation aborted at (eval 58) line 2. # Looks like you planned 116 tests but ran 1 extra. # Looks like you failed 1 test of 117 run. t/LocalDB/SeqFeature.t ....................... 1..116 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::DB::SeqFeature::Store; not ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader; ok 4 - use Bio::Root::IO; ok 5 - use Bio::DB::Fasta; ok 6 - use File::Copy; ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 70 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 71 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 72 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 73 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 74 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 75 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 76 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 77 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 78 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 79 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 80 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 81 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 82 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 83 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 84 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 85 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 86 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 87 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 88 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 89 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 90 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 91 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 92 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 93 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 94 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 95 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 96 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 97 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 98 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 99 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 100 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 101 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 102 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 103 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 104 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 105 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 106 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 107 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 108 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 109 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 110 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 111 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 112 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 113 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 114 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 115 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 116 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # ok 117 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 74) line 2. # at t/LocalDB/SeqFeature.t line 32 # Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 111 skipped subtests: 4 okay) ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- Bio::DB::Taxonomy: flatfile cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- For more information about the Bio::DB::Taxonomy system please see the Bio::DB::Taxonomy docs. This includes ways of checking for formats at compile time, not run time. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\TFBS\transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- Bio::DB::TFBS: transfac_pro cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\TFBS\transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- For more information about the Bio::DB::TFBS system please see the Bio::DB::TFBS docs. This includes ways of checking for formats at compile time, not run time. # Failed test at t/LocalDB/transfac_pro.t line 25. Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33. # Looks like you planned 115 tests but ran 4. # Looks like you failed 1 test of 4 run. # Looks like your test exited with 2 just after 4. t/LocalDB/transfac_pro.t ..................... 1..115 ok 1 - use Bio::Matrix::PSM::IO; ok 2 - use Bio::DB::TFBS; ok 3 - use Bio::DB::Taxonomy; not ok 4 Dubious, test returned 2 (wstat 512, 0x200) Failed 112/115 subtests t/Map/Cyto.t ................................. 1..110 ok 1 - use Bio::Map::CytoMap; ok 2 - use Bio::Map::CytoPosition; ok 3 - use Bio::Map::CytoMarker; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Map::CytoPosition ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Range ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok t/Map/Linkage.t .............................. 1..18 ok 1 - use Bio::Map::LinkagePosition; ok 2 - use Bio::Map::Microsatellite; ok 3 - use Bio::Map::LinkageMap; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/Map/Map.t .................................. 1..267 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Marker; ok 3 - use Bio::Map::Position; ok 4 - use Bio::Map::Relative; ok 5 - use Bio::Map::Mappable; ok 6 ok 7 ok 8 ok 9 ok 10 - Length is 0 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 - use Bio::Map::Gene; ok 152 - use Bio::Map::GeneMap; ok 153 - use Bio::Map::TranscriptionFactor; ok 154 - use Bio::Map::GeneRelative; ok 155 - use Bio::Map::GenePosition; ok 156 - use Bio::Map::Prediction; ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok t/Map/MapIO.t ................................ 1..51 ok 1 - use Bio::MapIO; ok 2 ok 3 - The object isa Bio::Map::MapI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok t/Map/MicrosatelliteMarker.t ................. 1..8 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Position; ok 3 - use Bio::Map::Microsatellite; ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Map/Physical.t ............................. 1..39 ok 1 - use Bio::Map::Physical; ok 2 - use Bio::MapIO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - code holds and returns a string, definition requires a boolean ok 13 - code holds and returns a string, definition requires a boolean ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok t/Matrix/IO/masta.t .......................... 1..16 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok t/Matrix/IO/psm.t ............................ 1..63 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok t/Matrix/InstanceSite.t ...................... 1..6 ok 1 - use Bio::Matrix::PSM::InstanceSite; ok 2 ok 3 ok 4 ok 5 ok 6 ok t/Matrix/Matrix.t ............................ 1..77 ok 1 - use Bio::Matrix::Generic; ok 2 - use Bio::Matrix::IO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 - The object isa Bio::Matrix::Scoring ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 - The object isa Bio::Matrix::Scoring ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok t/Matrix/ProtMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::ProtMatrix; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok t/Matrix/ProtPsm.t ........................... 1..14 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 # skip TODO: Module incomplete ok 6 # skip TODO: Module incomplete ok 7 # skip TODO: Module incomplete ok 8 # skip TODO: Module incomplete ok 9 # skip TODO: Module incomplete ok 10 # skip TODO: Module incomplete ok 11 # skip TODO: Module incomplete ok 12 # skip TODO: Module incomplete ok 13 # skip TODO: Module incomplete ok 14 # skip TODO: Module incomplete ok t/Matrix/SiteMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::SiteMatrix; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok t/Ontology/GOterm.t .......................... 1..62 ok 1 - use Bio::Ontology::GOterm; ok 2 - use Bio::Ontology::Ontology; ok 3 - use Bio::Annotation::DBLink; ok 4 - The object isa Bio::Ontology::GOterm ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok t/Ontology/GraphAdaptor.t .................... 1..28 ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok t/Ontology/IO/go.t ........................... 1..102 ok 1 - use Bio::OntologyIO; ok 2 ok 3 - The object isa Bio::Ontology::OntologyI ok 4 ok 5 - The object isa Bio::Ontology::OntologyEngineI ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok t/Ontology/IO/interpro.t ..................... 1..69 ok 1 - use Bio::OntologyIO; ok 2 - The object isa Bio::OntologyIO::InterProParser ok 3 ok 4 - get_dbxrefs on leaf terms is non-empty ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty ok 11 - get_members on leaf terms is non-empty ok 12 - class_list on leaf terms is non-empty ok 13 - get_examples on leaf terms is non-empty ok 14 - get_external_documents on leaf terms is non-empty ok 15 - get_references on leaf terms is non-empty ok 16 - protein_count on leaf terms is non-empty ok 17 - to_string looks reasonable ok 18 - There are 8 root InterPro terms ok 19 - The object isa Bio::Ontology::Ontology ok 20 - term Integrins alpha chain in ontology InterPro ok 21 - The object isa Bio::Ontology::Ontology ok 22 - term post-translational modification in ontology InterPro ok 23 - The object isa Bio::Ontology::Ontology ok 24 - term Repeat in ontology InterPro ok 25 - The object isa Bio::Ontology::Ontology ok 26 - term Binding Site in ontology InterPro ok 27 - The object isa Bio::Ontology::Ontology ok 28 - term Cdc20/Fizzy in ontology InterPro ok 29 - The object isa Bio::Ontology::Ontology ok 30 - term Conserved Site in ontology InterPro ok 31 - The object isa Bio::Ontology::Ontology ok 32 - term Region in ontology InterPro ok 33 - The object isa Bio::Ontology::Ontology ok 34 - term Kringle in ontology InterPro ok 35 - The object isa Bio::Ontology::Ontology ok 36 - term Helix-turn-helix, AraC type in ontology InterPro ok 37 - The object isa Bio::Ontology::Ontology ok 38 - term Active Site in ontology InterPro ok 39 - The object isa Bio::Ontology::Ontology ok 40 - term Active Site in ontology InterPro ok 41 - The object isa Bio::Ontology::Ontology ok 42 - term Binding Site in ontology InterPro ok 43 - The object isa Bio::Ontology::Ontology ok 44 - term Conserved Site in ontology InterPro ok 45 - The object isa Bio::Ontology::Ontology ok 46 - term Domain in ontology InterPro ok 47 - The object isa Bio::Ontology::Ontology ok 48 - term Family in ontology InterPro ok 49 - The object isa Bio::Ontology::Ontology ok 50 - term Region in ontology InterPro ok 51 - The object isa Bio::Ontology::Ontology ok 52 - term Repeat in ontology InterPro ok 53 - The object isa Bio::Ontology::Ontology ok 54 - term post-translational modification in ontology InterPro ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 - Integrins alpha chain term has one parent ok 62 - Integrins alpha chain term has one ancestor ok 63 - Cdc20/Fizzy term has one parent ok 64 - Cdc20/Fizzy term has one ancestor ok 65 - Kringle term has one parent ok 66 - Kringle term has one ancestor ok 67 - Helix-turn-helix, AraC type term has one parent ok 68 - Helix-turn-helix, AraC type term has one ancestor ok 69 - secondary accession map has 2 keys ok t/Ontology/IO/obo.t .......................... 1..92 ok 1 - use Bio::OntologyIO; ok 2 - use Bio::Ontology::RelationshipType; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - got a ontology IO handler isa Bio::OntologyIO ok 47 - got ontology parser2 isa Bio::Ontology::Ontology ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine ok 49 - got ontology parser2 isa Bio::Ontology::Ontology ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine ok 51 - got ontology parser2 isa Bio::Ontology::Ontology ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine ok 53 - Gene ontology ok 54 - biological process ok 55 - molecular function ok 56 - Got root ok 57 - Got root ok 58 - Got regulates # from gene_ontology ok 59 - Got # positively regulates from gene_ontology ok 60 - Got # regulates from biological_process ok 61 - Got # positively regulates from biological_process ok 62 - Got predicates for gene_ontology ok 63 - Got predicates for biological_process ok 64 - Got regulates predicate ok 65 - Got positively regulates predicate ok 66 - Got relationships for biological_process ok 67 - Got relationships for molecular_function ok 68 - Got is a relationship from # molecular_function ok 69 - Got term object isa Bio::Ontology::Term ok 70 - Got term id ok 71 - Got term name ok 72 - Got regulated object isa Bio::Ontology::Term ok 73 - Got regulated term1 id ok 74 - Got term1 object isa Bio::Ontology::Term ok 75 - Got back the child ok 76 - Got term object isa Bio::Ontology::Term ok 77 - Got term id ok 78 - Got term name ok 79 - Got regulated object isa Bio::Ontology::Term ok 80 - Got regulated term1 id ok 81 - Got identical regulation ok 82 - Got term1 object isa Bio::Ontology::Term ok 83 - Got back the child ok 84 - got a ontology IO handler isa Bio::OntologyIO ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok t/Ontology/Ontology.t ........................ 1..55 ok 1 - use Bio::OntologyIO; ok 2 - use Bio::Ontology::RelationshipType; ok 3 - The object isa Bio::Ontology::Ontology ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 - Interpro XML file interpro.xml can be parsed ok 54 - Interpro XML file interpro_sample.xml can be parsed ok 55 - Interpro XML file interpro_relationship.xml can be parsed ok Subroutine new redefined at Bio\Ontology\Relationship.pm line 139. Subroutine init redefined at Bio\Ontology\Relationship.pm line 190. Subroutine identifier redefined at Bio\Ontology\Relationship.pm line 215. Subroutine subject_term redefined at Bio\Ontology\Relationship.pm line 245. Subroutine object_term redefined at Bio\Ontology\Relationship.pm line 276. Subroutine predicate_term redefined at Bio\Ontology\Relationship.pm line 307. Subroutine ontology redefined at Bio\Ontology\Relationship.pm line 333. Subroutine to_string redefined at Bio\Ontology\Relationship.pm line 361. Subroutine _check_class redefined at Bio\Ontology\Relationship.pm line 383. Subroutine Bio::Ontology::Relationship::child_term redefined at Bio\Ontology\Relationship.pm line 409. Subroutine Bio::Ontology::Relationship::parent_term redefined at Bio\Ontology\Relationship.pm line 410. Subroutine Bio::Ontology::Relationship::relationship_type redefined at Bio\Ontology\Relationship.pm line 411. t/Ontology/OntologyEngine.t .................. 1..31 ok 1 - use Bio::Ontology::Term; ok 2 - use Bio::Ontology::Relationship; ok 3 - use Bio::Ontology::RelationshipType; ok 4 - use Bio::Ontology::SimpleOntologyEngine; ok 5 - use Bio::Ontology::Ontology; ok 6 - The object isa Bio::Ontology::OntologyEngineI ok 7 ok 8 - adding a relationship with an undef object term fails ok 9 - adding a relationship with an undef object term fails ok 10 - adding a relationship with an undef subject term fails ok 11 - adding a relationship with an undef subject term fails ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested t/Ontology/Relationship.t .................... 1..12 ok 1 - use Bio::Ontology::Relationship; ok 2 - use Bio::Ontology::GOterm; ok 3 - use Bio::Ontology::RelationshipType; ok 4 - The object isa Bio::Ontology::RelationshipType ok 5 - The object isa Bio::Ontology::GOterm ok 6 - The object isa Bio::Ontology::GOterm ok 7 - The object isa Bio::Ontology::Relationship ok 8 ok 9 ok 10 ok 11 ok 12 ok t/Ontology/RelationshipType.t ................ 1..23 ok 1 - use Bio::Ontology::RelationshipType; ok 2 - use Bio::Ontology::Ontology; ok 3 - The object isa Bio::Ontology::RelationshipType ok 4 - The object isa Bio::Ontology::TermI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok Constant subroutine Bio::Ontology::Term::TRUE redefined at C:\cpanfly-5.12\var\megalib/constant.pm line 131. Constant subroutine Bio::Ontology::Term::FALSE redefined at C:\cpanfly-5.12\var\megalib/constant.pm line 131. Subroutine new redefined at Bio\Ontology\Term.pm line 145. Subroutine init redefined at Bio\Ontology\Term.pm line 176. Subroutine identifier redefined at Bio\Ontology\Term.pm line 207. Subroutine name redefined at Bio\Ontology\Term.pm line 227. Subroutine definition redefined at Bio\Ontology\Term.pm line 247. Subroutine ontology redefined at Bio\Ontology\Term.pm line 275. Subroutine version redefined at Bio\Ontology\Term.pm line 305. Subroutine is_obsolete redefined at Bio\Ontology\Term.pm line 324. Subroutine comment redefined at Bio\Ontology\Term.pm line 344. Subroutine get_synonyms redefined at Bio\Ontology\Term.pm line 361. Subroutine add_synonym redefined at Bio\Ontology\Term.pm line 381. Subroutine remove_synonyms redefined at Bio\Ontology\Term.pm line 405. Subroutine get_dblinks redefined at Bio\Ontology\Term.pm line 428. Subroutine get_dbxrefs redefined at Bio\Ontology\Term.pm line 454. Subroutine get_dblink_context redefined at Bio\Ontology\Term.pm line 479. Subroutine get_dbxref_context redefined at Bio\Ontology\Term.pm line 495. Subroutine add_dblink redefined at Bio\Ontology\Term.pm line 515. Subroutine add_dbxref redefined at Bio\Ontology\Term.pm line 542. Subroutine has_dblink redefined at Bio\Ontology\Term.pm line 581. Subroutine has_dbxref redefined at Bio\Ontology\Term.pm line 599. Subroutine add_dblink_context redefined at Bio\Ontology\Term.pm line 630. Subroutine remove_dblinks redefined at Bio\Ontology\Term.pm line 651. Subroutine remove_dbxrefs redefined at Bio\Ontology\Term.pm line 668. Subroutine get_references redefined at Bio\Ontology\Term.pm line 690. Subroutine add_reference redefined at Bio\Ontology\Term.pm line 706. Subroutine remove_references redefined at Bio\Ontology\Term.pm line 729. Subroutine get_secondary_ids redefined at Bio\Ontology\Term.pm line 750. Subroutine add_secondary_id redefined at Bio\Ontology\Term.pm line 770. Subroutine remove_secondary_ids redefined at Bio\Ontology\Term.pm line 794. Subroutine _is_true_or_false redefined at Bio\Ontology\Term.pm line 808. Subroutine object_id redefined at Bio\Ontology\Term.pm line 833. Subroutine authority redefined at Bio\Ontology\Term.pm line 854. Subroutine namespace redefined at Bio\Ontology\Term.pm line 883. Subroutine display_name redefined at Bio\Ontology\Term.pm line 907. Subroutine description redefined at Bio\Ontology\Term.pm line 931. Subroutine each_dblink redefined at Bio\Ontology\Term.pm line 945. Subroutine add_dblinks redefined at Bio\Ontology\Term.pm line 946. Subroutine Bio::Ontology::Term::add_dbxrefs redefined at Bio\Ontology\Term.pm line 566. Subroutine Bio::Ontology::Term::each_synonym redefined at Bio\Ontology\Term.pm line 947. Subroutine Bio::Ontology::Term::add_synonyms redefined at Bio\Ontology\Term.pm line 948. t/Ontology/Term.t ............................ 1..54 ok 1 - use Bio::Ontology::Term; ok 2 - use Bio::Ontology::TermFactory; ok 3 - use Bio::Annotation::DBLink; ok 4 - The object isa Bio::Ontology::TermI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 - The object isa Bio::Ontology::TermI ok 45 ok 46 - The object isa Bio::Ontology::TermI ok 47 - The object isa Bio::Ontology::GOterm ok 48 ok 49 ok 50 - The object isa Bio::Ontology::TermI ok 51 - The object isa Bio::AnnotationI ok 52 ok 53 ok 54 ok t/Perl.t ..................................... 1..29 ok 1 - use Bio::Perl; ok 2 ok 3 - The object isa Bio::SeqI ok 4 ok 5 - The object isa Bio::SeqI ok 6 ok 7 - The object isa Bio::SeqI ok 8 - The object isa Bio::SeqI ok 9 ok 10 ok 11 - The object isa Bio::SeqI ok 12 ok 13 - The object isa Bio::SeqI ok 14 ok 15 - The object isa Bio::PrimarySeqI ok 16 ok 17 ok 18 ok 19 ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok t/Phenotype/Correlate.t ...................... 1..17 ok 1 - use Bio::Phenotype::Correlate; ok 2 - use Bio::Species; ok 3 - The object isa Bio::Phenotype::Correlate ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok t/Phenotype/MeSH.t ........................... 1..24 ok 1 - use Bio::Phenotype::MeSH::Term; ok 2 - use Bio::Phenotype::MeSH::Twig; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok t/Phenotype/Measure.t ........................ 1..21 ok 1 - use Bio::Phenotype::Measure; ok 2 - The object isa Bio::Phenotype::Measure ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok t/Phenotype/MiniMIMentry.t ................... 1..15 ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry; ok 2 - The object isa Bio::Phenotype::OMIM::MiniMIMentry ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok t/Phenotype/OMIMentry.t ...................... 1..153 ok 1 - use Bio::Phenotype::OMIM::OMIMentry; ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry; ok 3 - use Bio::Species; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Map::CytoPosition; ok 6 - use Bio::Phenotype::Correlate; ok 7 - use Bio::Phenotype::Measure; ok 8 - use Bio::Annotation::DBLink; ok 9 - The object isa Bio::Phenotype::OMIM::OMIMentry ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 - operator overloading in AnnotationI is deprecated ok 80 - operator overloading in AnnotationI is deprecated ok 81 ok 82 ok 83 - operator overloading in AnnotationI is deprecated ok 84 - operator overloading in AnnotationI is deprecated ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 - operator overloading in AnnotationI is deprecated ok 137 - operator overloading in AnnotationI is deprecated ok 138 ok 139 ok 140 - operator overloading in AnnotationI is deprecated ok 141 - operator overloading in AnnotationI is deprecated ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok t/Phenotype/OMIMentryAllelicVariant.t ........ 1..27 ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; ok 2 - The object isa Bio::Phenotype::OMIM::OMIMentryAllelicVariant ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok t/Phenotype/OMIMparser.t ..................... 1..175 ok 1 - use Bio::Phenotype::OMIM::OMIMparser; ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 - The object isa Bio::Phenotype::OMIM::MiniMIMentry ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 - The object isa Bio::Phenotype::OMIM::OMIMentry ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 - The object isa Bio::Phenotype::OMIM::MiniMIMentry ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 - missing linebreak caught ok t/Phenotype/Phenotype.t ...................... 1..116 ok 1 - use Bio::Phenotype::Phenotype; ok 2 - use Bio::Species; ok 3 - use Bio::Annotation::Reference; ok 4 - use Bio::Map::CytoPosition; ok 5 - use Bio::Phenotype::Correlate; ok 6 - use Bio::Phenotype::Measure; ok 7 - use Bio::Annotation::DBLink; ok 8 - The object isa Bio::Phenotype::PhenotypeI ok 9 - The object isa Bio::Phenotype::Phenotype ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 - operator overloading in AnnotationI is deprecated ok 43 - operator overloading in AnnotationI is deprecated ok 44 ok 45 ok 46 - operator overloading in AnnotationI is deprecated ok 47 - operator overloading in AnnotationI is deprecated ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 - operator overloading in AnnotationI is deprecated ok 100 - operator overloading in AnnotationI is deprecated ok 101 ok 102 ok 103 - operator overloading in AnnotationI is deprecated ok 104 - operator overloading in AnnotationI is deprecated ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok t/PodSyntax.t ................................ 1..1011 ok 1 - POD test for Bio\AlignIO.pm ok 2 - POD test for Bio\AnalysisI.pm ok 3 - POD test for Bio\AnalysisParserI.pm ok 4 - POD test for Bio\AnalysisResultI.pm ok 5 - POD test for Bio\AnnotatableI.pm ok 6 - POD test for Bio\AnnotationCollectionI.pm ok 7 - POD test for Bio\AnnotationI.pm ok 8 - POD test for Bio\Biblio.pm ok 9 - POD test for Bio\ClusterI.pm ok 10 - POD test for Bio\ClusterIO.pm ok 11 - POD test for Bio\DasI.pm ok 12 - POD test for Bio\DBLinkContainerI.pm ok 13 - POD test for Bio\DescribableI.pm ok 14 - POD test for Bio\FeatureHolderI.pm ok 15 - POD test for Bio\FeatureIO.pm ok 16 - POD test for Bio\HandlerBaseI.pm ok 17 - POD test for Bio\IdCollectionI.pm ok 18 - POD test for Bio\IdentifiableI.pm ok 19 - POD test for Bio\LocatableSeq.pm ok 20 - POD test for Bio\LocationI.pm ok 21 - POD test for Bio\MapIO.pm ok 22 - POD test for Bio\NexmlIO.pm ok 23 - POD test for Bio\OntologyIO.pm ok 24 - POD test for Bio\ParameterBaseI.pm ok 25 - POD test for Bio\Perl.pm ok 26 - POD test for Bio\PhyloNetwork.pm ok 27 - POD test for Bio\PrimarySeq.pm ok 28 - POD test for Bio\PrimarySeqI.pm ok 29 - POD test for Bio\PullParserI.pm ok 30 - POD test for Bio\Range.pm ok 31 - POD test for Bio\RangeI.pm ok 32 - POD test for Bio\SearchDist.pm ok 33 - POD test for Bio\SearchIO.pm ok 34 - POD test for Bio\Seq.pm ok 35 - POD test for Bio\SeqAnalysisParserI.pm ok 36 - POD test for Bio\SeqFeatureI.pm ok 37 - POD test for Bio\SeqI.pm ok 38 - POD test for Bio\SeqIO.pm ok 39 - POD test for Bio\SeqUtils.pm ok 40 - POD test for Bio\SimpleAlign.pm ok 41 - POD test for Bio\SimpleAnalysisI.pm ok 42 - POD test for Bio\Species.pm ok 43 - POD test for Bio\Taxon.pm ok 44 - POD test for Bio\Taxonomy.pm ok 45 - POD test for Bio\TreeIO.pm ok 46 - POD test for Bio\UpdateableSeqI.pm ok 47 - POD test for Bio\WebAgent.pm ok 48 - POD test for examples\bioperl.pl (no pod) ok 49 - POD test for examples\generate_random_seq.pl (no pod) ok 50 - POD test for examples\longorf.pl ok 51 - POD test for examples\make_primers.pl (no pod) ok 52 - POD test for examples\revcom_dir.pl (no pod) ok 53 - POD test for examples\rev_and_trans.pl (no pod) ok 54 - POD test for examples\subsequence.cgi (no pod) ok 55 - POD test for maintenance\authors.pl ok 56 - POD test for maintenance\check_NAME.pl ok 57 - POD test for maintenance\check_URLs.pl ok 58 - POD test for maintenance\cvs2cl_by_file.pl ok 59 - POD test for maintenance\dependencies.pl ok 60 - POD test for maintenance\deprecated.pl ok 61 - POD test for maintenance\find_mod_deps.pl ok 62 - POD test for maintenance\modules.pl ok 63 - POD test for maintenance\module_usage.pl (no pod) ok 64 - POD test for maintenance\ncbi_blast_switches.pl (no pod) ok 65 - POD test for maintenance\pod.pl ok 66 - POD test for maintenance\symlink_script.pl ok 67 - POD test for maintenance\version.pl ok 68 - POD test for Bio\Align\AlignI.pm ok 69 - POD test for Bio\Align\DNAStatistics.pm ok 70 - POD test for Bio\Align\Graphics.pm ok 71 - POD test for Bio\Align\PairwiseStatistics.pm ok 72 - POD test for Bio\Align\ProteinStatistics.pm ok 73 - POD test for Bio\Align\StatisticsI.pm ok 74 - POD test for Bio\Align\Utilities.pm ok 75 - POD test for Bio\AlignIO\arp.pm ok 76 - POD test for Bio\AlignIO\bl2seq.pm ok 77 - POD test for Bio\AlignIO\clustalw.pm ok 78 - POD test for Bio\AlignIO\emboss.pm ok 79 - POD test for Bio\AlignIO\fasta.pm ok 80 - POD test for Bio\AlignIO\largemultifasta.pm ok 81 - POD test for Bio\AlignIO\maf.pm ok 82 - POD test for Bio\AlignIO\mase.pm ok 83 - POD test for Bio\AlignIO\mega.pm ok 84 - POD test for Bio\AlignIO\meme.pm ok 85 - POD test for Bio\AlignIO\metafasta.pm ok 86 - POD test for Bio\AlignIO\msf.pm ok 87 - POD test for Bio\AlignIO\nexml.pm ok 88 - POD test for Bio\AlignIO\nexus.pm ok 89 - POD test for Bio\AlignIO\pfam.pm ok 90 - POD test for Bio\AlignIO\phylip.pm ok 91 - POD test for Bio\AlignIO\po.pm ok 92 - POD test for Bio\AlignIO\proda.pm ok 93 - POD test for Bio\AlignIO\prodom.pm ok 94 - POD test for Bio\AlignIO\psi.pm ok 95 - POD test for Bio\AlignIO\selex.pm ok 96 - POD test for Bio\AlignIO\stockholm.pm ok 97 - POD test for Bio\AlignIO\xmfa.pm ok 98 - POD test for Bio\Annotation\AnnotationFactory.pm ok 99 - POD test for Bio\Annotation\Collection.pm ok 100 - POD test for Bio\Annotation\Comment.pm ok 101 - POD test for Bio\Annotation\DBLink.pm ok 102 - POD test for Bio\Annotation\OntologyTerm.pm ok 103 - POD test for Bio\Annotation\Reference.pm ok 104 - POD test for Bio\Annotation\Relation.pm ok 105 - POD test for Bio\Annotation\SimpleValue.pm ok 106 - POD test for Bio\Annotation\StructuredValue.pm ok 107 - POD test for Bio\Annotation\TagTree.pm ok 108 - POD test for Bio\Annotation\Target.pm ok 109 - POD test for Bio\Annotation\Tree.pm ok 110 - POD test for Bio\Annotation\TypeManager.pm ok 111 - POD test for Bio\Assembly\Contig.pm ok 112 - POD test for Bio\Assembly\ContigAnalysis.pm ok 113 - POD test for Bio\Assembly\IO.pm ok 114 - POD test for Bio\Assembly\Scaffold.pm ok 115 - POD test for Bio\Assembly\ScaffoldI.pm ok 116 - POD test for Bio\Assembly\Singlet.pm ok 117 - POD test for Bio\Biblio\Article.pm ok 118 - POD test for Bio\Biblio\BiblioBase.pm ok 119 - POD test for Bio\Biblio\Book.pm ok 120 - POD test for Bio\Biblio\BookArticle.pm ok 121 - POD test for Bio\Biblio\IO.pm ok 122 - POD test for Bio\Biblio\Journal.pm ok 123 - POD test for Bio\Biblio\JournalArticle.pm ok 124 - POD test for Bio\Biblio\MedlineArticle.pm ok 125 - POD test for Bio\Biblio\MedlineBook.pm ok 126 - POD test for Bio\Biblio\MedlineBookArticle.pm ok 127 - POD test for Bio\Biblio\MedlineJournal.pm ok 128 - POD test for Bio\Biblio\MedlineJournalArticle.pm ok 129 - POD test for Bio\Biblio\Organisation.pm ok 130 - POD test for Bio\Biblio\Patent.pm ok 131 - POD test for Bio\Biblio\Person.pm ok 132 - POD test for Bio\Biblio\Proceeding.pm ok 133 - POD test for Bio\Biblio\Provider.pm ok 134 - POD test for Bio\Biblio\PubmedArticle.pm ok 135 - POD test for Bio\Biblio\PubmedBookArticle.pm ok 136 - POD test for Bio\Biblio\PubmedJournalArticle.pm ok 137 - POD test for Bio\Biblio\Ref.pm ok 138 - POD test for Bio\Biblio\Service.pm ok 139 - POD test for Bio\Biblio\TechReport.pm ok 140 - POD test for Bio\Biblio\Thesis.pm ok 141 - POD test for Bio\Biblio\WebResource.pm ok 142 - POD test for Bio\Cluster\ClusterFactory.pm ok 143 - POD test for Bio\Cluster\FamilyI.pm ok 144 - POD test for Bio\Cluster\SequenceFamily.pm ok 145 - POD test for Bio\Cluster\UniGene.pm ok 146 - POD test for Bio\Cluster\UniGeneI.pm ok 147 - POD test for Bio\ClusterIO\dbsnp.pm ok 148 - POD test for Bio\ClusterIO\unigene.pm ok 149 - POD test for Bio\CodonUsage\IO.pm ok 150 - POD test for Bio\CodonUsage\Table.pm ok 151 - POD test for Bio\Coordinate\Chain.pm ok 152 - POD test for Bio\Coordinate\Collection.pm ok 153 - POD test for Bio\Coordinate\ExtrapolatingPair.pm ok 154 - POD test for Bio\Coordinate\GeneMapper.pm ok 155 - POD test for Bio\Coordinate\Graph.pm ok 156 - POD test for Bio\Coordinate\MapperI.pm ok 157 - POD test for Bio\Coordinate\Pair.pm ok 158 - POD test for Bio\Coordinate\Result.pm ok 159 - POD test for Bio\Coordinate\ResultI.pm ok 160 - POD test for Bio\Coordinate\Utils.pm ok 161 - POD test for Bio\Das\FeatureTypeI.pm ok 162 - POD test for Bio\Das\SegmentI.pm ok 163 - POD test for Bio\DB\Ace.pm ok 164 - POD test for Bio\DB\BiblioI.pm ok 165 - POD test for Bio\DB\BioFetch.pm ok 166 - POD test for Bio\DB\CUTG.pm ok 167 - POD test for Bio\DB\DBFetch.pm ok 168 - POD test for Bio\DB\EMBL.pm ok 169 - POD test for Bio\DB\EntrezGene.pm ok 170 - POD test for Bio\DB\EUtilities.pm ok 171 - POD test for Bio\DB\Expression.pm ok 172 - POD test for Bio\DB\Failover.pm ok 173 - POD test for Bio\DB\Fasta.pm ok 174 - POD test for Bio\DB\FileCache.pm ok 175 - POD test for Bio\DB\Flat.pm ok 176 - POD test for Bio\DB\GenBank.pm ok 177 - POD test for Bio\DB\GenericWebAgent.pm ok 178 - POD test for Bio\DB\GenPept.pm ok 179 - POD test for Bio\DB\GFF.pm ok 180 - POD test for Bio\DB\HIV.pm ok 181 - POD test for Bio\DB\InMemoryCache.pm ok 182 - POD test for Bio\DB\LocationI.pm ok 183 - POD test for Bio\DB\MeSH.pm ok 184 - POD test for Bio\DB\NCBIHelper.pm ok 185 - POD test for Bio\DB\Qual.pm ok 186 - POD test for Bio\DB\QueryI.pm ok 187 - POD test for Bio\DB\RandomAccessI.pm ok 188 - POD test for Bio\DB\ReferenceI.pm ok 189 - POD test for Bio\DB\RefSeq.pm ok 190 - POD test for Bio\DB\Registry.pm ok 191 - POD test for Bio\DB\SeqFeature.pm ok 192 - POD test for Bio\DB\SeqHound.pm ok 193 - POD test for Bio\DB\SeqI.pm ok 194 - POD test for Bio\DB\SeqVersion.pm ok 195 - POD test for Bio\DB\SwissProt.pm ok 196 - POD test for Bio\DB\Taxonomy.pm ok 197 - POD test for Bio\DB\TFBS.pm ok 198 - POD test for Bio\DB\Universal.pm ok 199 - POD test for Bio\DB\UpdateableSeqI.pm ok 200 - POD test for Bio\DB\WebDBSeqI.pm ok 201 - POD test for Bio\Draw\Pictogram.pm ok 202 - POD test for Bio\Event\EventGeneratorI.pm ok 203 - POD test for Bio\Event\EventHandlerI.pm ok 204 - POD test for Bio\Factory\AnalysisI.pm ok 205 - POD test for Bio\Factory\ApplicationFactoryI.pm ok 206 - POD test for Bio\Factory\DriverFactory.pm ok 207 - POD test for Bio\Factory\FTLocationFactory.pm ok 208 - POD test for Bio\Factory\LocationFactoryI.pm ok 209 - POD test for Bio\Factory\MapFactoryI.pm ok 210 - POD test for Bio\Factory\ObjectBuilderI.pm ok 211 - POD test for Bio\Factory\ObjectFactory.pm ok 212 - POD test for Bio\Factory\ObjectFactoryI.pm ok 213 - POD test for Bio\Factory\SeqAnalysisParserFactory.pm ok 214 - POD test for Bio\Factory\SeqAnalysisParserFactoryI.pm ok 215 - POD test for Bio\Factory\SequenceFactoryI.pm ok 216 - POD test for Bio\Factory\SequenceProcessorI.pm ok 217 - POD test for Bio\Factory\SequenceStreamI.pm ok 218 - POD test for Bio\Factory\TreeFactoryI.pm ok 219 - POD test for Bio\FeatureIO\bed.pm ok 220 - POD test for Bio\FeatureIO\gff.pm ok 221 - POD test for Bio\FeatureIO\gtf.pm ok 222 - POD test for Bio\FeatureIO\interpro.pm ok 223 - POD test for Bio\FeatureIO\ptt.pm ok 224 - POD test for Bio\FeatureIO\vecscreen_simple.pm ok 225 - POD test for Bio\Index\Abstract.pm ok 226 - POD test for Bio\Index\AbstractSeq.pm ok 227 - POD test for Bio\Index\Blast.pm ok 228 - POD test for Bio\Index\BlastTable.pm ok 229 - POD test for Bio\Index\EMBL.pm ok 230 - POD test for Bio\Index\Fasta.pm ok 231 - POD test for Bio\Index\Fastq.pm ok 232 - POD test for Bio\Index\GenBank.pm ok 233 - POD test for Bio\Index\Hmmer.pm ok 234 - POD test for Bio\Index\Qual.pm ok 235 - POD test for Bio\Index\Stockholm.pm ok 236 - POD test for Bio\Index\SwissPfam.pm ok 237 - POD test for Bio\Index\Swissprot.pm ok 238 - POD test for Bio\LiveSeq\AARange.pm ok 239 - POD test for Bio\LiveSeq\Chain.pm ok 240 - POD test for Bio\LiveSeq\ChainI.pm ok 241 - POD test for Bio\LiveSeq\DNA.pm ok 242 - POD test for Bio\LiveSeq\Exon.pm ok 243 - POD test for Bio\LiveSeq\Gene.pm ok 244 - POD test for Bio\LiveSeq\Intron.pm ok 245 - POD test for Bio\LiveSeq\Mutation.pm ok 246 - POD test for Bio\LiveSeq\Mutator.pm ok 247 - POD test for Bio\LiveSeq\Prim_Transcript.pm ok 248 - POD test for Bio\LiveSeq\Range.pm ok 249 - POD test for Bio\LiveSeq\Repeat_Region.pm ok 250 - POD test for Bio\LiveSeq\Repeat_Unit.pm ok 251 - POD test for Bio\LiveSeq\SeqI.pm ok 252 - POD test for Bio\LiveSeq\Transcript.pm ok 253 - POD test for Bio\LiveSeq\Translation.pm ok 254 - POD test for Bio\Location\Atomic.pm ok 255 - POD test for Bio\Location\AvWithinCoordPolicy.pm ok 256 - POD test for Bio\Location\CoordinatePolicyI.pm ok 257 - POD test for Bio\Location\Fuzzy.pm ok 258 - POD test for Bio\Location\FuzzyLocationI.pm ok 259 - POD test for Bio\Location\NarrowestCoordPolicy.pm ok 260 - POD test for Bio\Location\Simple.pm ok 261 - POD test for Bio\Location\Split.pm ok 262 - POD test for Bio\Location\SplitLocationI.pm ok 263 - POD test for Bio\Location\WidestCoordPolicy.pm ok 264 - POD test for Bio\Map\Clone.pm ok 265 - POD test for Bio\Map\Contig.pm ok 266 - POD test for Bio\Map\CytoMap.pm ok 267 - POD test for Bio\Map\CytoMarker.pm ok 268 - POD test for Bio\Map\CytoPosition.pm ok 269 - POD test for Bio\Map\EntityI.pm ok 270 - POD test for Bio\Map\FPCMarker.pm ok 271 - POD test for Bio\Map\Gene.pm ok 272 - POD test for Bio\Map\GeneMap.pm ok 273 - POD test for Bio\Map\GenePosition.pm ok 274 - POD test for Bio\Map\GeneRelative.pm ok 275 - POD test for Bio\Map\LinkageMap.pm ok 276 - POD test for Bio\Map\LinkagePosition.pm ok 277 - POD test for Bio\Map\MapI.pm ok 278 - POD test for Bio\Map\Mappable.pm ok 279 - POD test for Bio\Map\MappableI.pm ok 280 - POD test for Bio\Map\Marker.pm ok 281 - POD test for Bio\Map\MarkerI.pm ok 282 - POD test for Bio\Map\Microsatellite.pm ok 283 - POD test for Bio\Map\OrderedPosition.pm ok 284 - POD test for Bio\Map\OrderedPositionWithDistance.pm ok 285 - POD test for Bio\Map\Physical.pm ok 286 - POD test for Bio\Map\Position.pm ok 287 - POD test for Bio\Map\PositionHandler.pm ok 288 - POD test for Bio\Map\PositionHandlerI.pm ok 289 - POD test for Bio\Map\PositionI.pm ok 290 - POD test for Bio\Map\PositionWithSequence.pm ok 291 - POD test for Bio\Map\Prediction.pm ok 292 - POD test for Bio\Map\Relative.pm ok 293 - POD test for Bio\Map\RelativeI.pm ok 294 - POD test for Bio\Map\SimpleMap.pm ok 295 - POD test for Bio\Map\TranscriptionFactor.pm ok 296 - POD test for Bio\MapIO\fpc.pm ok 297 - POD test for Bio\MapIO\mapmaker.pm ok 298 - POD test for Bio\Matrix\Generic.pm ok 299 - POD test for Bio\Matrix\IO.pm ok 300 - POD test for Bio\Matrix\MatrixI.pm ok 301 - POD test for Bio\Matrix\Mlagan.pm ok 302 - POD test for Bio\Matrix\PhylipDist.pm ok 303 - POD test for Bio\Matrix\Scoring.pm ok 304 - POD test for Bio\MolEvol\CodonModel.pm ok 305 - POD test for Bio\Nexml\Factory.pm ok 306 - POD test for Bio\Ontology\DocumentRegistry.pm ok 307 - POD test for Bio\Ontology\GOterm.pm ok 308 - POD test for Bio\Ontology\InterProTerm.pm ok 309 - POD test for Bio\Ontology\OBOEngine.pm ok 310 - POD test for Bio\Ontology\OBOterm.pm ok 311 - POD test for Bio\Ontology\Ontology.pm ok 312 - POD test for Bio\Ontology\OntologyEngineI.pm ok 313 - POD test for Bio\Ontology\OntologyI.pm ok 314 - POD test for Bio\Ontology\OntologyStore.pm ok 315 - POD test for Bio\Ontology\Path.pm ok 316 - POD test for Bio\Ontology\PathI.pm ok 317 - POD test for Bio\Ontology\Relationship.pm ok 318 - POD test for Bio\Ontology\RelationshipFactory.pm ok 319 - POD test for Bio\Ontology\RelationshipI.pm ok 320 - POD test for Bio\Ontology\RelationshipType.pm ok 321 - POD test for Bio\Ontology\SimpleOntologyEngine.pm ok 322 - POD test for Bio\Ontology\Term.pm ok 323 - POD test for Bio\Ontology\TermFactory.pm ok 324 - POD test for Bio\Ontology\TermI.pm ok 325 - POD test for Bio\OntologyIO\dagflat.pm ok 326 - POD test for Bio\OntologyIO\goflat.pm ok 327 - POD test for Bio\OntologyIO\InterProParser.pm ok 328 - POD test for Bio\OntologyIO\obo.pm ok 329 - POD test for Bio\OntologyIO\simplehierarchy.pm ok 330 - POD test for Bio\OntologyIO\soflat.pm ok 331 - POD test for Bio\Phenotype\Correlate.pm ok 332 - POD test for Bio\Phenotype\Measure.pm ok 333 - POD test for Bio\Phenotype\Phenotype.pm ok 334 - POD test for Bio\Phenotype\PhenotypeI.pm ok 335 - POD test for Bio\PhyloNetwork\Factory.pm ok 336 - POD test for Bio\PhyloNetwork\FactoryX.pm ok 337 - POD test for Bio\PhyloNetwork\GraphViz.pm ok 338 - POD test for Bio\PhyloNetwork\muVector.pm ok 339 - POD test for Bio\PhyloNetwork\RandomFactory.pm ok 340 - POD test for Bio\PhyloNetwork\TreeFactory.pm ok 341 - POD test for Bio\PhyloNetwork\TreeFactoryMulti.pm ok 342 - POD test for Bio\PhyloNetwork\TreeFactoryX.pm ok 343 - POD test for Bio\PopGen\Genotype.pm ok 344 - POD test for Bio\PopGen\GenotypeI.pm ok 345 - POD test for Bio\PopGen\HtSNP.pm ok 346 - POD test for Bio\PopGen\Individual.pm ok 347 - POD test for Bio\PopGen\IndividualI.pm ok 348 - POD test for Bio\PopGen\IO.pm ok 349 - POD test for Bio\PopGen\Marker.pm ok 350 - POD test for Bio\PopGen\MarkerI.pm ok 351 - POD test for Bio\PopGen\PopStats.pm ok 352 - POD test for Bio\PopGen\Population.pm ok 353 - POD test for Bio\PopGen\PopulationI.pm ok 354 - POD test for Bio\PopGen\Statistics.pm ok 355 - POD test for Bio\PopGen\TagHaplotype.pm ok 356 - POD test for Bio\PopGen\Utilities.pm ok 357 - POD test for Bio\Restriction\Analysis.pm ok 358 - POD test for Bio\Restriction\Enzyme.pm ok 359 - POD test for Bio\Restriction\EnzymeCollection.pm ok 360 - POD test for Bio\Restriction\EnzymeI.pm ok 361 - POD test for Bio\Restriction\IO.pm ok 362 - POD test for Bio\Root\Build.pm ok 363 - POD test for Bio\Root\Exception.pm ok 364 - POD test for Bio\Root\HTTPget.pm ok 365 - POD test for Bio\Root\IO.pm ok 366 - POD test for Bio\Root\Root.pm ok 367 - POD test for Bio\Root\RootI.pm ok 368 - POD test for Bio\Root\Storable.pm ok 369 - POD test for Bio\Root\Test.pm ok 370 - POD test for Bio\Root\Utilities.pm ok 371 - POD test for Bio\Root\Version.pm ok 372 - POD test for Bio\Search\BlastStatistics.pm ok 373 - POD test for Bio\Search\BlastUtils.pm ok 374 - POD test for Bio\Search\DatabaseI.pm ok 375 - POD test for Bio\Search\GenericDatabase.pm ok 376 - POD test for Bio\Search\GenericStatistics.pm ok 377 - POD test for Bio\Search\Processor.pm ok 378 - POD test for Bio\Search\SearchUtils.pm ok 379 - POD test for Bio\Search\StatisticsI.pm ok 380 - POD test for Bio\SearchIO\axt.pm ok 381 - POD test for Bio\SearchIO\blast.pm ok 382 - POD test for Bio\SearchIO\blasttable.pm ok 383 - POD test for Bio\SearchIO\blastxml.pm ok 384 - POD test for Bio\SearchIO\blast_pull.pm ok 385 - POD test for Bio\SearchIO\cross_match.pm ok 386 - POD test for Bio\SearchIO\erpin.pm ok 387 - POD test for Bio\SearchIO\EventHandlerI.pm ok 388 - POD test for Bio\SearchIO\exonerate.pm ok 389 - POD test for Bio\SearchIO\fasta.pm ok 390 - POD test for Bio\SearchIO\FastHitEventBuilder.pm ok 391 - POD test for Bio\SearchIO\gmap_f9.pm ok 392 - POD test for Bio\SearchIO\hmmer.pm ok 393 - POD test for Bio\SearchIO\hmmer2.pm ok 394 - POD test for Bio\SearchIO\hmmer3.pm ok 395 - POD test for Bio\SearchIO\hmmer_pull.pm ok 396 - POD test for Bio\SearchIO\infernal.pm ok 397 - POD test for Bio\SearchIO\IteratedSearchResultEventBuilder.pm ok 398 - POD test for Bio\SearchIO\megablast.pm ok 399 - POD test for Bio\SearchIO\psl.pm ok 400 - POD test for Bio\SearchIO\rnamotif.pm ok 401 - POD test for Bio\SearchIO\SearchResultEventBuilder.pm ok 402 - POD test for Bio\SearchIO\SearchWriterI.pm ok 403 - POD test for Bio\SearchIO\sim4.pm ok 404 - POD test for Bio\SearchIO\waba.pm ok 405 - POD test for Bio\SearchIO\wise.pm ok 406 - POD test for Bio\Seq\BaseSeqProcessor.pm ok 407 - POD test for Bio\Seq\EncodedSeq.pm ok 408 - POD test for Bio\Seq\LargeLocatableSeq.pm ok 409 - POD test for Bio\Seq\LargePrimarySeq.pm ok 410 - POD test for Bio\Seq\LargeSeq.pm ok 411 - POD test for Bio\Seq\LargeSeqI.pm ok 412 - POD test for Bio\Seq\Meta.pm ok 413 - POD test for Bio\Seq\MetaI.pm ok 414 - POD test for Bio\Seq\PrimaryQual.pm ok 415 - POD test for Bio\Seq\PrimedSeq.pm ok 416 - POD test for Bio\Seq\QualI.pm ok 417 - POD test for Bio\Seq\Quality.pm ok 418 - POD test for Bio\Seq\RichSeq.pm ok 419 - POD test for Bio\Seq\RichSeqI.pm ok 420 - POD test for Bio\Seq\SeqBuilder.pm ok 421 - POD test for Bio\Seq\SeqFactory.pm ok 422 - POD test for Bio\Seq\SeqFastaSpeedFactory.pm ok 423 - POD test for Bio\Seq\SequenceTrace.pm ok 424 - POD test for Bio\Seq\SeqWithQuality.pm ok 425 - POD test for Bio\Seq\TraceI.pm ok 426 - POD test for Bio\SeqEvolution\DNAPoint.pm ok 427 - POD test for Bio\SeqEvolution\EvolutionI.pm ok 428 - POD test for Bio\SeqEvolution\Factory.pm ok 429 - POD test for Bio\SeqFeature\Annotated.pm ok 430 - POD test for Bio\SeqFeature\AnnotationAdaptor.pm ok 431 - POD test for Bio\SeqFeature\Collection.pm ok 432 - POD test for Bio\SeqFeature\CollectionI.pm ok 433 - POD test for Bio\SeqFeature\Computation.pm ok 434 - POD test for Bio\SeqFeature\FeaturePair.pm ok 435 - POD test for Bio\SeqFeature\Generic.pm ok 436 - POD test for Bio\SeqFeature\Lite.pm ok 437 - POD test for Bio\SeqFeature\PositionProxy.pm ok 438 - POD test for Bio\SeqFeature\Primer.pm ok 439 - POD test for Bio\SeqFeature\Similarity.pm ok 440 - POD test for Bio\SeqFeature\SimilarityPair.pm ok 441 - POD test for Bio\SeqFeature\TypedSeqFeatureI.pm ok 442 - POD test for Bio\SeqIO\abi.pm ok 443 - POD test for Bio\SeqIO\ace.pm ok 444 - POD test for Bio\SeqIO\agave.pm ok 445 - POD test for Bio\SeqIO\alf.pm ok 446 - POD test for Bio\SeqIO\asciitree.pm ok 447 - POD test for Bio\SeqIO\bsml.pm ok 448 - POD test for Bio\SeqIO\bsml_sax.pm ok 449 - POD test for Bio\SeqIO\chadoxml.pm ok 450 - POD test for Bio\SeqIO\chaos.pm ok 451 - POD test for Bio\SeqIO\chaosxml.pm ok 452 - POD test for Bio\SeqIO\ctf.pm ok 453 - POD test for Bio\SeqIO\embl.pm ok 454 - POD test for Bio\SeqIO\embldriver.pm ok 455 - POD test for Bio\SeqIO\entrezgene.pm ok 456 - POD test for Bio\SeqIO\excel.pm ok 457 - POD test for Bio\SeqIO\exp.pm ok 458 - POD test for Bio\SeqIO\fasta.pm ok 459 - POD test for Bio\SeqIO\fastq.pm ok 460 - POD test for Bio\SeqIO\flybase_chadoxml.pm ok 461 - POD test for Bio\SeqIO\FTHelper.pm ok 462 - POD test for Bio\SeqIO\game.pm ok 463 - POD test for Bio\SeqIO\gbdriver.pm ok 464 - POD test for Bio\SeqIO\gbxml.pm ok 465 - POD test for Bio\SeqIO\gcg.pm ok 466 - POD test for Bio\SeqIO\genbank.pm ok 467 - POD test for Bio\SeqIO\interpro.pm ok 468 - POD test for Bio\SeqIO\kegg.pm ok 469 - POD test for Bio\SeqIO\largefasta.pm ok 470 - POD test for Bio\SeqIO\lasergene.pm ok 471 - POD test for Bio\SeqIO\locuslink.pm ok 472 - POD test for Bio\SeqIO\mbsout.pm ok 473 - POD test for Bio\SeqIO\metafasta.pm ok 474 - POD test for Bio\SeqIO\msout.pm ok 475 - POD test for Bio\SeqIO\MultiFile.pm ok 476 - POD test for Bio\SeqIO\nexml.pm ok 477 - POD test for Bio\SeqIO\phd.pm ok 478 - POD test for Bio\SeqIO\pir.pm ok 479 - POD test for Bio\SeqIO\pln.pm ok 480 - POD test for Bio\SeqIO\qual.pm ok 481 - POD test for Bio\SeqIO\raw.pm ok 482 - POD test for Bio\SeqIO\scf.pm ok 483 - POD test for Bio\SeqIO\seqxml.pm ok 484 - POD test for Bio\SeqIO\strider.pm ok 485 - POD test for Bio\SeqIO\swiss.pm ok 486 - POD test for Bio\SeqIO\swissdriver.pm ok 487 - POD test for Bio\SeqIO\tab.pm ok 488 - POD test for Bio\SeqIO\table.pm ok 489 - POD test for Bio\SeqIO\tigr.pm ok 490 - POD test for Bio\SeqIO\tigrxml.pm ok 491 - POD test for Bio\SeqIO\tinyseq.pm ok 492 - POD test for Bio\SeqIO\ztr.pm ok 493 - POD test for Bio\Structure\Atom.pm ok 494 - POD test for Bio\Structure\Chain.pm ok 495 - POD test for Bio\Structure\Entry.pm ok 496 - POD test for Bio\Structure\IO.pm ok 497 - POD test for Bio\Structure\Model.pm ok 498 - POD test for Bio\Structure\Residue.pm ok 499 - POD test for Bio\Structure\StructureI.pm ok 500 - POD test for Bio\Symbol\Alphabet.pm ok 501 - POD test for Bio\Symbol\AlphabetI.pm ok 502 - POD test for Bio\Symbol\DNAAlphabet.pm ok 503 - POD test for Bio\Symbol\ProteinAlphabet.pm ok 504 - POD test for Bio\Symbol\Symbol.pm ok 505 - POD test for Bio\Symbol\SymbolI.pm ok 506 - POD test for Bio\Taxonomy\FactoryI.pm ok 507 - POD test for Bio\Taxonomy\Node.pm ok 508 - POD test for Bio\Taxonomy\Taxon.pm ok 509 - POD test for Bio\Taxonomy\Tree.pm ok 510 - POD test for Bio\Tools\AlignFactory.pm ok 511 - POD test for Bio\Tools\AnalysisResult.pm ok 512 - POD test for Bio\Tools\Blat.pm ok 513 - POD test for Bio\Tools\CodonTable.pm ok 514 - POD test for Bio\Tools\Coil.pm ok 515 - POD test for Bio\Tools\dpAlign.pm ok 516 - POD test for Bio\Tools\ECnumber.pm ok 517 - POD test for Bio\Tools\EPCR.pm ok 518 - POD test for Bio\Tools\Eponine.pm ok 519 - POD test for Bio\Tools\ERPIN.pm ok 520 - POD test for Bio\Tools\Est2Genome.pm ok 521 - POD test for Bio\Tools\ESTScan.pm ok 522 - POD test for Bio\Tools\EUtilities.pm ok 523 - POD test for Bio\Tools\Fgenesh.pm ok 524 - POD test for Bio\Tools\FootPrinter.pm ok 525 - POD test for Bio\Tools\Gel.pm ok 526 - POD test for Bio\Tools\Geneid.pm ok 527 - POD test for Bio\Tools\Genemark.pm ok 528 - POD test for Bio\Tools\Genewise.pm ok 529 - POD test for Bio\Tools\Genomewise.pm ok 530 - POD test for Bio\Tools\Genscan.pm ok 531 - POD test for Bio\Tools\GFF.pm ok 532 - POD test for Bio\Tools\Glimmer.pm ok 533 - POD test for Bio\Tools\Grail.pm ok 534 - POD test for Bio\Tools\GuessSeqFormat.pm ok 535 - POD test for Bio\Tools\Hmmpfam.pm ok 536 - POD test for Bio\Tools\Infernal.pm ok 537 - POD test for Bio\Tools\ipcress.pm ok 538 - POD test for Bio\Tools\isPcr.pm ok 539 - POD test for Bio\Tools\IUPAC.pm ok 540 - POD test for Bio\Tools\Lucy.pm ok 541 - POD test for Bio\Tools\Match.pm ok 542 - POD test for Bio\Tools\MZEF.pm ok 543 - POD test for Bio\Tools\OddCodes.pm ok 544 - POD test for Bio\Tools\pICalculator.pm ok 545 - POD test for Bio\Tools\Primer3.pm ok 546 - POD test for Bio\Tools\Prints.pm ok 547 - POD test for Bio\Tools\Profile.pm ok 548 - POD test for Bio\Tools\Promoterwise.pm ok 549 - POD test for Bio\Tools\PrositeScan.pm ok 550 - POD test for Bio\Tools\Protparam.pm ok 551 - POD test for Bio\Tools\Pseudowise.pm ok 552 - POD test for Bio\Tools\pSW.pm ok 553 - POD test for Bio\Tools\QRNA.pm ok 554 - POD test for Bio\Tools\RandomDistFunctions.pm ok 555 - POD test for Bio\Tools\RepeatMasker.pm ok 556 - POD test for Bio\Tools\RNAMotif.pm ok 557 - POD test for Bio\Tools\Seg.pm ok 558 - POD test for Bio\Tools\SeqPattern.pm ok 559 - POD test for Bio\Tools\SeqStats.pm ok 560 - POD test for Bio\Tools\SeqWords.pm ok 561 - POD test for Bio\Tools\Sigcleave.pm ok 562 - POD test for Bio\Tools\Signalp.pm ok 563 - POD test for Bio\Tools\SiRNA.pm ok 564 - POD test for Bio\Tools\TandemRepeatsFinder.pm ok 565 - POD test for Bio\Tools\TargetP.pm ok 566 - POD test for Bio\Tools\Tmhmm.pm ok 567 - POD test for Bio\Tools\tRNAscanSE.pm ok 568 - POD test for Bio\Tree\AlleleNode.pm ok 569 - POD test for Bio\Tree\AnnotatableNode.pm ok 570 - POD test for Bio\Tree\Compatible.pm ok 571 - POD test for Bio\Tree\DistanceFactory.pm ok 572 - POD test for Bio\Tree\Node.pm ok 573 - POD test for Bio\Tree\NodeI.pm ok 574 - POD test for Bio\Tree\NodeNHX.pm ok 575 - POD test for Bio\Tree\RandomFactory.pm ok 576 - POD test for Bio\Tree\Statistics.pm ok 577 - POD test for Bio\Tree\Tree.pm ok 578 - POD test for Bio\Tree\TreeFunctionsI.pm ok 579 - POD test for Bio\Tree\TreeI.pm ok 580 - POD test for Bio\TreeIO\cluster.pm ok 581 - POD test for Bio\TreeIO\lintree.pm ok 582 - POD test for Bio\TreeIO\newick.pm ok 583 - POD test for Bio\TreeIO\NewickParser.pm ok 584 - POD test for Bio\TreeIO\nexml.pm ok 585 - POD test for Bio\TreeIO\nexus.pm ok 586 - POD test for Bio\TreeIO\nhx.pm ok 587 - POD test for Bio\TreeIO\pag.pm ok 588 - POD test for Bio\TreeIO\phyloxml.pm ok 589 - POD test for Bio\TreeIO\svggraph.pm ok 590 - POD test for Bio\TreeIO\tabtree.pm ok 591 - POD test for Bio\TreeIO\TreeEventBuilder.pm ok 592 - POD test for Bio\Variation\AAChange.pm ok 593 - POD test for Bio\Variation\AAReverseMutate.pm ok 594 - POD test for Bio\Variation\Allele.pm ok 595 - POD test for Bio\Variation\DNAMutation.pm ok 596 - POD test for Bio\Variation\IO.pm ok 597 - POD test for Bio\Variation\RNAChange.pm ok 598 - POD test for Bio\Variation\SeqDiff.pm ok 599 - POD test for Bio\Variation\SNP.pm ok 600 - POD test for Bio\Variation\VariantI.pm ok 601 - POD test for scripts\biblio\biblio.PLS ok 602 - POD test for scripts\Bio-DB-EUtilities\einfo.PLS ok 603 - POD test for scripts\Bio-DB-GFF\bulk_load_gff.PLS ok 604 - POD test for scripts\Bio-DB-GFF\fast_load_gff.PLS ok 605 - POD test for scripts\Bio-DB-GFF\genbank2gff.PLS ok 606 - POD test for scripts\Bio-DB-GFF\genbank2gff3.PLS ok 607 - POD test for scripts\Bio-DB-GFF\generate_histogram.PLS ok 608 - POD test for scripts\Bio-DB-GFF\load_gff.PLS ok 609 - POD test for scripts\Bio-DB-GFF\meta_gff.PLS ok 610 - POD test for scripts\Bio-DB-GFF\process_gadfly.PLS ok 611 - POD test for scripts\Bio-DB-GFF\process_sgd.PLS ok 612 - POD test for scripts\Bio-DB-GFF\process_wormbase.PLS ok 613 - POD test for scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_delete.PLS (no pod) ok 614 - POD test for scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_gff3.PLS (no pod) ok 615 - POD test for scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_load.PLS ok 616 - POD test for scripts\das\das_server.pl (no pod) ok 617 - POD test for scripts\DB\biofetch_genbank_proxy.PLS ok 618 - POD test for scripts\DB\bioflat_index.PLS ok 619 - POD test for scripts\DB\biogetseq.PLS ok 620 - POD test for scripts\DB\flanks.PLS ok 621 - POD test for scripts\DB-HIV\hivq.PLS ok 622 - POD test for scripts\index\bp_fetch.PLS ok 623 - POD test for scripts\index\bp_index.PLS ok 624 - POD test for scripts\index\bp_seqret.PLS ok 625 - POD test for scripts\popgen\composite_LD.PLS ok 626 - POD test for scripts\popgen\heterogeneity_test.PLS ok 627 - POD test for scripts\searchio\fastam9_to_table.PLS ok 628 - POD test for scripts\searchio\filter_search.PLS ok 629 - POD test for scripts\searchio\hmmer_to_table.PLS ok 630 - POD test for scripts\searchio\parse_hmmsearch.PLS ok 631 - POD test for scripts\searchio\search2table.PLS ok 632 - POD test for scripts\seq\extract_feature_seq.PLS ok 633 - POD test for scripts\seq\make_mrna_protein.PLS ok 634 - POD test for scripts\seq\seqconvert.PLS ok 635 - POD test for scripts\seq\seqretsplit.PLS ok 636 - POD test for scripts\seq\split_seq.PLS ok 637 - POD test for scripts\seq\translate_seq.PLS ok 638 - POD test for scripts\seq\unflatten_seq.PLS ok 639 - POD test for scripts\seqstats\aacomp.PLS ok 640 - POD test for scripts\seqstats\chaos_plot.PLS ok 641 - POD test for scripts\seqstats\gccalc.PLS ok 642 - POD test for scripts\seqstats\oligo_count.PLS ok 643 - POD test for scripts\taxa\classify_hits_kingdom.PLS ok 644 - POD test for scripts\taxa\local_taxonomydb_query.PLS ok 645 - POD test for scripts\taxa\query_entrez_taxa.PLS ok 646 - POD test for scripts\taxa\taxid4species.PLS ok 647 - POD test for scripts\taxa\taxonomy2tree.PLS ok 648 - POD test for scripts\tree\blast2tree.PLS ok 649 - POD test for scripts\tree\nexus2nh.PLS ok 650 - POD test for scripts\tree\tree2pag.PLS ok 651 - POD test for scripts\utilities\bp_mrtrans.PLS ok 652 - POD test for scripts\utilities\bp_netinstall.PLS ok 653 - POD test for scripts\utilities\bp_nrdb.PLS ok 654 - POD test for scripts\utilities\bp_sreformat.PLS ok 655 - POD test for scripts\utilities\dbsplit.PLS ok 656 - POD test for scripts\utilities\download_query_genbank.PLS ok 657 - POD test for scripts\utilities\mask_by_search.PLS ok 658 - POD test for scripts\utilities\mutate.PLS ok 659 - POD test for scripts\utilities\pairwise_kaks.PLS ok 660 - POD test for scripts\utilities\remote_blast.PLS ok 661 - POD test for scripts\utilities\revtrans-motif.PLS ok 662 - POD test for scripts\utilities\search2alnblocks.PLS ok 663 - POD test for scripts\utilities\search2BSML.PLS ok 664 - POD test for scripts\utilities\search2gff.PLS ok 665 - POD test for scripts\utilities\search2tribe.PLS ok 666 - POD test for scripts\utilities\seq_length.PLS ok 667 - POD test for examples\align\aligntutorial.pl (no pod) ok 668 - POD test for examples\align\align_on_codons.pl (no pod) ok 669 - POD test for examples\align\clustalw.pl (no pod) ok 670 - POD test for examples\align\simplealign.pl (no pod) ok 671 - POD test for examples\biblio\biblio-eutils-example.pl ok 672 - POD test for examples\biblio\biblio-soap-example.pl ok 673 - POD test for examples\biblio\biblio_soap.pl (no pod) ok 674 - POD test for examples\Bio-DB-GFF\load_ucsc.pl (no pod) ok 675 - POD test for examples\cluster\dbsnp.pl (no pod) ok 676 - POD test for examples\contributed\nmrpdb_parse.pl (no pod) ok 677 - POD test for examples\contributed\prosite2perl.pl (no pod) ok 678 - POD test for examples\contributed\rebase2list.pl (no pod) ok 679 - POD test for examples\db\dbfetch ok 680 - POD test for examples\db\est_tissue_query.pl (no pod) ok 681 - POD test for examples\db\gb2features.pl (no pod) ok 682 - POD test for examples\db\getGenBank.pl (no pod) ok 683 - POD test for examples\db\get_seqs.pl (no pod) ok 684 - POD test for examples\db\rfetch.pl (no pod) ok 685 - POD test for examples\db\use_registry.pl (no pod) ok 686 - POD test for examples\liveseq\change_gene.pl (no pod) ok 687 - POD test for examples\popgen\parse_calc_stats.pl (no pod) ok 688 - POD test for examples\quality\svgtrace.pl (no pod) ok 689 - POD test for examples\root\exceptions1.pl (no pod) ok 690 - POD test for examples\root\exceptions2.pl (no pod) ok 691 - POD test for examples\root\exceptions3.pl (no pod) ok 692 - POD test for examples\root\exceptions4.pl (no pod) ok 693 - POD test for examples\searchio\blast_example.pl (no pod) ok 694 - POD test for examples\searchio\custom_writer.pl (no pod) ok 695 - POD test for examples\searchio\hitwriter.pl (no pod) ok 696 - POD test for examples\searchio\hspwriter.pl (no pod) ok 697 - POD test for examples\searchio\htmlwriter.pl (no pod) ok 698 - POD test for examples\searchio\psiblast_features.pl (no pod) ok 699 - POD test for examples\searchio\psiblast_iterations.pl (no pod) ok 700 - POD test for examples\searchio\rawwriter.pl (no pod) ok 701 - POD test for examples\searchio\resultwriter.pl (no pod) ok 702 - POD test for examples\searchio\waba2gff.pl (no pod) ok 703 - POD test for examples\searchio\waba2gff3.pl ok 704 - POD test for examples\sirna\rnai_finder.cgi ok 705 - POD test for examples\structure\structure-io.pl (no pod) ok 706 - POD test for examples\tk\gsequence.pl (no pod) ok 707 - POD test for examples\tk\hitdisplay.pl (no pod) ok 708 - POD test for examples\tools\extract_genes.pl ok 709 - POD test for examples\tools\gb_to_gff.pl (no pod) ok 710 - POD test for examples\tools\gff2ps.pl ok 711 - POD test for examples\tools\parse_codeml.pl (no pod) ok 712 - POD test for examples\tools\psw.pl (no pod) ok 713 - POD test for examples\tools\reverse-translate.pl ok 714 - POD test for examples\tools\run_genscan.pl (no pod) ok 715 - POD test for examples\tools\run_primer3.pl ok 716 - POD test for examples\tools\seq_pattern.pl (no pod) ok 717 - POD test for examples\tools\standaloneblast.pl (no pod) ok 718 - POD test for examples\tree\paup2phylip.pl (no pod) ok 719 - POD test for Bio\AlignIO\Handler\GenericAlignHandler.pm ok 720 - POD test for Bio\Assembly\IO\ace.pm ok 721 - POD test for Bio\Assembly\IO\bowtie.pm ok 722 - POD test for Bio\Assembly\IO\maq.pm ok 723 - POD test for Bio\Assembly\IO\phrap.pm ok 724 - POD test for Bio\Assembly\IO\sam.pm ok 725 - POD test for Bio\Assembly\IO\tigr.pm ok 726 - POD test for Bio\Assembly\Tools\ContigSpectrum.pm ok 727 - POD test for Bio\Biblio\IO\medline2ref.pm ok 728 - POD test for Bio\Biblio\IO\medlinexml.pm ok 729 - POD test for Bio\Biblio\IO\pubmed2ref.pm ok 730 - POD test for Bio\Biblio\IO\pubmedxml.pm ok 731 - POD test for Bio\Coordinate\Result\Gap.pm ok 732 - POD test for Bio\Coordinate\Result\Match.pm ok 733 - POD test for Bio\DB\Biblio\biofetch.pm ok 734 - POD test for Bio\DB\Biblio\eutils.pm ok 735 - POD test for Bio\DB\Biblio\soap.pm ok 736 - POD test for Bio\DB\Expression\geo.pm ok 737 - POD test for Bio\DB\Flat\BDB.pm ok 738 - POD test for Bio\DB\Flat\BinarySearch.pm ok 739 - POD test for Bio\DB\GFF\Aggregator.pm ok 740 - POD test for Bio\DB\GFF\Featname.pm ok 741 - POD test for Bio\DB\GFF\Feature.pm ok 742 - POD test for Bio\DB\GFF\Homol.pm ok 743 - POD test for Bio\DB\GFF\RelSegment.pm ok 744 - POD test for Bio\DB\GFF\Segment.pm ok 745 - POD test for Bio\DB\GFF\Typename.pm ok 746 - POD test for Bio\DB\HIV\HIVAnnotProcessor.pm ok 747 - POD test for Bio\DB\HIV\HIVQueryHelper.pm ok 748 - POD test for Bio\DB\Query\GenBank.pm ok 749 - POD test for Bio\DB\Query\HIVQuery.pm ok 750 - POD test for Bio\DB\Query\WebQuery.pm ok 751 - POD test for Bio\DB\SeqFeature\NormalizedFeature.pm ok 752 - POD test for Bio\DB\SeqFeature\NormalizedFeatureI.pm ok 753 - POD test for Bio\DB\SeqFeature\NormalizedTableFeatureI.pm ok 754 - POD test for Bio\DB\SeqFeature\Segment.pm ok 755 - POD test for Bio\DB\SeqFeature\Store.pm ok 756 - POD test for Bio\DB\SeqVersion\gi.pm ok 757 - POD test for Bio\DB\Taxonomy\entrez.pm ok 758 - POD test for Bio\DB\Taxonomy\flatfile.pm ok 759 - POD test for Bio\DB\Taxonomy\list.pm ok 760 - POD test for Bio\DB\TFBS\transfac_pro.pm ok 761 - POD test for Bio\LiveSeq\IO\BioPerl.pm ok 762 - POD test for Bio\LiveSeq\IO\Loader.pm ok 763 - POD test for Bio\Matrix\IO\mlagan.pm ok 764 - POD test for Bio\Matrix\IO\phylip.pm ok 765 - POD test for Bio\Matrix\IO\scoring.pm ok 766 - POD test for Bio\Matrix\PSM\InstanceSite.pm ok 767 - POD test for Bio\Matrix\PSM\InstanceSiteI.pm ok 768 - POD test for Bio\Matrix\PSM\IO.pm ok 769 - POD test for Bio\Matrix\PSM\ProtMatrix.pm ok 770 - POD test for Bio\Matrix\PSM\ProtPsm.pm ok 771 - POD test for Bio\Matrix\PSM\Psm.pm ok 772 - POD test for Bio\Matrix\PSM\PsmHeader.pm ok 773 - POD test for Bio\Matrix\PSM\PsmHeaderI.pm ok 774 - POD test for Bio\Matrix\PSM\PsmI.pm ok 775 - POD test for Bio\Matrix\PSM\SiteMatrix.pm ok 776 - POD test for Bio\Matrix\PSM\SiteMatrixI.pm ok 777 - POD test for Bio\Ontology\SimpleGOEngine\GraphAdaptor.pm ok 778 - POD test for Bio\Ontology\SimpleGOEngine\GraphAdaptor02.pm ok 779 - POD test for Bio\OntologyIO\Handlers\BaseSAXHandler.pm ok 780 - POD test for Bio\OntologyIO\Handlers\InterProHandler.pm ok 781 - POD test for Bio\OntologyIO\Handlers\InterPro_BioSQL_Handler.pm ok 782 - POD test for Bio\Phenotype\MeSH\Term.pm ok 783 - POD test for Bio\Phenotype\MeSH\Twig.pm ok 784 - POD test for Bio\Phenotype\OMIM\MiniMIMentry.pm ok 785 - POD test for Bio\Phenotype\OMIM\OMIMentry.pm ok 786 - POD test for Bio\Phenotype\OMIM\OMIMentryAllelicVariant.pm ok 787 - POD test for Bio\Phenotype\OMIM\OMIMparser.pm ok 788 - POD test for Bio\PopGen\IO\csv.pm ok 789 - POD test for Bio\PopGen\IO\hapmap.pm ok 790 - POD test for Bio\PopGen\IO\phase.pm ok 791 - POD test for Bio\PopGen\IO\prettybase.pm ok 792 - POD test for Bio\PopGen\Simulation\Coalescent.pm ok 793 - POD test for Bio\PopGen\Simulation\GeneticDrift.pm ok 794 - POD test for Bio\Restriction\Enzyme\MultiCut.pm ok 795 - POD test for Bio\Restriction\Enzyme\MultiSite.pm ok 796 - POD test for Bio\Restriction\IO\bairoch.pm ok 797 - POD test for Bio\Restriction\IO\base.pm ok 798 - POD test for Bio\Restriction\IO\itype2.pm ok 799 - POD test for Bio\Restriction\IO\prototype.pm ok 800 - POD test for Bio\Restriction\IO\withrefm.pm ok 801 - POD test for Bio\Root\Test\Warn.pm ok 802 - POD test for Bio\Search\Hit\BlastHit.pm ok 803 - POD test for Bio\Search\Hit\BlastPullHit.pm ok 804 - POD test for Bio\Search\Hit\Fasta.pm ok 805 - POD test for Bio\Search\Hit\GenericHit.pm ok 806 - POD test for Bio\Search\Hit\HitFactory.pm ok 807 - POD test for Bio\Search\Hit\HitI.pm ok 808 - POD test for Bio\Search\Hit\hmmer3Hit.pm ok 809 - POD test for Bio\Search\Hit\HMMERHit.pm ok 810 - POD test for Bio\Search\Hit\HmmpfamHit.pm ok 811 - POD test for Bio\Search\Hit\ModelHit.pm ok 812 - POD test for Bio\Search\Hit\PsiBlastHit.pm ok 813 - POD test for Bio\Search\Hit\PullHitI.pm ok 814 - POD test for Bio\Search\HSP\BlastHSP.pm ok 815 - POD test for Bio\Search\HSP\BlastPullHSP.pm ok 816 - POD test for Bio\Search\HSP\FastaHSP.pm ok 817 - POD test for Bio\Search\HSP\GenericHSP.pm ok 818 - POD test for Bio\Search\HSP\hmmer3HSP.pm ok 819 - POD test for Bio\Search\HSP\HMMERHSP.pm ok 820 - POD test for Bio\Search\HSP\HmmpfamHSP.pm ok 821 - POD test for Bio\Search\HSP\HSPFactory.pm ok 822 - POD test for Bio\Search\HSP\HSPI.pm ok 823 - POD test for Bio\Search\HSP\ModelHSP.pm ok 824 - POD test for Bio\Search\HSP\PsiBlastHSP.pm ok 825 - POD test for Bio\Search\HSP\PSLHSP.pm ok 826 - POD test for Bio\Search\HSP\PullHSPI.pm ok 827 - POD test for Bio\Search\HSP\WABAHSP.pm ok 828 - POD test for Bio\Search\Iteration\GenericIteration.pm ok 829 - POD test for Bio\Search\Iteration\IterationI.pm ok 830 - POD test for Bio\Search\Result\BlastPullResult.pm ok 831 - POD test for Bio\Search\Result\BlastResult.pm ok 832 - POD test for Bio\Search\Result\CrossMatchResult.pm ok 833 - POD test for Bio\Search\Result\GenericResult.pm ok 834 - POD test for Bio\Search\Result\hmmer3Result.pm ok 835 - POD test for Bio\Search\Result\HMMERResult.pm ok 836 - POD test for Bio\Search\Result\HmmpfamResult.pm ok 837 - POD test for Bio\Search\Result\PullResultI.pm ok 838 - POD test for Bio\Search\Result\ResultFactory.pm ok 839 - POD test for Bio\Search\Result\ResultI.pm ok 840 - POD test for Bio\Search\Result\WABAResult.pm ok 841 - POD test for Bio\Search\Tiling\MapTileUtils.pm ok 842 - POD test for Bio\Search\Tiling\MapTiling.pm ok 843 - POD test for Bio\Search\Tiling\TilingI.pm ok 844 - POD test for Bio\SearchIO\Writer\BSMLResultWriter.pm ok 845 - POD test for Bio\SearchIO\Writer\GbrowseGFF.pm ok 846 - POD test for Bio\SearchIO\Writer\HitTableWriter.pm ok 847 - POD test for Bio\SearchIO\Writer\HSPTableWriter.pm ok 848 - POD test for Bio\SearchIO\Writer\HTMLResultWriter.pm ok 849 - POD test for Bio\SearchIO\Writer\ResultTableWriter.pm ok 850 - POD test for Bio\SearchIO\Writer\TextResultWriter.pm ok 851 - POD test for Bio\SearchIO\XML\BlastHandler.pm ok 852 - POD test for Bio\SearchIO\XML\PsiBlastHandler.pm ok 853 - POD test for Bio\Seq\Meta\Array.pm ok 854 - POD test for Bio\SeqFeature\Gene\Exon.pm ok 855 - POD test for Bio\SeqFeature\Gene\ExonI.pm ok 856 - POD test for Bio\SeqFeature\Gene\GeneStructure.pm ok 857 - POD test for Bio\SeqFeature\Gene\GeneStructureI.pm ok 858 - POD test for Bio\SeqFeature\Gene\Intron.pm ok 859 - POD test for Bio\SeqFeature\Gene\NC_Feature.pm ok 860 - POD test for Bio\SeqFeature\Gene\Poly_A_site.pm ok 861 - POD test for Bio\SeqFeature\Gene\Promoter.pm ok 862 - POD test for Bio\SeqFeature\Gene\Transcript.pm ok 863 - POD test for Bio\SeqFeature\Gene\TranscriptI.pm ok 864 - POD test for Bio\SeqFeature\Gene\UTR.pm ok 865 - POD test for Bio\SeqFeature\SiRNA\Oligo.pm ok 866 - POD test for Bio\SeqFeature\SiRNA\Pair.pm ok 867 - POD test for Bio\SeqFeature\Tools\FeatureNamer.pm ok 868 - POD test for Bio\SeqFeature\Tools\IDHandler.pm ok 869 - POD test for Bio\SeqFeature\Tools\TypeMapper.pm ok 870 - POD test for Bio\SeqFeature\Tools\Unflattener.pm ok 871 - POD test for Bio\SeqIO\game\featHandler.pm ok 872 - POD test for Bio\SeqIO\game\gameHandler.pm ok 873 - POD test for Bio\SeqIO\game\gameSubs.pm ok 874 - POD test for Bio\SeqIO\game\gameWriter.pm ok 875 - POD test for Bio\SeqIO\game\seqHandler.pm ok 876 - POD test for Bio\SeqIO\Handler\GenericRichSeqHandler.pm ok 877 - POD test for Bio\SeqIO\tinyseq\tinyseqHandler.pm ok 878 - POD test for Bio\Structure\IO\pdb.pm ok 879 - POD test for Bio\Tools\Alignment\Consed.pm ok 880 - POD test for Bio\Tools\Alignment\Trim.pm ok 881 - POD test for Bio\Tools\Analysis\SimpleAnalysisBase.pm ok 882 - POD test for Bio\Tools\EMBOSS\Palindrome.pm ok 883 - POD test for Bio\Tools\EUtilities\EUtilDataI.pm ok 884 - POD test for Bio\Tools\EUtilities\EUtilParameters.pm ok 885 - POD test for Bio\Tools\EUtilities\History.pm ok 886 - POD test for Bio\Tools\EUtilities\HistoryI.pm ok 887 - POD test for Bio\Tools\EUtilities\Info.pm ok 888 - POD test for Bio\Tools\EUtilities\Link.pm ok 889 - POD test for Bio\Tools\EUtilities\Query.pm ok 890 - POD test for Bio\Tools\EUtilities\Summary.pm ok 891 - POD test for Bio\Tools\HMMER\Domain.pm ok 892 - POD test for Bio\Tools\HMMER\Results.pm ok 893 - POD test for Bio\Tools\HMMER\Set.pm ok 894 - POD test for Bio\Tools\Phylo\Gerp.pm ok 895 - POD test for Bio\Tools\Phylo\Gumby.pm ok 896 - POD test for Bio\Tools\Phylo\Molphy.pm ok 897 - POD test for Bio\Tools\Phylo\PAML.pm ok 898 - POD test for Bio\Tools\Prediction\Exon.pm ok 899 - POD test for Bio\Tools\Prediction\Gene.pm ok 900 - POD test for Bio\Tools\Primer\AssessorI.pm ok 901 - POD test for Bio\Tools\Primer\Feature.pm ok 902 - POD test for Bio\Tools\Primer\Pair.pm ok 903 - POD test for Bio\Tools\Run\GenericParameters.pm ok 904 - POD test for Bio\Tools\Run\hmmer3.pm (no pod) ok 905 - POD test for Bio\Tools\Run\ParametersI.pm ok 906 - POD test for Bio\Tools\Run\RemoteBlast.pm ok 907 - POD test for Bio\Tools\Run\StandAloneBlast.pm ok 908 - POD test for Bio\Tools\Run\StandAloneNCBIBlast.pm ok 909 - POD test for Bio\Tools\Run\StandAloneWUBlast.pm ok 910 - POD test for Bio\Tools\Run\WrapperBase.pm ok 911 - POD test for Bio\Tools\SeqPattern\Backtranslate.pm ok 912 - POD test for Bio\Tools\Signalp\ExtendedSignalp.pm ok 913 - POD test for Bio\Tools\Sim4\Exon.pm ok 914 - POD test for Bio\Tools\Sim4\Results.pm ok 915 - POD test for Bio\Tools\Spidey\Exon.pm ok 916 - POD test for Bio\Tools\Spidey\Results.pm ok 917 - POD test for Bio\Tree\Draw\Cladogram.pm ok 918 - POD test for Bio\Variation\IO\flat.pm ok 919 - POD test for Bio\Variation\IO\xml.pm ok 920 - POD test for examples\root\lib\TestInterface.pm ok 921 - POD test for examples\root\lib\TestObject.pm ok 922 - POD test for Bio\DB\Flat\BDB\embl.pm ok 923 - POD test for Bio\DB\Flat\BDB\fasta.pm ok 924 - POD test for Bio\DB\Flat\BDB\genbank.pm ok 925 - POD test for Bio\DB\Flat\BDB\swiss.pm ok 926 - POD test for Bio\DB\GFF\Adaptor\ace.pm ok 927 - POD test for Bio\DB\GFF\Adaptor\berkeleydb.pm ok 928 - POD test for Bio\DB\GFF\Adaptor\biofetch.pm ok 929 - POD test for Bio\DB\GFF\Adaptor\biofetch_oracle.pm ok 930 - POD test for Bio\DB\GFF\Adaptor\dbi.pm ok 931 - POD test for Bio\DB\GFF\Adaptor\memory.pm ok 932 - POD test for Bio\DB\GFF\Aggregator\alignment.pm ok 933 - POD test for Bio\DB\GFF\Aggregator\clone.pm ok 934 - POD test for Bio\DB\GFF\Aggregator\coding.pm ok 935 - POD test for Bio\DB\GFF\Aggregator\gene.pm ok 936 - POD test for Bio\DB\GFF\Aggregator\match.pm ok 937 - POD test for Bio\DB\GFF\Aggregator\none.pm ok 938 - POD test for Bio\DB\GFF\Aggregator\orf.pm ok 939 - POD test for Bio\DB\GFF\Aggregator\processed_transcript.pm ok 940 - POD test for Bio\DB\GFF\Aggregator\so_transcript.pm ok 941 - POD test for Bio\DB\GFF\Aggregator\transcript.pm ok 942 - POD test for Bio\DB\GFF\Aggregator\ucsc_acembly.pm ok 943 - POD test for Bio\DB\GFF\Aggregator\ucsc_ensgene.pm ok 944 - POD test for Bio\DB\GFF\Aggregator\ucsc_genscan.pm ok 945 - POD test for Bio\DB\GFF\Aggregator\ucsc_refgene.pm ok 946 - POD test for Bio\DB\GFF\Aggregator\ucsc_sanger22.pm ok 947 - POD test for Bio\DB\GFF\Aggregator\ucsc_sanger22pseudo.pm ok 948 - POD test for Bio\DB\GFF\Aggregator\ucsc_softberry.pm ok 949 - POD test for Bio\DB\GFF\Aggregator\ucsc_twinscan.pm ok 950 - POD test for Bio\DB\GFF\Aggregator\ucsc_unigene.pm ok 951 - POD test for Bio\DB\GFF\Util\Binning.pm ok 952 - POD test for Bio\DB\GFF\Util\Rearrange.pm ok 953 - POD test for Bio\DB\SeqFeature\Store\bdb.pm ok 954 - POD test for Bio\DB\SeqFeature\Store\berkeleydb.pm ok 955 - POD test for Bio\DB\SeqFeature\Store\berkeleydb3.pm ok 956 - POD test for Bio\DB\SeqFeature\Store\FeatureFileLoader.pm ok 957 - POD test for Bio\DB\SeqFeature\Store\GFF2Loader.pm ok 958 - POD test for Bio\DB\SeqFeature\Store\GFF3Loader.pm ok 959 - POD test for Bio\DB\SeqFeature\Store\Loader.pm ok 960 - POD test for Bio\DB\SeqFeature\Store\LoadHelper.pm ok 961 - POD test for Bio\DB\SeqFeature\Store\memory.pm ok 962 - POD test for Bio\Matrix\PSM\IO\mast.pm ok 963 - POD test for Bio\Matrix\PSM\IO\masta.pm ok 964 - POD test for Bio\Matrix\PSM\IO\meme.pm ok 965 - POD test for Bio\Matrix\PSM\IO\psiblast.pm ok 966 - POD test for Bio\Matrix\PSM\IO\transfac.pm ok 967 - POD test for Bio\Structure\SecStr\DSSP\Res.pm ok 968 - POD test for Bio\Structure\SecStr\STRIDE\Res.pm ok 969 - POD test for Bio\Tools\Analysis\DNA\ESEfinder.pm ok 970 - POD test for Bio\Tools\Analysis\Protein\Domcut.pm ok 971 - POD test for Bio\Tools\Analysis\Protein\ELM.pm ok 972 - POD test for Bio\Tools\Analysis\Protein\GOR4.pm ok 973 - POD test for Bio\Tools\Analysis\Protein\HNN.pm ok 974 - POD test for Bio\Tools\Analysis\Protein\Mitoprot.pm ok 975 - POD test for Bio\Tools\Analysis\Protein\NetPhos.pm ok 976 - POD test for Bio\Tools\Analysis\Protein\Scansite.pm ok 977 - POD test for Bio\Tools\Analysis\Protein\Sopma.pm ok 978 - POD test for Bio\Tools\EUtilities\Info\FieldInfo.pm ok 979 - POD test for Bio\Tools\EUtilities\Info\LinkInfo.pm ok 980 - POD test for Bio\Tools\EUtilities\Link\LinkSet.pm ok 981 - POD test for Bio\Tools\EUtilities\Link\UrlLink.pm ok 982 - POD test for Bio\Tools\EUtilities\Query\GlobalQuery.pm ok 983 - POD test for Bio\Tools\EUtilities\Summary\DocSum.pm ok 984 - POD test for Bio\Tools\EUtilities\Summary\Item.pm ok 985 - POD test for Bio\Tools\EUtilities\Summary\ItemContainerI.pm ok 986 - POD test for Bio\Tools\Phylo\Molphy\Result.pm ok 987 - POD test for Bio\Tools\Phylo\PAML\Codeml.pm ok 988 - POD test for Bio\Tools\Phylo\PAML\ModelResult.pm ok 989 - POD test for Bio\Tools\Phylo\PAML\Result.pm ok 990 - POD test for Bio\Tools\Phylo\Phylip\ProtDist.pm ok 991 - POD test for Bio\Tools\Primer\Assessor\Base.pm ok 992 - POD test for Bio\Tools\Run\WrapperBase\CommandExts.pm ok 993 - POD test for Bio\Tools\SiRNA\Ruleset\saigo.pm ok 994 - POD test for Bio\Tools\SiRNA\Ruleset\tuschl.pm ok 995 - POD test for Bio\DB\GFF\Adaptor\berkeleydb\iterator.pm ok 996 - POD test for Bio\DB\GFF\Adaptor\dbi\caching_handle.pm ok 997 - POD test for Bio\DB\GFF\Adaptor\dbi\iterator.pm ok 998 - POD test for Bio\DB\GFF\Adaptor\dbi\mysql.pm ok 999 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlace.pm ok 1000 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlcmap.pm ok 1001 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlopt.pm ok 1002 - POD test for Bio\DB\GFF\Adaptor\dbi\oracle.pm ok 1003 - POD test for Bio\DB\GFF\Adaptor\dbi\oracleace.pm ok 1004 - POD test for Bio\DB\GFF\Adaptor\dbi\pg.pm ok 1005 - POD test for Bio\DB\GFF\Adaptor\dbi\pg_fts.pm ok 1006 - POD test for Bio\DB\GFF\Adaptor\memory\feature_serializer.pm ok 1007 - POD test for Bio\DB\GFF\Adaptor\memory\iterator.pm ok 1008 - POD test for Bio\DB\SeqFeature\Store\DBI\Iterator.pm ok 1009 - POD test for Bio\DB\SeqFeature\Store\DBI\mysql.pm ok 1010 - POD test for Bio\DB\SeqFeature\Store\DBI\Pg.pm ok 1011 - POD test for Bio\DB\SeqFeature\Store\DBI\SQLite.pm ok Subroutine new redefined at Bio\Tree\Tree.pm line 131. Subroutine nodelete redefined at Bio\Tree\Tree.pm line 179. Subroutine get_nodes redefined at Bio\Tree\Tree.pm line 196. Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 230. Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 245. Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 269. Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 283. Subroutine id redefined at Bio\Tree\Tree.pm line 306. Subroutine score redefined at Bio\Tree\Tree.pm line 327. Subroutine as_text redefined at Bio\Tree\Tree.pm line 375. Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 411. Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 432. Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 452. Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 472. Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 488. Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 504. Subroutine has_tag redefined at Bio\Tree\Tree.pm line 520. Subroutine clone redefined at Bio\Tree\Tree.pm line 540. Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 558. Subroutine new redefined at Bio\Tree\Node.pm line 110. Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 163. Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 221. Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 259. Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 322. Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 357. Subroutine ancestor redefined at Bio\Tree\Node.pm line 396. Subroutine branch_length redefined at Bio\Tree\Node.pm line 437. Subroutine bootstrap redefined at Bio\Tree\Node.pm line 461. Subroutine description redefined at Bio\Tree\Node.pm line 482. Subroutine id redefined at Bio\Tree\Node.pm line 511. Subroutine internal_id redefined at Bio\Tree\Node.pm line 553. Subroutine _creation_id redefined at Bio\Tree\Node.pm line 567. Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 588. Subroutine height redefined at Bio\Tree\Node.pm line 606. Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 631. Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 652. Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 674. Subroutine remove_tag redefined at Bio\Tree\Node.pm line 695. Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 715. Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 731. Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 749. Subroutine has_tag redefined at Bio\Tree\Node.pm line 765. Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 770. Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 800. t/PopGen/Coalescent.t ........................ 1..13 ok 1 - use Bio::PopGen::Simulation::Coalescent; ok 2 - use Bio::PopGen::Statistics; ok 3 - use Bio::TreeIO; ok 4 ok 5 ok 6 - pi ok 7 - theta ok 8 - tajimaD ok 9 - all the mutations should be polymorphic (by definition) ok 10 - fu and li D ok 11 - fu and li D* ok 12 - fu and li F ok 13 - fu and li F ok t/PopGen/HtSNP.t ............................. 1..8 ok 1 - use Bio::PopGen::HtSNP; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok t/PopGen/MK.t ................................ 1..46 ok 1 - use Bio::AlignIO; ok 2 - use Bio::PopGen::Statistics; ok 3 - use Bio::PopGen::Utilities; ok 4 - The object isa Bio::PopGen::Statistics ok 5 - The object isa Bio::SimpleAlign ok 6 - The object isa Bio::PopGen::Population ok 7 - Marker Names ok 8 - Number of Inds ok 9 - number of ingroup sequences ok 10 - number of outgroup1 sequences ok 11 - number of outgroup2 sequences ok 12 - NSpoly ok 13 - NSfixed ok 14 - Spoly ok 15 - Sfixed ok 16 - McDonald Kreitman ok 17 - NSpoly ok 18 - NSfixed ok 19 - Spoly ok 20 - Sfixed ok 21 - McDonald Kreitman ok 22 - NSpoly ok 23 - NSfixed ok 24 - Spoly ok 25 - Sfixed ok 26 - The object isa Bio::SimpleAlign ok 27 - The object isa Bio::PopGen::Population ok 28 - Marker Names ok 29 - Number of Inds ok 30 - number of ingroup sequences ok 31 - number of outgroup1 sequences ok 32 - number of outgroup2 sequences ok 33 - NSpoly ok 34 - NSfixed ok 35 - Spoly ok 36 - Sfixed ok 37 - McDonald Kreitman ok 38 - NSpoly ok 39 - NSfixed ok 40 - Spoly ok 41 - Sfixed ok 42 - McDonald Kreitman ok 43 - NSpoly ok 44 - NSfixed ok 45 - Spoly ok 46 - Sfixed ok t/PopGen/PopGen.t ............................ 1..100 ok 1 - use Bio::PopGen::Individual; ok 2 - use Bio::PopGen::Genotype; ok 3 - use Bio::PopGen::Population; ok 4 - use Bio::PopGen::IO; ok 5 - use Bio::PopGen::PopStats; ok 6 - use Bio::AlignIO; ok 7 - use Bio::PopGen::Statistics; ok 8 - use Bio::PopGen::Utilities; ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - mrsa,mssa aflp1 ok 38 - all pops, aflp1 ok 39 - mrsa,envpop aflp1,aflp2 ok 40 ok 41 ok 42 ok 43 - mssa,mrsa all_bands ok 44 - env,mssa mkr1 ok 45 - env,mssa,mrsa all bands ok 46 - env,mssa,mrsa mkr2 ok 47 - mrsa,nc all_bands ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 - Pi on 3-allele data ok 100 - Theta on 3-allele data ok t/PopGen/PopGenSims.t ........................ 1..23 ok 1 - use Bio::PopGen::Simulation::GeneticDrift; ok 2 - Allele freqs should sum to 1 ok 3 - Allele freqs should sum to 1 ok 4 - Allele freqs should sum to 1 ok 5 - Allele freqs should sum to 1 ok 6 - Allele freqs should sum to 1 ok 7 - Allele freqs should sum to 1 ok 8 - Allele freqs should sum to 1 ok 9 - Allele freqs should sum to 1 ok 10 - Allele freqs should sum to 1 ok 11 - Allele freqs should sum to 1 ok 12 ok 13 - All frequencies should be <= 1 ok 14 - Allele freqs should sum to 1 ok 15 - Allele freqs should sum to 1 ok 16 - Allele freqs should sum to 1 ok 17 - Allele freqs should sum to 1 ok 18 - Allele freqs should sum to 1 ok 19 - Allele freqs should sum to 1 ok 20 - Allele freqs should sum to 1 ok 21 - Allele freqs should sum to 1 ok 22 - Allele freqs should sum to 1 ok 23 - Allele freqs should sum to 1 ok t/PopGen/TagHaplotype.t ...................... 1..3 ok 1 - use Bio::PopGen::TagHaplotype; ok 2 ok 3 ok t/RemoteDB/BioFetch.t ........................ skipped: Network tests have not been requested t/RemoteDB/CUTG.t ............................ 1..37 ok 1 - use Bio::DB::CUTG; ok 2 - use Bio::CodonUsage::Table; ok 3 - use Bio::CodonUsage::IO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Tools::SeqStats; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok 31 # skip Network tests have not been requested ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested t/RemoteDB/EUtilities.t ...................... skipped: Valid email not provided; required for tests t/RemoteDB/EntrezGene.t ...................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/RemoteDB/GenBank.t ......................... skipped: Network tests have not been requested t/RemoteDB/GenPept.t ......................... skipped: Network tests have not been requested t/RemoteDB/HIV/HIV.t ......................... 1..30 ok 1 - use Bio::DB::HIV; ok 2 - use Bio::DB::WebDBSeqI; ok 3 - use Bio::DB::HIV::HIVAnnotProcessor; ok 4 - The object isa Bio::DB::HIV ok 5 - The object isa Bio::Root::Root ok 6 - Bio::DB::HIV->can(...) ok 7 - Bio::DB::HIV->can(...) ok 8 - Bio::DB::HIV->can(...) ok 9 - lanl_base set in default object ok 10 - map_db set in default object ok 11 - make_search_if set in default object ok 12 - search_ set in default object ok 13 - url_base_address set in default object ok 14 - default sequence request format (fasta) ok 15 - sorry till implemented ok 16 - sorry till implemented ok 17 - HIVQuery type exception check ok 18 # skip Network tests have not been requested ok 19 # skip Network tests have not been requested ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok t/RemoteDB/HIV/HIVAnnotProcessor.t ........... 1..11 ok 1 - use Bio::Seq; ok 2 - use Bio::SeqIO; ok 3 - use Bio::DB::HIV::HIVAnnotProcessor; ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor ok 5 - The object isa Bio::Root::Root ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...) ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query') ok 8 - bad type set exception ok 9 - attach stream ok 10 - write exception ok 11 - access stream ok Use of uninitialized value $rest[0] in join or string at (eval 75) line 15. t/RemoteDB/HIV/HIVQuery.t .................... 1..41 ok 1 - use Bio::DB::Query::HIVQuery; ok 2 - use Bio::DB::HIV; ok 3 - use Bio::Annotation::Collection; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::Reference; ok 6 - use Bio::DB::HIV::HIVQueryHelper; ok 7 - The object isa Bio::DB::Query::HIVQuery ok 8 - The object isa Bio::Root::Root ok 9 - Bio::DB::Query::HIVQuery->can(...) ok 10 - Bio::DB::Query::HIVQuery->can(...) ok 11 - Bio::DB::Query::HIVQuery->can(...) ok 12 - _map_db_uri set in default object ok 13 - _make_search_if_uri set in default object ok 14 - _search_uri set in default object ok 15 - _schema_file set in default object ok 16 - _run_option set in default object ok 17 - annotations container available ok 18 - query syntax check 1 ok 19 - query syntax check 2 ok 20 - query syntax check 3 ok 21 - query parser check ok 22 - multiquery parse check ok 23 - use HTML::Parser; ok 24 - help html to file ok 25 - help html parsed ok 26 - bad field exception check ok 27 - bad match data exception check ok 28 - empty field not ok exception check ok 29 - uninitialized schema exception check ok 30 - query not run (level 1) warning check ok 31 - query not run (level 2) warning check ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok 38 # skip Network tests have not been requested ok 39 # skip Network tests have not been requested ok 40 # skip Network tests have not been requested ok 41 # skip Network tests have not been requested ok t/RemoteDB/HIV/HIVQueryHelper.t .............. 1..40 ok 1 - use Bio::DB::HIV::HIVQueryHelper; ok 2 - The object isa HIVSchema ok 3 - The object isa QRY ok 4 - The object isa R ok 5 - The object isa Q ok 6 - schema load ok 7 - HIVSchema->can(...) ok 8 - fields complete ok 9 - tables complete ok 10 - aliases complete ok 11 ok 12 - test field syntax ok ok 13 - test field syntax ok ok 14 - test alias by field name ok 15 - correct primary key for SequenceEntry ok 16 - correct number of foreign keys for AUthor ok 17 - correct foreign table for au_pub_id ok 18 - correct annotation key hash ok 19 - QRY->can(...) ok 20 - R->can(...) ok 21 - Q->can(...) ok 22 - null QRY ok 23 - null R (request object) ok 24 - null Q (atomic query object) ok 25 - R obj create and init (1) ok 26 - R obj create and init (2) ok 27 - R::In ok 28 - !R::In ok 29 - R::Eq ok 30 - QRY obj create and init (1) ok 31 - QRY obj create and init (2) ok 32 - QRY obj create and init (3) ok 33 - QRY overload | ok 34 - QRY overload & ok 35 - QRY nontrivial & ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} ok 37 - make: 2 queries returned ok 38 - {annotation fields} parsed correctly ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} ok 40 - above query is null ok t/RemoteDB/MeSH.t ............................ skipped: Network tests have not been requested t/RemoteDB/Query/GenBank.t ................... skipped: Network tests have not been requested t/RemoteDB/RefSeq.t .......................... 1..16 ok 1 - use Bio::DB::RefSeq; ok 2 - use Bio::DB::GenBank; ok 3 - use Bio::DB::EMBL; ok 4 ok 5 ok 6 ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok 15 # skip Network tests have not been requested ok 16 # skip Network tests have not been requested ok t/RemoteDB/SeqHound.t ........................ skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail.t .................... skipped: Network tests have not been requested t/RemoteDB/SeqVersion.t ...................... 1..10 ok 1 - use Bio::DB::SeqVersion; ok 2 ok 3 # skip Network tests have not been requested ok 4 # skip Network tests have not been requested ok 5 # skip Network tests have not been requested ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok t/RemoteDB/SwissProt.t ....................... skipped: Network tests have not been requested ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/RemoteDB/Taxonomy.t:24 ----------------------------------------------------------- Bio::DB::Taxonomy: flatfile cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.900-jmg4Mb C:\cpanfly-5.12\var\megalib C:/cpanfly-5.12/var/megalib C:/Perl64-5.12/site/lib C:/Perl64-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/RemoteDB/Taxonomy.t:24 ----------------------------------------------------------- For more information about the Bio::DB::Taxonomy system please see the Bio::DB::Taxonomy docs. This includes ways of checking for formats at compile time, not run time. # Failed test at t/RemoteDB/Taxonomy.t line 24. Use of uninitialized value $db in string eq at t/RemoteDB/Taxonomy.t line 32. Can't call method "get_taxon" on an undefined value at t/RemoteDB/Taxonomy.t line 124. # Looks like you planned 103 tests but ran 82. # Looks like you failed 1 test of 82 run. # Looks like your test exited with 255 just after 82. t/RemoteDB/Taxonomy.t ........................ 1..103 ok 1 - use Bio::DB::Taxonomy; ok 2 - use Bio::Tree::Tree; ok 3 not ok 4 ok 5 # skip Network tests have not been requested ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok 15 # skip Network tests have not been requested ok 16 # skip Network tests have not been requested ok 17 # skip Network tests have not been requested ok 18 # skip Network tests have not been requested ok 19 # skip Network tests have not been requested ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok 31 # skip Network tests have not been requested ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok 38 # skip Network tests have not been requested ok 39 # skip Network tests have not been requested ok 40 # skip Network tests have not been requested ok 41 # skip Network tests have not been requested ok 42 # skip Network tests have not been requested ok 43 # skip Unable to connect to entrez database; no network or server busy? ok 44 # skip Unable to connect to entrez database; no network or server busy? ok 45 # skip Unable to connect to entrez database; no network or server busy? ok 46 # skip Unable to connect to entrez database; no network or server busy? ok 47 # skip Unable to connect to entrez database; no network or server busy? ok 48 # skip Unable to connect to entrez database; no network or server busy? ok 49 # skip Unable to connect to entrez database; no network or server busy? ok 50 # skip Unable to connect to entrez database; no network or server busy? ok 51 # skip Unable to connect to entrez database; no network or server busy? ok 52 # skip Unable to connect to entrez database; no network or server busy? ok 53 # skip Unable to connect to entrez database; no network or server busy? ok 54 # skip Unable to connect to entrez database; no network or server busy? ok 55 # skip Unable to connect to entrez database; no network or server busy? ok 56 # skip Unable to connect to entrez database; no network or server busy? ok 57 # skip Unable to connect to entrez database; no network or server busy? ok 58 # skip Unable to connect to entrez database; no network or server busy? ok 59 # skip Unable to connect to entrez database; no network or server busy? ok 60 # skip Unable to connect to entrez database; no network or server busy? ok 61 # skip Unable to connect to entrez database; no network or server busy? ok 62 # skip Unable to connect to entrez database; no network or server busy? ok 63 # skip Unable to connect to entrez database; no network or server busy? ok 64 # skip Unable to connect to entrez database; no network or server busy? ok 65 # skip Unable to connect to entrez database; no network or server busy? ok 66 # skip Unable to connect to entrez database; no network or server busy? ok 67 # skip Unable to connect to entrez database; no network or server busy? ok 68 # skip Unable to connect to entrez database; no network or server busy? ok 69 # skip Unable to connect to entrez database; no network or server busy? ok 70 # skip Unable to connect to entrez database; no network or server busy? ok 71 # skip Unable to connect to entrez database; no network or server busy? ok 72 # skip Unable to connect to entrez database; no network or server busy? ok 73 # skip Unable to connect to entrez database; no network or server busy? ok 74 # skip Unable to connect to entrez database; no network or server busy? ok 75 # skip Unable to connect to entrez database; no network or server busy? ok 76 # skip Unable to connect to entrez database; no network or server busy? ok 77 # skip Unable to connect to entrez database; no network or server busy? ok 78 # skip Unable to connect to entrez database; no network or server busy? ok 79 # skip Unable to connect to entrez database; no network or server busy? ok 80 # skip Unable to connect to entrez database; no network or server busy? ok 81 ok 82 Dubious, test returned 255 (wstat 65280, 0xff00) Failed 22/103 subtests (less 76 skipped subtests: 5 okay) t/Restriction/Analysis-refac.t ............... 1..91 ok 1 - use Bio::Restriction::IO; ok 2 - use Bio::Restriction::Analysis; ok 3 - use Bio::Restriction::EnzymeCollection; ok 4 - use Bio::Restriction::Enzyme; ok 5 - read withrefm file ok 6 - parse withrefm file ok 7 - HindIII: nonambiguous intrasite cutter ok 8 - AarI: nonambiguous extrasite cutter ok 9 - AasI: ambiguous intrasite cutter ok 10 - BceSI: ambiguous extrasite cutter ok 11 - AjuI: cutter with central recog site ok 12 - TaqII: multi-extrasite cutter ok 13 ok 14 - HindIII plus ok 15 - HindIII minus ok 16 - AasI plus ok 17 - AasI minus ok 18 - AarI plus ok 19 - AarI minus ok 20 - BceSI plus ok 21 - BceSI minus ok 22 - AjuI plus ok 23 - AjuI minus ok 24 - TaqII plus ok 25 - TaqII minus ok 26 - build real B:R::Analysis object ok 27 - 13 fragments ok 28 - circularize ok 29 - recut ok 30 - circ: AasI # site at origin ok 31 - circ: still 13 fragments (cut site at origin) ok 32 - use Bio::Restriction::IO; ok 33 - use Bio::Restriction::Analysis; ok 34 - read withrefm file ok 35 - parse withrefm file ok 36 - Collection initiated ok 37 - AbeI: found ok into collection ok 38 - AccBSI: found ok into collection ok 39 - AciI: found ok into collection ok 40 - Asp26HI: found ok into collection ok 41 - BmgBI: found ok into collection ok 42 - AbeI plus ok 43 - AbeI minus ok 44 - AbeI fragment ok 45 - AbeI positions ok 46 - AbeI Overhang ok 47 - AbeI name ok 48 - AbeI site ok 49 - AbeI revcom_site ok 50 - AbeI cut ok 51 - AbeI complementary_cut ok 52 - AccBSI plus ok 53 - AccBSI minus ok 54 - AccBSI fragment ok 55 - AccBSI positions ok 56 - AccBSI Overhang ok 57 - AccBSI name ok 58 - AccBSI site ok 59 - AccBSI revcom_site ok 60 - AccBSI cut ok 61 - AccBSI complementary_cut ok 62 - AciI plus ok 63 - AciI minus ok 64 - AciI fragment ok 65 - AciI positions ok 66 - AciI Overhang ok 67 - AciI name ok 68 - AciI site ok 69 - AciI revcom_site ok 70 - AciI cut ok 71 - AciI complementary_cut ok 72 - Asp26HI plus ok 73 - Asp26HI minus ok 74 - Asp26HI fragment ok 75 - Asp26HI positions ok 76 - Asp26HI Overhang ok 77 - Asp26HI name ok 78 - Asp26HI site ok 79 - Asp26HI revcom_site ok 80 - Asp26HI cut ok 81 - Asp26HI complementary_cut ok 82 - BmgBI plus ok 83 - BmgBI minus ok 84 - BmgBI fragment ok 85 - BmgBI positions ok 86 - BmgBI Overhang ok 87 - BmgBI name ok 88 - BmgBI site ok 89 - BmgBI revcom_site ok 90 - BmgBI cut ok 91 - BmgBI complementary_cut ok t/Restriction/Analysis.t ..................... 1..182 ok 1 - use Bio::Restriction::Enzyme; ok 2 - use Bio::Restriction::Enzyme::MultiCut; ok 3 - use Bio::Restriction::Enzyme::MultiSite; ok 4 - use Bio::Restriction::EnzymeCollection; ok 5 - use Bio::Restriction::Analysis; ok 6 - use Bio::SeqIO; ok 7 ok 8 - The object isa Bio::Restriction::EnzymeI ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 - The object isa Bio::PrimarySeqI ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 - bug 2179 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 - The object isa Bio::Restriction::EnzymeI ok 77 - The object isa Bio::Restriction::EnzymeI ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 - The object isa Bio::Restriction::EnzymeI ok 88 - The object isa Bio::Restriction::EnzymeI ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 - The object isa Bio::Restriction::Enzyme ok 100 ok 101 ok 102 - The object isa Bio::Restriction::Enzyme ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 - number of unique cutters ok 119 - number of RsaI fragments ok 120 - number of maximum cutters ok 121 - number of zero cutters ok 122 - number of cutters ok 123 - number of 3x cutters ok 124 - 4 MseI fragments ok 125 - 3 MseI cut sites ok 126 - expected 2 PspEI fragments ok 127 ok 128 ok 129 - expected 2 sizes for PspEI ok 130 ok 131 - expected 2 sizes for PspEI ok 132 ok 133 - not circular expected 1 fragments for MwoI as it doesnt cut ok 134 ok 135 ok 136 - number of RsaI fragments ok 137 - 3 circular MseI fragments ok 138 - 3 circular MseI cut sites ok 139 - number for AciI a non-palindromic enzyme ok 140 - 1 fragment for MwoI as it cuts across the circ point ok 141 ok 142 ok 143 ok 144 ok 145 - 7 fragments in the multiple digest ok 146 - 7 positions in the multiple digest ok 147 - 7 sizes in the multiple digest ok 148 ok 149 - expected 9 cuts for HindI ok 150 - expect 9 fragment maps for HindI ok 151 - sequence for GT ok 152 - start at 40 ok 153 - end at 41 ok 154 - sequence for GGATTAAAAAAAGAGT ok 155 - start at 42 ok 156 - end at 57 ok 157 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT ok 158 - start at 58 ok 159 - end at 92 ok 160 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA ok 161 - start at 93 ok 162 - end at 123 ok 163 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA ok 164 - start at 124 ok 165 - end at 155 ok 166 - sequence for CAGACAGATAAAAATTACAGAGTACA ok 167 - start at 156 ok 168 - end at 181 ok 169 - sequence for CAACATCCATGAAACGCATTAGCA ok 170 - start at 182 ok 171 - end at 205 ok 172 - sequence for CCA ok 173 - start at 206 ok 174 - end at 208 ok 175 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT ok 176 - start at 209 ok 177 - end at 39 ok 178 ok 179 - bug 2139 ok 180 - number of HindIII fragments ok 181 - number of EcoRI fragments ok 182 - number of RsaI fragments ok t/Restriction/Gel.t .......................... 1..9 ok 1 - use Bio::PrimarySeq; ok 2 - use Bio::Restriction::Analysis; ok 3 - use Bio::Tools::Gel; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok Subroutine new redefined at Bio/Restriction/IO/base.pm line 90, line 532. Subroutine _initialize redefined at Bio/Restriction/IO/base.pm line 114, line 532. Subroutine read redefined at Bio/Restriction/IO/base.pm line 144, line 532. Subroutine _xln_sub redefined at Bio/Restriction/IO/base.pm line 172, line 532. Subroutine write redefined at Bio/Restriction/IO/base.pm line 189, line 532. Subroutine verify_prototype redefined at Bio/Restriction/IO/base.pm line 221, line 532. Subroutine _cuts_from_site redefined at Bio/Restriction/IO/base.pm line 258, line 532. Subroutine _meth redefined at Bio/Restriction/IO/base.pm line 279, line 532. Subroutine _coordinate_shift_to_cut redefined at Bio/Restriction/IO/base.pm line 305, line 532. Subroutine _make_multisites redefined at Bio/Restriction/IO/base.pm line 327, line 532. Subroutine _make_multicuts redefined at Bio/Restriction/IO/base.pm line 412, line 532. Subroutine _companies redefined at Bio/Restriction/IO/base.pm line 441, line 532. t/Restriction/IO.t ........................... 1..18 ok 1 - use Bio::Restriction::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT! # Failed (TODO) test at t/Restriction/IO.t line 31. ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 # skip Network tests have not been requested ok 17 # skip Network tests have not been requested ok 18 # skip Network tests have not been requested ok t/Root/Exception.t ........................... 1..8 ok 1 - use TestObject; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Root/HTTPget.t ............................. skipped: Network tests have not been requested t/Root/RootI.t ............................... 1..63 ok 1 - use Bio::Root::Root; ok 2 - use Bio::Seq; ok 3 ok 4 - The object isa Bio::Root::RootI ok 5 - threw Regexp ((?-xism:Testing throw)) ok 6 - threw Regexp ((?-xism:EXCEPTION: Bio::Root::NotImplemented)) ok 7 - threw Regexp ((?-xism:EXCEPTION )) ok 8 - threw Regexp ((?-xism:Testing throw)) ok 9 ok 10 - threw Regexp ((?-xism:Testing throw)) ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 - simple ok 17 - simple ok 18 - warns for versions below current version 1.0069 ok 19 - warns for versions below current version 1.0069 ok 20 - throws for versions above 1.0069 ok 21 - throws for versions above 1.0069 ok 22 - throws for versions equal to 1.0069 ok 23 - simple ok 24 - simple ok 25 - warns for versions below current version 1.0069 ok 26 - warns for versions below current version 1.0069 ok 27 - throws for versions above 1.0069 ok 28 - throws for versions above 1.0069 ok 29 - arg callable since method was created ok 30 - mal-formed arg callable since method was created with good name ok 31 - Bio::Foo2->can('t3') ok 32 - Methods don't pollute original Bio::Root::Root namespace ok 33 - Bio::Foo2->can('test_4') ok 34 - Methods don't pollute original Bio::Root::Root namespace ok 35 - Bio::Foo3->can('t5') ok 36 - arg not in method list not created ok 37 - Bio::Foo3->can('t5') ok 38 - Methods don't pollute original Bio::Root::Root namespace ok 39 - verbose was set correctly ok 40 - synonym was set correctly ok 41 - real method of synonym was set correctly ok 42 - mal-formed arg correctly resolved to created method ok 43 - synonym of set method was set correctly ok 44 - Bio::Foo4->can('t7') ok 45 - Methods don't pollute original Bio::Root::Root namespace ok 46 - Bio::Foo4->can('test7') ok 47 - Methods don't pollute original Bio::Root::Root namespace ok 48 - Bio::Foo4->can('test_8') ok 49 - Methods don't pollute original Bio::Root::Root namespace ok 50 - Bio::Foo4->can('t8') ok 51 - Methods don't pollute original Bio::Root::Root namespace ok 52 - clone ok 53 - clone ok 54 - clone ok 55 - clone changed, original didn't ok 56 - parameters passed to clone() modify object ok 57 - original is not modified ok 58 - must use proper versioning scheme ok 59 - warns for versions >= 1.0069 ok 60 - warns for versions >= 1.0069 ok 61 - throws for versions >= 1.0069 ok 62 - throws for versions >= 1.0069 ok 63 - No warnings/exceptions below 1.0069 ok # Failed test 'executable file' # at t/Root/RootIO.t line 55. Can't do inplace edit without backup at Bio/Root/IO.pm line 513. # Looks like you planned 67 tests but ran 43. # Looks like you failed 1 test of 43 run. # Looks like your test exited with 25 just after 43. Error removing C:\cpanfly-5.12\var\tmp\XlUP8jdIvN at C:\cpanfly-5.12\var\megalib/File/Temp.pm line 890. t/Root/RootIO.t .............................. 1..67 ok 1 - use Bio::Root::IO; ok 2 ok 3 - throw() ok 4 - throw() verbose(-1) ok 5 - warn() ok 6 - throw() verbose(1) ok 7 - stack_trace() ok 8 - set verbosity to 1 ok 9 ok 10 not ok 11 - executable file ok 12 - non-executable file ok 13 - executable dir ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 - filename, read ok 20 ok 21 ok 22 - filename, write ok 23 ok 24 ok 25 ok 26 ok 27 - handle, read ok 28 ok 29 ok 30 - handle, write ok 31 ok 32 - is a write handle ok 33 - no warnings ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 - _print ok 43 Dubious, test returned 25 (wstat 6400, 0x1900) Failed 25/67 subtests t/Root/Storable.t ............................ 1..35 ok 1 - use Bio::Root::Storable; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok t/Root/Tempfile.t ............................ 1..18 ok 1 - use Bio::Root::IO; ok 2 ok 3 - The object isa Bio::Root::IO ok 4 ok 5 ok 6 - auto UNLINK => 1 ok 7 ok 8 ok 9 - tempfile deleted ok 10 ok 11 - UNLINK => 0 ok 12 ok 13 ok 14 ok 15 - tempfile suffix ok 16 ok 17 - tempfile() in scalar context ok 18 ok t/Root/Utilities.t ........................... 1..56 ok 1 - use Bio::Root::Utilities; ok 2 - The object isa Bio::Root::Utilities ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - file_date() ok 38 - unix (\n or 012 or ^J) ok 39 - date format ok 40 - date format ok 41 - date format ok 42 - date format ok 43 - date format ok 44 ok 45 # skip gzip not found, skipping gzip tests ok 46 # skip gzip not found, skipping gzip tests ok 47 # skip gzip not found, skipping gzip tests ok 48 # skip gzip not found, skipping gzip tests ok 49 # skip gzip not found, skipping gzip tests ok 50 # skip gzip not found, skipping gzip tests ok 51 # skip gzip not found, skipping gzip tests ok 52 # skip gzip not found, skipping gzip tests ok 53 # skip gzip not found, skipping gzip tests ok 54 # skip gzip not found, skipping gzip tests ok 55 # skip gzip not found, skipping gzip tests ok 56 # skip gzip not found, skipping gzip tests ok t/SearchDist.t ............................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 434. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 434. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 434. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 434. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 434. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 434. t/SearchIO/CigarString.t ..................... 1..4 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok t/SearchIO/SearchIO.t ........................ 1..19 ok 1 - use Bio::SearchIO; ok 2 - blastxml for f.blastxml ok 3 - fasta for f.fy ok 4 - exonerate for f.exonerate ok 5 - blast for f.tblx ok 6 - fasta for f.fx ok 7 - fasta for f.osearch ok 8 - blast for filename.bls ok 9 - exonerate for f.exon ok 10 - fasta for f.SSEARCH.m9 ok 11 - blast for filename.blast ok 12 - fasta for f.m9 ok 13 - blast for f.blx ok 14 - blastxml for f.xml ok 15 - fasta for f.fasta ok 16 - fasta for f.fa ok 17 - blast for fast.bls ok 18 - fasta for f.ssearch ok 19 - fasta for f.psearch ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 434. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 434. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 434. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 434. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 434. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 434. t/SearchIO/SimilarityPair.t .................. 1..12 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SeqIO; ok 3 ok 4 - The object isa Bio::SeqI ok 5 ok 6 - The object isa Bio::SearchIO ok 7 ok 8 - The object isa Bio::Search::Hit::HitI ok 9 ok 10 - The object isa Bio::SeqFeatureI ok 11 ok 12 ok Subroutine new redefined at Bio\Search\Hit\GenericHit.pm line 127. Subroutine add_hsp redefined at Bio\Search\Hit\GenericHit.pm line 204. Subroutine hsp_factory redefined at Bio\Search\Hit\GenericHit.pm line 228. Subroutine name redefined at Bio\Search\Hit\GenericHit.pm line 248. Subroutine accession redefined at Bio\Search\Hit\GenericHit.pm line 268. Subroutine description redefined at Bio\Search\Hit\GenericHit.pm line 288. Subroutine length redefined at Bio\Search\Hit\GenericHit.pm line 308. Subroutine algorithm redefined at Bio\Search\Hit\GenericHit.pm line 333. Subroutine raw_score redefined at Bio\Search\Hit\GenericHit.pm line 355. Subroutine score redefined at Bio\Search\Hit\GenericHit.pm line 385. Subroutine significance redefined at Bio\Search\Hit\GenericHit.pm line 400. Subroutine bits redefined at Bio\Search\Hit\GenericHit.pm line 430. Subroutine next_hsp redefined at Bio\Search\Hit\GenericHit.pm line 458. Subroutine hsps redefined at Bio\Search\Hit\GenericHit.pm line 494. Subroutine num_hsps redefined at Bio\Search\Hit\GenericHit.pm line 517. Subroutine rewind redefined at Bio\Search\Hit\GenericHit.pm line 538. Subroutine ambiguous_aln redefined at Bio\Search\Hit\GenericHit.pm line 564. Subroutine overlap redefined at Bio\Search\Hit\GenericHit.pm line 576. Subroutine n redefined at Bio\Search\Hit\GenericHit.pm line 605. Subroutine p redefined at Bio\Search\Hit\GenericHit.pm line 652. Subroutine hsp redefined at Bio\Search\Hit\GenericHit.pm line 694. Subroutine logical_length redefined at Bio\Search\Hit\GenericHit.pm line 740. Subroutine length_aln redefined at Bio\Search\Hit\GenericHit.pm line 786. Subroutine gaps redefined at Bio\Search\Hit\GenericHit.pm line 849. Subroutine matches redefined at Bio\Search\Hit\GenericHit.pm line 887. Subroutine start redefined at Bio\Search\Hit\GenericHit.pm line 948. Subroutine end redefined at Bio\Search\Hit\GenericHit.pm line 1025. Subroutine range redefined at Bio\Search\Hit\GenericHit.pm line 1093. Subroutine frac_identical redefined at Bio\Search\Hit\GenericHit.pm line 1150. Subroutine frac_conserved redefined at Bio\Search\Hit\GenericHit.pm line 1226. Subroutine frac_aligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1274. Subroutine frac_aligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1310. Subroutine num_unaligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1364. Subroutine num_unaligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1400. Subroutine seq_inds redefined at Bio\Search\Hit\GenericHit.pm line 1442. Subroutine strand redefined at Bio\Search\Hit\GenericHit.pm line 1473. Subroutine frame redefined at Bio\Search\Hit\GenericHit.pm line 1535. Subroutine rank redefined at Bio\Search\Hit\GenericHit.pm line 1574. Subroutine locus redefined at Bio\Search\Hit\GenericHit.pm line 1590. Subroutine each_accession_number redefined at Bio\Search\Hit\GenericHit.pm line 1618. Subroutine tiled_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1666. Subroutine query_length redefined at Bio\Search\Hit\GenericHit.pm line 1683. Subroutine ncbi_gi redefined at Bio\Search\Hit\GenericHit.pm line 1701. Subroutine sort_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1732. Subroutine iteration redefined at Bio\Search\Hit\GenericHit.pm line 1772. Subroutine found_again redefined at Bio\Search\Hit\GenericHit.pm line 1807. Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1333. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1341. Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\Search\Hit\BlastHit.pm line 105. Subroutine iteration redefined at Bio\Search\Hit\BlastHit.pm line 134. Subroutine found_again redefined at Bio\Search\Hit\BlastHit.pm line 169. Subroutine expect redefined at Bio\Search\Hit\BlastHit.pm line 176. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 2564. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 2564. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 2564. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 2564. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 2564. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 2564. t/SearchIO/Tiling.t .......................... 1..1141 ok 1 - use Bio::Search::Tiling::MapTiling; ok 2 - use Bio::Search::Tiling::MapTileUtils; ok 3 - use Bio::SearchIO; ok 4 - use Bio::Search::Hit::BlastHit; ok 5 - use File::Spec; ok 6 - parse data file ok 7 - got test hit ok 8 - create tiling ok 9 - The object isa Bio::Search::Tiling::TilingI ok 10 - implements 'next_tiling' ok 11 - implements 'rewind_tilings' ok 12 - implements 'identities' ok 13 - implements 'conserved' ok 14 - implements 'length' ok 15 - identities regression test ok 16 - conserved regression test ok 17 - tiling iterator regression test(1) ok 18 - tiling iterator regression test(2) ok 19 - tiling iterator regression test(3, rewind) ok 20 - ecolitst.wublastp ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 - dnaEbsub_ecoli.wublastx ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 - tricky.wublast ok 37 - tricky.wublast(1) ok 38 - tricky.wublast(2) ok 39 - tricky.wublast(3) ok 40 - tricky.wublast(4) ok 41 - ecolitst.bls ok 42 - tile ecolitst.bls hit 1 \#hsps 1 ok 43 - q id: est (0.98293) = fast (0.98293) ok 44 - q cn: est (0.98293) = fast (0.98293) ok 45 - h id: est (0.98293) = fast (0.98293) ok 46 - h cn: est (0.98293) = fast (0.98293) ok 47 - tile ecolitst.bls hit 2 \#hsps 1 ok 48 - q id: est (0.30074) = fast (0.30074) ok 49 - q cn: est (0.49876) = fast (0.49876) ok 50 - h id: est (0.30759) = fast (0.30759) ok 51 - h cn: est (0.51013) = fast (0.51013) ok 52 - tile ecolitst.bls hit 3 \#hsps 1 ok 53 - q id: est (0.31004) = fast (0.31004) ok 54 - q cn: est (0.49782) = fast (0.49782) ok 55 - h id: est (0.32054) = fast (0.32054) ok 56 - h cn: est (0.51467) = fast (0.51467) ok 57 - tile ecolitst.bls hit 4 \#hsps 1 ok 58 - q id: est (0.30435) = fast (0.30435) ok 59 - q cn: est (0.47826) = fast (0.47826) ok 60 - h id: est (0.29787) = fast (0.29787) ok 61 - h cn: est (0.46809) = fast (0.46809) ok 62 - tricky.wublast ok 63 - tile tricky.wublast hit 1 \#hsps 7 ok 64 - q id: exact (0.22153) ~ est (0.22153) ok 65 - q id: exact (0.22153) <= max (0.22153) ok 66 - q cn: exact (0.42760) ~ est (0.42760) ok 67 - q cn: exact (0.42760) <= max (0.42760) ok 68 - h id: exact (0.22704) ~ est (0.22704) ok 69 - h id: exact (0.22704) <= max (0.22704) ok 70 - h cn: exact (0.43335) ~ est (0.43335) ok 71 - h cn: exact (0.43335) <= max (0.43335) ok 72 - a_thaliana.blastn ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1 ok 74 - q id: est (0.96667) = fast (0.96667) ok 75 - q cn: est (0.96667) = fast (0.96667) ok 76 - h id: est (0.98305) = fast (0.98305) ok 77 - h cn: est (0.98305) = fast (0.98305) ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1 ok 79 - q id: est (0.96667) = fast (0.96667) ok 80 - q cn: est (0.96667) = fast (0.96667) ok 81 - h id: est (0.98305) = fast (0.98305) ok 82 - h cn: est (0.98305) = fast (0.98305) ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1 ok 84 - q id: est (1.00000) = fast (1.00000) ok 85 - q cn: est (1.00000) = fast (1.00000) ok 86 - h id: est (1.00000) = fast (1.00000) ok 87 - h cn: est (1.00000) = fast (1.00000) ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1 ok 89 - q id: est (1.00000) = fast (1.00000) ok 90 - q cn: est (1.00000) = fast (1.00000) ok 91 - h id: est (1.00000) = fast (1.00000) ok 92 - h cn: est (1.00000) = fast (1.00000) ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1 ok 94 - q id: est (0.92308) = fast (0.92308) ok 95 - q cn: est (0.92308) = fast (0.92308) ok 96 - h id: est (0.92308) = fast (0.92308) ok 97 - h cn: est (0.92308) = fast (0.92308) ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1 ok 99 - q id: est (1.00000) = fast (1.00000) ok 100 - q cn: est (1.00000) = fast (1.00000) ok 101 - h id: est (1.00000) = fast (1.00000) ok 102 - h cn: est (1.00000) = fast (1.00000) ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1 ok 104 - q id: est (1.00000) = fast (1.00000) ok 105 - q cn: est (1.00000) = fast (1.00000) ok 106 - h id: est (1.00000) = fast (1.00000) ok 107 - h cn: est (1.00000) = fast (1.00000) ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1 ok 109 - q id: est (1.00000) = fast (1.00000) ok 110 - q cn: est (1.00000) = fast (1.00000) ok 111 - h id: est (1.00000) = fast (1.00000) ok 112 - h cn: est (1.00000) = fast (1.00000) ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1 ok 114 - q id: est (1.00000) = fast (1.00000) ok 115 - q cn: est (1.00000) = fast (1.00000) ok 116 - h id: est (1.00000) = fast (1.00000) ok 117 - h cn: est (1.00000) = fast (1.00000) ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1 ok 119 - q id: est (1.00000) = fast (1.00000) ok 120 - q cn: est (1.00000) = fast (1.00000) ok 121 - h id: est (1.00000) = fast (1.00000) ok 122 - h cn: est (1.00000) = fast (1.00000) ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1 ok 124 - q id: est (1.00000) = fast (1.00000) ok 125 - q cn: est (1.00000) = fast (1.00000) ok 126 - h id: est (1.00000) = fast (1.00000) ok 127 - h cn: est (1.00000) = fast (1.00000) ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1 ok 129 - q id: est (1.00000) = fast (1.00000) ok 130 - q cn: est (1.00000) = fast (1.00000) ok 131 - h id: est (1.00000) = fast (1.00000) ok 132 - h cn: est (1.00000) = fast (1.00000) ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1 ok 134 - q id: est (1.00000) = fast (1.00000) ok 135 - q cn: est (1.00000) = fast (1.00000) ok 136 - h id: est (1.00000) = fast (1.00000) ok 137 - h cn: est (1.00000) = fast (1.00000) ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1 ok 139 - q id: est (1.00000) = fast (1.00000) ok 140 - q cn: est (1.00000) = fast (1.00000) ok 141 - h id: est (1.00000) = fast (1.00000) ok 142 - h cn: est (1.00000) = fast (1.00000) ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1 ok 144 - q id: est (1.00000) = fast (1.00000) ok 145 - q cn: est (1.00000) = fast (1.00000) ok 146 - h id: est (1.00000) = fast (1.00000) ok 147 - h cn: est (1.00000) = fast (1.00000) ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1 ok 149 - q id: est (1.00000) = fast (1.00000) ok 150 - q cn: est (1.00000) = fast (1.00000) ok 151 - h id: est (1.00000) = fast (1.00000) ok 152 - h cn: est (1.00000) = fast (1.00000) ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1 ok 154 - q id: est (1.00000) = fast (1.00000) ok 155 - q cn: est (1.00000) = fast (1.00000) ok 156 - h id: est (1.00000) = fast (1.00000) ok 157 - h cn: est (1.00000) = fast (1.00000) ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1 ok 159 - q id: est (1.00000) = fast (1.00000) ok 160 - q cn: est (1.00000) = fast (1.00000) ok 161 - h id: est (1.00000) = fast (1.00000) ok 162 - h cn: est (1.00000) = fast (1.00000) ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1 ok 164 - q id: est (1.00000) = fast (1.00000) ok 165 - q cn: est (1.00000) = fast (1.00000) ok 166 - h id: est (1.00000) = fast (1.00000) ok 167 - h cn: est (1.00000) = fast (1.00000) ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1 ok 169 - q id: est (0.95238) = fast (0.95238) ok 170 - q cn: est (0.95238) = fast (0.95238) ok 171 - h id: est (0.95238) = fast (0.95238) ok 172 - h cn: est (0.95238) = fast (0.95238) ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1 ok 174 - q id: est (1.00000) = fast (1.00000) ok 175 - q cn: est (1.00000) = fast (1.00000) ok 176 - h id: est (1.00000) = fast (1.00000) ok 177 - h cn: est (1.00000) = fast (1.00000) ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1 ok 179 - q id: est (0.95238) = fast (0.95238) ok 180 - q cn: est (0.95238) = fast (0.95238) ok 181 - h id: est (0.95238) = fast (0.95238) ok 182 - h cn: est (0.95238) = fast (0.95238) ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1 ok 184 - q id: est (1.00000) = fast (1.00000) ok 185 - q cn: est (1.00000) = fast (1.00000) ok 186 - h id: est (1.00000) = fast (1.00000) ok 187 - h cn: est (1.00000) = fast (1.00000) ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1 ok 189 - q id: est (0.95238) = fast (0.95238) ok 190 - q cn: est (0.95238) = fast (0.95238) ok 191 - h id: est (0.95238) = fast (0.95238) ok 192 - h cn: est (0.95238) = fast (0.95238) ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1 ok 194 - q id: est (1.00000) = fast (1.00000) ok 195 - q cn: est (1.00000) = fast (1.00000) ok 196 - h id: est (1.00000) = fast (1.00000) ok 197 - h cn: est (1.00000) = fast (1.00000) ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1 ok 199 - q id: est (1.00000) = fast (1.00000) ok 200 - q cn: est (1.00000) = fast (1.00000) ok 201 - h id: est (1.00000) = fast (1.00000) ok 202 - h cn: est (1.00000) = fast (1.00000) ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1 ok 204 - q id: est (1.00000) = fast (1.00000) ok 205 - q cn: est (1.00000) = fast (1.00000) ok 206 - h id: est (1.00000) = fast (1.00000) ok 207 - h cn: est (1.00000) = fast (1.00000) ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1 ok 209 - q id: est (1.00000) = fast (1.00000) ok 210 - q cn: est (1.00000) = fast (1.00000) ok 211 - h id: est (1.00000) = fast (1.00000) ok 212 - h cn: est (1.00000) = fast (1.00000) ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1 ok 214 - q id: est (1.00000) = fast (1.00000) ok 215 - q cn: est (1.00000) = fast (1.00000) ok 216 - h id: est (1.00000) = fast (1.00000) ok 217 - h cn: est (1.00000) = fast (1.00000) ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1 ok 219 - q id: est (1.00000) = fast (1.00000) ok 220 - q cn: est (1.00000) = fast (1.00000) ok 221 - h id: est (1.00000) = fast (1.00000) ok 222 - h cn: est (1.00000) = fast (1.00000) ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1 ok 224 - q id: est (1.00000) = fast (1.00000) ok 225 - q cn: est (1.00000) = fast (1.00000) ok 226 - h id: est (1.00000) = fast (1.00000) ok 227 - h cn: est (1.00000) = fast (1.00000) ok 228 - brassica_ATH.WUBLASTN ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3 ok 230 - q id: exact (0.82465) ~ est (0.82343) ok 231 - q id: exact (0.82465) <= max (0.83333) ok 232 - q cn: exact (0.85590) ~ est (0.85312) ok 233 - q cn: exact (0.85590) <= max (0.86458) ok 234 - h id: exact (0.83920) ~ est (0.83920) ok 235 - h id: exact (0.83920) <= max (0.83920) ok 236 - h cn: exact (0.86935) ~ est (0.86935) ok 237 - h cn: exact (0.86935) <= max (0.86935) ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2 ok 239 - q id: exact (0.82486) ~ est (0.82486) ok 240 - q id: exact (0.82486) <= max (0.82486) ok 241 - q cn: exact (0.85122) ~ est (0.85122) ok 242 - q cn: exact (0.85122) <= max (0.85122) ok 243 - h id: exact (0.82955) ~ est (0.82955) ok 244 - h id: exact (0.82955) <= max (0.82955) ok 245 - h cn: exact (0.85606) ~ est (0.85606) ok 246 - h cn: exact (0.85606) <= max (0.85606) ok 247 - no_hsps.blastp ok 248 - tile no_hsps.blastp hit 1 \#hsps 0 ok 249 - tile no_hsps.blastp hit 2 \#hsps 0 ok 250 - tile no_hsps.blastp hit 3 \#hsps 0 ok 251 - tile no_hsps.blastp hit 4 \#hsps 0 ok 252 - tile no_hsps.blastp hit 5 \#hsps 0 ok 253 - tile no_hsps.blastp hit 6 \#hsps 0 ok 254 - tile no_hsps.blastp hit 7 \#hsps 0 ok 255 - tile no_hsps.blastp hit 8 \#hsps 0 ok 256 - tile no_hsps.blastp hit 9 \#hsps 0 ok 257 - tile no_hsps.blastp hit 10 \#hsps 0 ok 258 - tile no_hsps.blastp hit 11 \#hsps 0 ok 259 - tile no_hsps.blastp hit 12 \#hsps 0 ok 260 - tile no_hsps.blastp hit 13 \#hsps 0 ok 261 - tile no_hsps.blastp hit 14 \#hsps 0 ok 262 - tile no_hsps.blastp hit 15 \#hsps 0 ok 263 - tile no_hsps.blastp hit 16 \#hsps 0 ok 264 - tile no_hsps.blastp hit 17 \#hsps 0 ok 265 - tile no_hsps.blastp hit 18 \#hsps 0 ok 266 - tile no_hsps.blastp hit 19 \#hsps 0 ok 267 - tile no_hsps.blastp hit 20 \#hsps 0 ok 268 - tile no_hsps.blastp hit 21 \#hsps 0 ok 269 - tile no_hsps.blastp hit 22 \#hsps 0 ok 270 - tile no_hsps.blastp hit 23 \#hsps 0 ok 271 - tile no_hsps.blastp hit 24 \#hsps 0 ok 272 - tile no_hsps.blastp hit 25 \#hsps 0 ok 273 - tile no_hsps.blastp hit 26 \#hsps 0 ok 274 - tile no_hsps.blastp hit 27 \#hsps 0 ok 275 - tile no_hsps.blastp hit 28 \#hsps 0 ok 276 - tile no_hsps.blastp hit 29 \#hsps 0 ok 277 - tile no_hsps.blastp hit 30 \#hsps 0 ok 278 - tile no_hsps.blastp hit 31 \#hsps 0 ok 279 - tile no_hsps.blastp hit 32 \#hsps 0 ok 280 - tile no_hsps.blastp hit 33 \#hsps 0 ok 281 - tile no_hsps.blastp hit 34 \#hsps 0 ok 282 - tile no_hsps.blastp hit 35 \#hsps 0 ok 283 - tile no_hsps.blastp hit 36 \#hsps 0 ok 284 - tile no_hsps.blastp hit 37 \#hsps 0 ok 285 - tile no_hsps.blastp hit 38 \#hsps 0 ok 286 - tile no_hsps.blastp hit 39 \#hsps 0 ok 287 - tile no_hsps.blastp hit 40 \#hsps 0 ok 288 - tile no_hsps.blastp hit 41 \#hsps 0 ok 289 - tile no_hsps.blastp hit 42 \#hsps 0 ok 290 - tile no_hsps.blastp hit 43 \#hsps 0 ok 291 - tile no_hsps.blastp hit 44 \#hsps 0 ok 292 - tile no_hsps.blastp hit 45 \#hsps 0 ok 293 - tile no_hsps.blastp hit 46 \#hsps 0 ok 294 - tile no_hsps.blastp hit 47 \#hsps 0 ok 295 - tile no_hsps.blastp hit 48 \#hsps 0 ok 296 - tile no_hsps.blastp hit 49 \#hsps 0 ok 297 - tile no_hsps.blastp hit 50 \#hsps 0 ok 298 - tile no_hsps.blastp hit 51 \#hsps 0 ok 299 - tile no_hsps.blastp hit 52 \#hsps 0 ok 300 - tile no_hsps.blastp hit 53 \#hsps 0 ok 301 - tile no_hsps.blastp hit 54 \#hsps 0 ok 302 - tile no_hsps.blastp hit 55 \#hsps 0 ok 303 - tile no_hsps.blastp hit 56 \#hsps 0 ok 304 - tile no_hsps.blastp hit 57 \#hsps 0 ok 305 - tile no_hsps.blastp hit 58 \#hsps 0 ok 306 - tile no_hsps.blastp hit 59 \#hsps 0 ok 307 - tile no_hsps.blastp hit 60 \#hsps 0 ok 308 - tile no_hsps.blastp hit 61 \#hsps 0 ok 309 - tile no_hsps.blastp hit 62 \#hsps 0 ok 310 - tile no_hsps.blastp hit 63 \#hsps 0 ok 311 - tile no_hsps.blastp hit 64 \#hsps 0 ok 312 - tile no_hsps.blastp hit 65 \#hsps 0 ok 313 - tile no_hsps.blastp hit 66 \#hsps 0 ok 314 - tile no_hsps.blastp hit 67 \#hsps 0 ok 315 - tile no_hsps.blastp hit 68 \#hsps 0 ok 316 - tile no_hsps.blastp hit 69 \#hsps 0 ok 317 - tile no_hsps.blastp hit 70 \#hsps 0 ok 318 - tile no_hsps.blastp hit 71 \#hsps 0 ok 319 - tile no_hsps.blastp hit 72 \#hsps 0 ok 320 - tile no_hsps.blastp hit 73 \#hsps 0 ok 321 - tile no_hsps.blastp hit 74 \#hsps 0 ok 322 - tile no_hsps.blastp hit 75 \#hsps 0 ok 323 - tile no_hsps.blastp hit 76 \#hsps 0 ok 324 - tile no_hsps.blastp hit 77 \#hsps 0 ok 325 - tile no_hsps.blastp hit 78 \#hsps 0 ok 326 - tile no_hsps.blastp hit 79 \#hsps 0 ok 327 - tile no_hsps.blastp hit 80 \#hsps 0 ok 328 - tile no_hsps.blastp hit 81 \#hsps 0 ok 329 - tile no_hsps.blastp hit 82 \#hsps 0 ok 330 - tile no_hsps.blastp hit 83 \#hsps 0 ok 331 - tile no_hsps.blastp hit 84 \#hsps 0 ok 332 - tile no_hsps.blastp hit 85 \#hsps 0 ok 333 - tile no_hsps.blastp hit 86 \#hsps 0 ok 334 - tile no_hsps.blastp hit 87 \#hsps 0 ok 335 - tile no_hsps.blastp hit 88 \#hsps 0 ok 336 - tile no_hsps.blastp hit 89 \#hsps 0 ok 337 - tile no_hsps.blastp hit 90 \#hsps 0 ok 338 - tile no_hsps.blastp hit 91 \#hsps 0 ok 339 - tile no_hsps.blastp hit 92 \#hsps 0 ok 340 - tile no_hsps.blastp hit 93 \#hsps 0 ok 341 - tile no_hsps.blastp hit 94 \#hsps 0 ok 342 - tile no_hsps.blastp hit 95 \#hsps 0 ok 343 - tile no_hsps.blastp hit 96 \#hsps 0 ok 344 - tile no_hsps.blastp hit 97 \#hsps 0 ok 345 - tile no_hsps.blastp hit 98 \#hsps 0 ok 346 - tile no_hsps.blastp hit 99 \#hsps 0 ok 347 - tile no_hsps.blastp hit 100 \#hsps 0 ok 348 - tile no_hsps.blastp hit 101 \#hsps 0 ok 349 - tile no_hsps.blastp hit 102 \#hsps 0 ok 350 - tile no_hsps.blastp hit 103 \#hsps 0 ok 351 - tile no_hsps.blastp hit 104 \#hsps 0 ok 352 - tile no_hsps.blastp hit 105 \#hsps 0 ok 353 - tile no_hsps.blastp hit 106 \#hsps 0 ok 354 - tile no_hsps.blastp hit 107 \#hsps 0 ok 355 - tile no_hsps.blastp hit 108 \#hsps 0 ok 356 - tile no_hsps.blastp hit 109 \#hsps 0 ok 357 - tile no_hsps.blastp hit 110 \#hsps 0 ok 358 - tile no_hsps.blastp hit 111 \#hsps 0 ok 359 - tile no_hsps.blastp hit 112 \#hsps 0 ok 360 - tile no_hsps.blastp hit 113 \#hsps 0 ok 361 - tile no_hsps.blastp hit 114 \#hsps 0 ok 362 - tile no_hsps.blastp hit 115 \#hsps 0 ok 363 - tile no_hsps.blastp hit 116 \#hsps 0 ok 364 - tile no_hsps.blastp hit 117 \#hsps 0 ok 365 - tile no_hsps.blastp hit 118 \#hsps 0 ok 366 - tile no_hsps.blastp hit 119 \#hsps 0 ok 367 - tile no_hsps.blastp hit 120 \#hsps 0 ok 368 - tile no_hsps.blastp hit 121 \#hsps 0 ok 369 - tile no_hsps.blastp hit 122 \#hsps 0 ok 370 - tile no_hsps.blastp hit 123 \#hsps 0 ok 371 - tile no_hsps.blastp hit 124 \#hsps 0 ok 372 - tile no_hsps.blastp hit 125 \#hsps 0 ok 373 - tile no_hsps.blastp hit 126 \#hsps 0 ok 374 - tile no_hsps.blastp hit 127 \#hsps 0 ok 375 - tile no_hsps.blastp hit 128 \#hsps 0 ok 376 - tile no_hsps.blastp hit 129 \#hsps 0 ok 377 - tile no_hsps.blastp hit 130 \#hsps 0 ok 378 - tile no_hsps.blastp hit 131 \#hsps 0 ok 379 - tile no_hsps.blastp hit 132 \#hsps 0 ok 380 - tile no_hsps.blastp hit 133 \#hsps 0 ok 381 - tile no_hsps.blastp hit 134 \#hsps 0 ok 382 - tile no_hsps.blastp hit 135 \#hsps 0 ok 383 - tile no_hsps.blastp hit 136 \#hsps 0 ok 384 - tile no_hsps.blastp hit 137 \#hsps 0 ok 385 - tile no_hsps.blastp hit 138 \#hsps 0 ok 386 - tile no_hsps.blastp hit 139 \#hsps 0 ok 387 - tile no_hsps.blastp hit 140 \#hsps 0 ok 388 - tile no_hsps.blastp hit 141 \#hsps 0 ok 389 - tile no_hsps.blastp hit 142 \#hsps 0 ok 390 - tile no_hsps.blastp hit 143 \#hsps 0 ok 391 - tile no_hsps.blastp hit 144 \#hsps 0 ok 392 - tile no_hsps.blastp hit 145 \#hsps 0 ok 393 - tile no_hsps.blastp hit 146 \#hsps 0 ok 394 - tile no_hsps.blastp hit 147 \#hsps 0 ok 395 - tile no_hsps.blastp hit 148 \#hsps 0 ok 396 - tile no_hsps.blastp hit 149 \#hsps 0 ok 397 - tile no_hsps.blastp hit 150 \#hsps 0 ok 398 - tile no_hsps.blastp hit 151 \#hsps 0 ok 399 - tile no_hsps.blastp hit 152 \#hsps 0 ok 400 - tile no_hsps.blastp hit 153 \#hsps 0 ok 401 - tile no_hsps.blastp hit 154 \#hsps 0 ok 402 - tile no_hsps.blastp hit 155 \#hsps 0 ok 403 - tile no_hsps.blastp hit 156 \#hsps 0 ok 404 - tile no_hsps.blastp hit 157 \#hsps 0 ok 405 - tile no_hsps.blastp hit 158 \#hsps 0 ok 406 - tile no_hsps.blastp hit 159 \#hsps 0 ok 407 - tile no_hsps.blastp hit 160 \#hsps 0 ok 408 - tile no_hsps.blastp hit 161 \#hsps 0 ok 409 - tile no_hsps.blastp hit 162 \#hsps 0 ok 410 - tile no_hsps.blastp hit 163 \#hsps 0 ok 411 - tile no_hsps.blastp hit 164 \#hsps 0 ok 412 - tile no_hsps.blastp hit 165 \#hsps 0 ok 413 - tile no_hsps.blastp hit 166 \#hsps 0 ok 414 - tile no_hsps.blastp hit 167 \#hsps 0 ok 415 - tile no_hsps.blastp hit 168 \#hsps 0 ok 416 - tile no_hsps.blastp hit 169 \#hsps 0 ok 417 - tile no_hsps.blastp hit 170 \#hsps 0 ok 418 - tile no_hsps.blastp hit 171 \#hsps 0 ok 419 - tile no_hsps.blastp hit 172 \#hsps 0 ok 420 - tile no_hsps.blastp hit 173 \#hsps 0 ok 421 - tile no_hsps.blastp hit 174 \#hsps 0 ok 422 - tile no_hsps.blastp hit 175 \#hsps 0 ok 423 - tile no_hsps.blastp hit 176 \#hsps 0 ok 424 - tile no_hsps.blastp hit 177 \#hsps 0 ok 425 - tile no_hsps.blastp hit 178 \#hsps 0 ok 426 - tile no_hsps.blastp hit 179 \#hsps 0 ok 427 - tile no_hsps.blastp hit 180 \#hsps 0 ok 428 - tile no_hsps.blastp hit 181 \#hsps 0 ok 429 - tile no_hsps.blastp hit 182 \#hsps 0 ok 430 - tile no_hsps.blastp hit 183 \#hsps 0 ok 431 - tile no_hsps.blastp hit 184 \#hsps 0 ok 432 - tile no_hsps.blastp hit 185 \#hsps 0 ok 433 - tile no_hsps.blastp hit 186 \#hsps 0 ok 434 - tile no_hsps.blastp hit 187 \#hsps 0 ok 435 - tile no_hsps.blastp hit 188 \#hsps 0 ok 436 - tile no_hsps.blastp hit 189 \#hsps 0 ok 437 - tile no_hsps.blastp hit 190 \#hsps 0 ok 438 - tile no_hsps.blastp hit 191 \#hsps 0 ok 439 - tile no_hsps.blastp hit 192 \#hsps 0 ok 440 - tile no_hsps.blastp hit 193 \#hsps 0 ok 441 - tile no_hsps.blastp hit 194 \#hsps 0 ok 442 - tile no_hsps.blastp hit 195 \#hsps 0 ok 443 - tile no_hsps.blastp hit 196 \#hsps 0 ok 444 - tile no_hsps.blastp hit 197 \#hsps 0 ok 445 - tile no_hsps.blastp hit 198 \#hsps 0 ok 446 - tile no_hsps.blastp hit 199 \#hsps 0 ok 447 - tile no_hsps.blastp hit 200 \#hsps 0 ok 448 - tile no_hsps.blastp hit 201 \#hsps 0 ok 449 - tile no_hsps.blastp hit 202 \#hsps 0 ok 450 - tile no_hsps.blastp hit 203 \#hsps 0 ok 451 - tile no_hsps.blastp hit 204 \#hsps 0 ok 452 - tile no_hsps.blastp hit 205 \#hsps 0 ok 453 - tile no_hsps.blastp hit 206 \#hsps 0 ok 454 - tile no_hsps.blastp hit 207 \#hsps 0 ok 455 - tile no_hsps.blastp hit 208 \#hsps 0 ok 456 - tile no_hsps.blastp hit 209 \#hsps 0 ok 457 - tile no_hsps.blastp hit 210 \#hsps 0 ok 458 - tile no_hsps.blastp hit 211 \#hsps 0 ok 459 - tile no_hsps.blastp hit 212 \#hsps 0 ok 460 - tile no_hsps.blastp hit 213 \#hsps 0 ok 461 - tile no_hsps.blastp hit 214 \#hsps 0 ok 462 - tile no_hsps.blastp hit 215 \#hsps 0 ok 463 - tile no_hsps.blastp hit 216 \#hsps 0 ok 464 - tile no_hsps.blastp hit 217 \#hsps 0 ok 465 - tile no_hsps.blastp hit 218 \#hsps 0 ok 466 - tile no_hsps.blastp hit 219 \#hsps 0 ok 467 - tile no_hsps.blastp hit 220 \#hsps 0 ok 468 - tile no_hsps.blastp hit 221 \#hsps 0 ok 469 - tile no_hsps.blastp hit 222 \#hsps 0 ok 470 - tile no_hsps.blastp hit 223 \#hsps 0 ok 471 - tile no_hsps.blastp hit 224 \#hsps 0 ok 472 - tile no_hsps.blastp hit 225 \#hsps 0 ok 473 - tile no_hsps.blastp hit 226 \#hsps 0 ok 474 - tile no_hsps.blastp hit 227 \#hsps 0 ok 475 - tile no_hsps.blastp hit 228 \#hsps 0 ok 476 - tile no_hsps.blastp hit 229 \#hsps 0 ok 477 - tile no_hsps.blastp hit 230 \#hsps 0 ok 478 - tile no_hsps.blastp hit 231 \#hsps 0 ok 479 - tile no_hsps.blastp hit 232 \#hsps 0 ok 480 - tile no_hsps.blastp hit 233 \#hsps 0 ok 481 - tile no_hsps.blastp hit 234 \#hsps 0 ok 482 - tile no_hsps.blastp hit 235 \#hsps 0 ok 483 - tile no_hsps.blastp hit 236 \#hsps 0 ok 484 - tile no_hsps.blastp hit 237 \#hsps 0 ok 485 - tile no_hsps.blastp hit 238 \#hsps 0 ok 486 - tile no_hsps.blastp hit 239 \#hsps 0 ok 487 - tile no_hsps.blastp hit 240 \#hsps 0 ok 488 - tile no_hsps.blastp hit 241 \#hsps 0 ok 489 - tile no_hsps.blastp hit 242 \#hsps 0 ok 490 - tile no_hsps.blastp hit 243 \#hsps 0 ok 491 - tile no_hsps.blastp hit 244 \#hsps 0 ok 492 - tile no_hsps.blastp hit 245 \#hsps 0 ok 493 - tile no_hsps.blastp hit 246 \#hsps 0 ok 494 - tile no_hsps.blastp hit 247 \#hsps 0 ok 495 - tile no_hsps.blastp hit 248 \#hsps 0 ok 496 - tile no_hsps.blastp hit 249 \#hsps 0 ok 497 - tile no_hsps.blastp hit 250 \#hsps 0 ok 498 - tile no_hsps.blastp hit 251 \#hsps 0 ok 499 - tile no_hsps.blastp hit 252 \#hsps 0 ok 500 - tile no_hsps.blastp hit 253 \#hsps 0 ok 501 - tile no_hsps.blastp hit 254 \#hsps 0 ok 502 - tile no_hsps.blastp hit 255 \#hsps 0 ok 503 - tile no_hsps.blastp hit 256 \#hsps 0 ok 504 - tile no_hsps.blastp hit 257 \#hsps 0 ok 505 - tile no_hsps.blastp hit 258 \#hsps 0 ok 506 - tile no_hsps.blastp hit 259 \#hsps 0 ok 507 - tile no_hsps.blastp hit 260 \#hsps 0 ok 508 - tile no_hsps.blastp hit 261 \#hsps 0 ok 509 - tile no_hsps.blastp hit 262 \#hsps 0 ok 510 - tile no_hsps.blastp hit 263 \#hsps 0 ok 511 - tile no_hsps.blastp hit 264 \#hsps 0 ok 512 - tile no_hsps.blastp hit 265 \#hsps 0 ok 513 - tile no_hsps.blastp hit 266 \#hsps 0 ok 514 - tile no_hsps.blastp hit 267 \#hsps 0 ok 515 - tile no_hsps.blastp hit 268 \#hsps 0 ok 516 - tile no_hsps.blastp hit 269 \#hsps 0 ok 517 - tile no_hsps.blastp hit 270 \#hsps 0 ok 518 - tile no_hsps.blastp hit 271 \#hsps 0 ok 519 - tile no_hsps.blastp hit 272 \#hsps 0 ok 520 - tile no_hsps.blastp hit 273 \#hsps 0 ok 521 - tile no_hsps.blastp hit 274 \#hsps 0 ok 522 - tile no_hsps.blastp hit 275 \#hsps 0 ok 523 - tile no_hsps.blastp hit 276 \#hsps 0 ok 524 - tile no_hsps.blastp hit 277 \#hsps 0 ok 525 - tile no_hsps.blastp hit 278 \#hsps 0 ok 526 - tile no_hsps.blastp hit 279 \#hsps 0 ok 527 - tile no_hsps.blastp hit 280 \#hsps 0 ok 528 - tile no_hsps.blastp hit 281 \#hsps 0 ok 529 - tile no_hsps.blastp hit 282 \#hsps 0 ok 530 - tile no_hsps.blastp hit 283 \#hsps 0 ok 531 - tile no_hsps.blastp hit 284 \#hsps 0 ok 532 - tile no_hsps.blastp hit 285 \#hsps 0 ok 533 - tile no_hsps.blastp hit 286 \#hsps 0 ok 534 - tile no_hsps.blastp hit 287 \#hsps 0 ok 535 - tile no_hsps.blastp hit 288 \#hsps 0 ok 536 - tile no_hsps.blastp hit 289 \#hsps 0 ok 537 - tile no_hsps.blastp hit 290 \#hsps 0 ok 538 - tile no_hsps.blastp hit 291 \#hsps 0 ok 539 - tile no_hsps.blastp hit 292 \#hsps 0 ok 540 - tile no_hsps.blastp hit 293 \#hsps 0 ok 541 - tile no_hsps.blastp hit 294 \#hsps 0 ok 542 - tile no_hsps.blastp hit 295 \#hsps 0 ok 543 - tile no_hsps.blastp hit 296 \#hsps 0 ok 544 - tile no_hsps.blastp hit 297 \#hsps 0 ok 545 - tile no_hsps.blastp hit 298 \#hsps 0 ok 546 - tile no_hsps.blastp hit 299 \#hsps 0 ok 547 - tile no_hsps.blastp hit 300 \#hsps 0 ok 548 - tile no_hsps.blastp hit 301 \#hsps 0 ok 549 - tile no_hsps.blastp hit 302 \#hsps 0 ok 550 - tile no_hsps.blastp hit 303 \#hsps 0 ok 551 - tile no_hsps.blastp hit 304 \#hsps 0 ok 552 - tile no_hsps.blastp hit 305 \#hsps 0 ok 553 - tile no_hsps.blastp hit 306 \#hsps 0 ok 554 - tile no_hsps.blastp hit 307 \#hsps 0 ok 555 - tile no_hsps.blastp hit 308 \#hsps 0 ok 556 - tile no_hsps.blastp hit 309 \#hsps 0 ok 557 - tile no_hsps.blastp hit 310 \#hsps 0 ok 558 - tile no_hsps.blastp hit 311 \#hsps 0 ok 559 - tile no_hsps.blastp hit 312 \#hsps 0 ok 560 - tile no_hsps.blastp hit 313 \#hsps 0 ok 561 - tile no_hsps.blastp hit 314 \#hsps 0 ok 562 - tile no_hsps.blastp hit 315 \#hsps 0 ok 563 - tile no_hsps.blastp hit 316 \#hsps 0 ok 564 - tile no_hsps.blastp hit 317 \#hsps 0 ok 565 - tile no_hsps.blastp hit 318 \#hsps 0 ok 566 - tile no_hsps.blastp hit 319 \#hsps 0 ok 567 - tile no_hsps.blastp hit 320 \#hsps 0 ok 568 - tile no_hsps.blastp hit 321 \#hsps 0 ok 569 - tile no_hsps.blastp hit 322 \#hsps 0 ok 570 - tile no_hsps.blastp hit 323 \#hsps 0 ok 571 - tile no_hsps.blastp hit 324 \#hsps 0 ok 572 - tile no_hsps.blastp hit 325 \#hsps 0 ok 573 - tile no_hsps.blastp hit 326 \#hsps 0 ok 574 - tile no_hsps.blastp hit 327 \#hsps 0 ok 575 - tile no_hsps.blastp hit 328 \#hsps 0 ok 576 - tile no_hsps.blastp hit 329 \#hsps 0 ok 577 - tile no_hsps.blastp hit 330 \#hsps 0 ok 578 - tile no_hsps.blastp hit 331 \#hsps 0 ok 579 - tile no_hsps.blastp hit 332 \#hsps 0 ok 580 - tile no_hsps.blastp hit 333 \#hsps 0 ok 581 - tile no_hsps.blastp hit 334 \#hsps 0 ok 582 - tile no_hsps.blastp hit 335 \#hsps 0 ok 583 - tile no_hsps.blastp hit 336 \#hsps 0 ok 584 - tile no_hsps.blastp hit 337 \#hsps 0 ok 585 - tile no_hsps.blastp hit 338 \#hsps 0 ok 586 - tile no_hsps.blastp hit 339 \#hsps 0 ok 587 - tile no_hsps.blastp hit 340 \#hsps 0 ok 588 - tile no_hsps.blastp hit 341 \#hsps 0 ok 589 - tile no_hsps.blastp hit 342 \#hsps 0 ok 590 - tile no_hsps.blastp hit 343 \#hsps 0 ok 591 - tile no_hsps.blastp hit 344 \#hsps 0 ok 592 - tile no_hsps.blastp hit 345 \#hsps 0 ok 593 - tile no_hsps.blastp hit 346 \#hsps 0 ok 594 - tile no_hsps.blastp hit 347 \#hsps 0 ok 595 - tile no_hsps.blastp hit 348 \#hsps 0 ok 596 - tile no_hsps.blastp hit 349 \#hsps 0 ok 597 - tile no_hsps.blastp hit 350 \#hsps 0 ok 598 - tile no_hsps.blastp hit 351 \#hsps 0 ok 599 - tile no_hsps.blastp hit 352 \#hsps 0 ok 600 - tile no_hsps.blastp hit 353 \#hsps 0 ok 601 - tile no_hsps.blastp hit 354 \#hsps 0 ok 602 - tile no_hsps.blastp hit 355 \#hsps 0 ok 603 - tile no_hsps.blastp hit 356 \#hsps 0 ok 604 - tile no_hsps.blastp hit 357 \#hsps 0 ok 605 - tile no_hsps.blastp hit 358 \#hsps 0 ok 606 - tile no_hsps.blastp hit 359 \#hsps 0 ok 607 - tile no_hsps.blastp hit 360 \#hsps 0 ok 608 - tile no_hsps.blastp hit 361 \#hsps 0 ok 609 - tile no_hsps.blastp hit 362 \#hsps 0 ok 610 - tile no_hsps.blastp hit 363 \#hsps 0 ok 611 - tile no_hsps.blastp hit 364 \#hsps 0 ok 612 - tile no_hsps.blastp hit 365 \#hsps 0 ok 613 - tile no_hsps.blastp hit 366 \#hsps 0 ok 614 - tile no_hsps.blastp hit 367 \#hsps 0 ok 615 - tile no_hsps.blastp hit 368 \#hsps 0 ok 616 - tile no_hsps.blastp hit 369 \#hsps 0 ok 617 - tile no_hsps.blastp hit 370 \#hsps 0 ok 618 - tile no_hsps.blastp hit 371 \#hsps 0 ok 619 - tile no_hsps.blastp hit 372 \#hsps 0 ok 620 - tile no_hsps.blastp hit 373 \#hsps 0 ok 621 - tile no_hsps.blastp hit 374 \#hsps 0 ok 622 - tile no_hsps.blastp hit 375 \#hsps 0 ok 623 - tile no_hsps.blastp hit 376 \#hsps 0 ok 624 - tile no_hsps.blastp hit 377 \#hsps 0 ok 625 - tile no_hsps.blastp hit 378 \#hsps 0 ok 626 - tile no_hsps.blastp hit 379 \#hsps 0 ok 627 - tile no_hsps.blastp hit 380 \#hsps 0 ok 628 - tile no_hsps.blastp hit 381 \#hsps 0 ok 629 - tile no_hsps.blastp hit 382 \#hsps 0 ok 630 - tile no_hsps.blastp hit 383 \#hsps 0 ok 631 - tile no_hsps.blastp hit 384 \#hsps 0 ok 632 - tile no_hsps.blastp hit 385 \#hsps 0 ok 633 - tile no_hsps.blastp hit 386 \#hsps 0 ok 634 - tile no_hsps.blastp hit 387 \#hsps 0 ok 635 - tile no_hsps.blastp hit 388 \#hsps 0 ok 636 - tile no_hsps.blastp hit 389 \#hsps 0 ok 637 - tile no_hsps.blastp hit 390 \#hsps 0 ok 638 - tile no_hsps.blastp hit 391 \#hsps 0 ok 639 - tile no_hsps.blastp hit 392 \#hsps 0 ok 640 - tile no_hsps.blastp hit 393 \#hsps 0 ok 641 - tile no_hsps.blastp hit 394 \#hsps 0 ok 642 - tile no_hsps.blastp hit 395 \#hsps 0 ok 643 - tile no_hsps.blastp hit 396 \#hsps 0 ok 644 - tile no_hsps.blastp hit 397 \#hsps 0 ok 645 - tile no_hsps.blastp hit 398 \#hsps 0 ok 646 - tile no_hsps.blastp hit 399 \#hsps 0 ok 647 - tile no_hsps.blastp hit 400 \#hsps 0 ok 648 - tile no_hsps.blastp hit 401 \#hsps 0 ok 649 - tile no_hsps.blastp hit 402 \#hsps 0 ok 650 - tile no_hsps.blastp hit 403 \#hsps 0 ok 651 - tile no_hsps.blastp hit 404 \#hsps 0 ok 652 - tile no_hsps.blastp hit 405 \#hsps 0 ok 653 - tile no_hsps.blastp hit 406 \#hsps 0 ok 654 - tile no_hsps.blastp hit 407 \#hsps 0 ok 655 - tile no_hsps.blastp hit 408 \#hsps 0 ok 656 - tile no_hsps.blastp hit 409 \#hsps 0 ok 657 - tile no_hsps.blastp hit 410 \#hsps 0 ok 658 - tile no_hsps.blastp hit 411 \#hsps 0 ok 659 - tile no_hsps.blastp hit 412 \#hsps 0 ok 660 - tile no_hsps.blastp hit 413 \#hsps 0 ok 661 - tile no_hsps.blastp hit 414 \#hsps 0 ok 662 - tile no_hsps.blastp hit 415 \#hsps 0 ok 663 - catalase-webblast.BLASTP ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1 ok 665 - q id: est (1.00000) = fast (1.00000) ok 666 - q cn: est (1.00000) = fast (1.00000) ok 667 - h id: est (1.00000) = fast (1.00000) ok 668 - h cn: est (1.00000) = fast (1.00000) ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1 ok 670 - q id: est (0.80973) = fast (0.80973) ok 671 - q cn: est (0.89006) = fast (0.89006) ok 672 - h id: est (0.82543) = fast (0.82543) ok 673 - h cn: est (0.90733) = fast (0.90733) ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1 ok 675 - q id: est (0.71670) = fast (0.71670) ok 676 - q cn: est (0.84144) = fast (0.84144) ok 677 - h id: est (0.72747) = fast (0.72747) ok 678 - h cn: est (0.85408) = fast (0.85408) ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1 ok 680 - q id: est (0.58910) = fast (0.58910) ok 681 - q cn: est (0.70860) = fast (0.70860) ok 682 - h id: est (0.65654) = fast (0.65654) ok 683 - h cn: est (0.78972) = fast (0.78972) ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1 ok 685 - q id: est (0.49245) = fast (0.49245) ok 686 - q cn: est (0.65257) = fast (0.65257) ok 687 - h id: est (0.49544) = fast (0.49544) ok 688 - h cn: est (0.65653) = fast (0.65653) ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1 ok 690 - q id: est (0.44366) = fast (0.44366) ok 691 - q cn: est (0.58920) = fast (0.58920) ok 692 - h id: est (0.44787) = fast (0.44787) ok 693 - h cn: est (0.59479) = fast (0.59479) ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1 ok 695 - q id: est (0.42564) = fast (0.42564) ok 696 - q cn: est (0.61282) = fast (0.61282) ok 697 - h id: est (0.43229) = fast (0.43229) ok 698 - h cn: est (0.62240) = fast (0.62240) ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1 ok 700 - q id: est (0.48358) = fast (0.48358) ok 701 - q cn: est (0.63881) = fast (0.63881) ok 702 - h id: est (0.48943) = fast (0.48943) ok 703 - h cn: est (0.64653) = fast (0.64653) ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1 ok 705 - q id: est (0.42308) = fast (0.42308) ok 706 - q cn: est (0.61282) = fast (0.61282) ok 707 - h id: est (0.42969) = fast (0.42969) ok 708 - h cn: est (0.62240) = fast (0.62240) ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1 ok 710 - q id: est (0.39675) = fast (0.39675) ok 711 - q cn: est (0.58933) = fast (0.58933) ok 712 - h id: est (0.39767) = fast (0.39767) ok 713 - h cn: est (0.59070) = fast (0.59070) ok 714 - dcr1_sp.WUBLASTP ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1 ok 716 - q id: est (1.00000) = fast (1.00000) ok 717 - q cn: est (1.00000) = fast (1.00000) ok 718 - h id: est (1.00000) = fast (1.00000) ok 719 - h cn: est (1.00000) = fast (1.00000) ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4 ok 721 - q id: exact (0.36876) ~ est (0.36973) ok 722 - q id: exact (0.36876) <= max (0.37070) ok 723 - q cn: exact (0.55022) ~ est (0.55041) ok 724 - q cn: exact (0.55022) <= max (0.55105) ok 725 - h id: exact (0.35111) ~ est (0.35111) ok 726 - h id: exact (0.35111) <= max (0.35111) ok 727 - h cn: exact (0.52305) ~ est (0.52305) ok 728 - h cn: exact (0.52305) <= max (0.52305) ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1 ok 730 - q id: est (0.38685) = fast (0.38685) ok 731 - q cn: est (0.55397) = fast (0.55397) ok 732 - h id: est (0.37613) = fast (0.37613) ok 733 - h cn: est (0.53863) = fast (0.53863) ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1 ok 735 - q id: est (0.38247) = fast (0.38247) ok 736 - q cn: est (0.55068) = fast (0.55068) ok 737 - h id: est (0.37306) = fast (0.37306) ok 738 - h cn: est (0.53715) = fast (0.53715) ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5 ok 740 - q id: exact (0.35010) ~ est (0.35010) ok 741 - q id: exact (0.35010) <= max (0.35010) ok 742 - q cn: exact (0.53183) ~ est (0.53183) ok 743 - q cn: exact (0.53183) <= max (0.53183) ok 744 - h id: exact (0.35082) ~ est (0.35082) ok 745 - h id: exact (0.35082) <= max (0.35082) ok 746 - h cn: exact (0.53292) ~ est (0.53292) ok 747 - h cn: exact (0.53292) <= max (0.53292) ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8 ok 749 - q id: exact (0.30547) ~ est (0.30659) ok 750 - q id: exact (0.30547) <= max (0.30623) ok 751 - q cn: exact (0.50076) ~ est (0.50205) ok 752 - q cn: exact (0.50076) <= max (0.50076) ok 753 - h id: exact (0.31390) ~ est (0.31179) ok 754 - h id: exact (0.31390) <= max (0.31795) ok 755 - h cn: exact (0.50531) ~ est (0.50557) ok 756 - h cn: exact (0.50531) <= max (0.51091) ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7 ok 758 - q id: exact (0.30136) ~ est (0.30184) ok 759 - q id: exact (0.30136) <= max (0.30498) ok 760 - q cn: exact (0.48688) ~ est (0.48742) ok 761 - q cn: exact (0.48688) <= max (0.49140) ok 762 - h id: exact (0.30944) ~ est (0.31034) ok 763 - h id: exact (0.30944) <= max (0.30988) ok 764 - h cn: exact (0.50178) ~ est (0.50277) ok 765 - h cn: exact (0.50178) <= max (0.50223) ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10 ok 767 - q id: exact (0.28918) ~ est (0.28961) ok 768 - q id: exact (0.28918) <= max (0.28955) ok 769 - q cn: exact (0.46418) ~ est (0.46247) ok 770 - q cn: exact (0.46418) <= max (0.46866) ok 771 - h id: exact (0.30166) ~ est (0.30299) ok 772 - h id: exact (0.30166) <= max (0.30800) ok 773 - h cn: exact (0.48179) ~ est (0.48439) ok 774 - h cn: exact (0.48179) <= max (0.48535) ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8 ok 776 - q id: exact (0.30289) ~ est (0.30238) ok 777 - q id: exact (0.30289) <= max (0.30651) ok 778 - q cn: exact (0.49955) ~ est (0.49787) ok 779 - q cn: exact (0.49955) <= max (0.50362) ok 780 - h id: exact (0.31395) ~ est (0.31347) ok 781 - h id: exact (0.31395) <= max (0.31721) ok 782 - h cn: exact (0.51535) ~ est (0.51578) ok 783 - h cn: exact (0.51535) <= max (0.51814) ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5 ok 785 - q id: exact (0.29334) ~ est (0.29534) ok 786 - q id: exact (0.29334) <= max (0.29810) ok 787 - q cn: exact (0.46617) ~ est (0.46719) ok 788 - q cn: exact (0.46617) <= max (0.47040) ok 789 - h id: exact (0.31176) ~ est (0.31176) ok 790 - h id: exact (0.31176) <= max (0.31176) ok 791 - h cn: exact (0.49299) ~ est (0.49299) ok 792 - h cn: exact (0.49299) <= max (0.49299) ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7 ok 794 - q id: exact (0.30456) ~ est (0.30514) ok 795 - q id: exact (0.30456) <= max (0.30650) ok 796 - q cn: exact (0.48739) ~ est (0.48879) ok 797 - q cn: exact (0.48739) <= max (0.49370) ok 798 - h id: exact (0.32062) ~ est (0.31987) ok 799 - h id: exact (0.32062) <= max (0.32932) ok 800 - h cn: exact (0.51071) ~ est (0.51306) ok 801 - h cn: exact (0.51071) <= max (0.52410) ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8 ok 803 - q id: exact (0.29615) ~ est (0.29879) ok 804 - q id: exact (0.29615) <= max (0.30009) ok 805 - q cn: exact (0.47419) ~ est (0.47394) ok 806 - q cn: exact (0.47419) <= max (0.48119) ok 807 - h id: exact (0.31611) ~ est (0.31482) ok 808 - h id: exact (0.31611) <= max (0.32227) ok 809 - h cn: exact (0.49779) ~ est (0.49788) ok 810 - h cn: exact (0.49779) <= max (0.50616) ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8 ok 812 - q id: exact (0.30390) ~ est (0.30440) ok 813 - q id: exact (0.30390) <= max (0.30701) ok 814 - q cn: exact (0.45874) ~ est (0.45993) ok 815 - q cn: exact (0.45874) <= max (0.45963) ok 816 - h id: exact (0.32282) ~ est (0.32324) ok 817 - h id: exact (0.32282) <= max (0.32560) ok 818 - h cn: exact (0.48052) ~ est (0.48136) ok 819 - h cn: exact (0.48052) <= max (0.48330) ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6 ok 821 - q id: exact (0.29769) ~ est (0.29851) ok 822 - q id: exact (0.29769) <= max (0.29769) ok 823 - q cn: exact (0.48480) ~ est (0.48628) ok 824 - q cn: exact (0.48480) <= max (0.48637) ok 825 - h id: exact (0.30704) ~ est (0.30810) ok 826 - h id: exact (0.30704) <= max (0.30917) ok 827 - h cn: exact (0.50107) ~ est (0.50292) ok 828 - h cn: exact (0.50107) <= max (0.50320) ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6 ok 830 - q id: exact (0.27854) ~ est (0.27854) ok 831 - q id: exact (0.27854) <= max (0.27854) ok 832 - q cn: exact (0.48174) ~ est (0.48174) ok 833 - q cn: exact (0.48174) <= max (0.48174) ok 834 - h id: exact (0.28514) ~ est (0.28623) ok 835 - h id: exact (0.28514) <= max (0.28594) ok 836 - h cn: exact (0.49197) ~ est (0.49154) ok 837 - h cn: exact (0.49197) <= max (0.49237) ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8 ok 839 - q id: exact (0.30362) ~ est (0.30824) ok 840 - q id: exact (0.30362) <= max (0.30852) ok 841 - q cn: exact (0.47111) ~ est (0.47587) ok 842 - q cn: exact (0.47111) <= max (0.47405) ok 843 - h id: exact (0.32347) ~ est (0.32392) ok 844 - h id: exact (0.32347) <= max (0.32643) ok 845 - h cn: exact (0.49310) ~ est (0.49360) ok 846 - h cn: exact (0.49310) <= max (0.49606) ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4 ok 848 - q id: exact (0.29174) ~ est (0.29174) ok 849 - q id: exact (0.29174) <= max (0.29174) ok 850 - q cn: exact (0.46230) ~ est (0.46230) ok 851 - q cn: exact (0.46230) <= max (0.46230) ok 852 - h id: exact (0.30204) ~ est (0.30204) ok 853 - h id: exact (0.30204) <= max (0.30204) ok 854 - h cn: exact (0.47862) ~ est (0.47862) ok 855 - h cn: exact (0.47862) <= max (0.47862) ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6 ok 857 - q id: exact (0.29064) ~ est (0.29089) ok 858 - q id: exact (0.29064) <= max (0.29115) ok 859 - q cn: exact (0.48765) ~ est (0.48670) ok 860 - q cn: exact (0.48765) <= max (0.48868) ok 861 - h id: exact (0.29848) ~ est (0.29887) ok 862 - h id: exact (0.29848) <= max (0.29902) ok 863 - h cn: exact (0.50108) ~ est (0.50116) ok 864 - h cn: exact (0.50108) <= max (0.50163) ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5 ok 866 - q id: exact (0.29510) ~ est (0.29505) ok 867 - q id: exact (0.29510) <= max (0.29510) ok 868 - q cn: exact (0.48982) ~ est (0.49039) ok 869 - q cn: exact (0.48982) <= max (0.49029) ok 870 - h id: exact (0.30019) ~ est (0.30019) ok 871 - h id: exact (0.30019) <= max (0.30019) ok 872 - h cn: exact (0.49906) ~ est (0.49906) ok 873 - h cn: exact (0.49906) <= max (0.49906) ok 874 - 503384.MEGABLAST.2 ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5 ok 876 - q id: exact (0.91435) ~ est (0.91435) ok 877 - q id: exact (0.91435) <= max (0.91435) ok 878 - q cn: exact (0.91435) ~ est (0.91435) ok 879 - q cn: exact (0.91435) <= max (0.91435) ok 880 - h id: exact (0.91157) ~ est (0.91157) ok 881 - h id: exact (0.91157) <= max (0.91157) ok 882 - h cn: exact (0.91157) ~ est (0.91157) ok 883 - h cn: exact (0.91157) <= max (0.91157) ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9 ok 885 - q id: exact (0.92895) ~ est (0.92895) ok 886 - q id: exact (0.92895) <= max (0.92895) ok 887 - q cn: exact (0.92895) ~ est (0.92895) ok 888 - q cn: exact (0.92895) <= max (0.92895) ok 889 - h id: exact (0.92854) ~ est (0.92854) ok 890 - h id: exact (0.92854) <= max (0.92854) ok 891 - h cn: exact (0.92854) ~ est (0.92854) ok 892 - h cn: exact (0.92854) <= max (0.92854) ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3 ok 894 - q id: exact (0.93516) ~ est (0.93516) ok 895 - q id: exact (0.93516) <= max (0.93516) ok 896 - q cn: exact (0.93516) ~ est (0.93516) ok 897 - q cn: exact (0.93516) <= max (0.93516) ok 898 - h id: exact (0.93651) ~ est (0.93651) ok 899 - h id: exact (0.93651) <= max (0.93651) ok 900 - h cn: exact (0.93651) ~ est (0.93651) ok 901 - h cn: exact (0.93651) <= max (0.93651) ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3 ok 903 - q id: exact (0.93064) ~ est (0.93064) ok 904 - q id: exact (0.93064) <= max (0.93064) ok 905 - q cn: exact (0.93064) ~ est (0.93064) ok 906 - q cn: exact (0.93064) <= max (0.93064) ok 907 - h id: exact (0.92885) ~ est (0.92885) ok 908 - h id: exact (0.92885) <= max (0.92885) ok 909 - h cn: exact (0.92885) ~ est (0.92885) ok 910 - h cn: exact (0.92885) <= max (0.92885) ok 911 - bl2seq.blastx.out ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6 ok 913 - q id: est (0.71429) = fast (0.71429) ok 914 - q cn: est (1.00000) = fast (1.00000) ok 915 - q id: exact (0.70536) ~ est (0.70495) ok 916 - q id: exact (0.70536) <= max (0.94286) ok 917 - q cn: exact (0.78810) ~ est (0.78803) ok 918 - q cn: exact (0.78810) <= max (0.96429) ok 919 - q id: est (0.35714) = fast (0.35714) ok 920 - q cn: est (0.57143) = fast (0.57143) ok 921 - h id: exact (0.61923) ~ est (0.61955) ok 922 - h id: exact (0.61923) <= max (0.64231) ok 923 - h cn: exact (0.73077) ~ est (0.73077) ok 924 - h cn: exact (0.73077) <= max (0.75000) ok 925 - dnaEbsub_ecoli.wublastx ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1 ok 927 - q id: est (0.36386) = fast (0.36386) ok 928 - q cn: est (0.53735) = fast (0.53735) ok 929 - h id: est (0.36562) = fast (0.36562) ok 930 - h cn: est (0.53995) = fast (0.53995) ok 931 - tblastn.out ok 932 - tile tblastn.out hit 1 \#hsps 2 ok 933 - q id: exact (0.31250) ~ est (0.33325) ok 934 - q id: exact (0.31250) <= max (0.33333) ok 935 - q cn: exact (0.44792) ~ est (0.47055) ok 936 - q cn: exact (0.44792) <= max (0.45833) ok 937 - h id: exact (0.33333) ~ est (0.33333) ok 938 - h id: exact (0.33333) <= max (0.33333) ok 939 - h cn: exact (0.47059) ~ est (0.47059) ok 940 - h cn: exact (0.47059) <= max (0.47059) ok 941 - tile tblastn.out hit 2 \#hsps 2 ok 942 - q id: exact (0.68750) ~ est (0.68750) ok 943 - q id: exact (0.68750) <= max (0.68750) ok 944 - q cn: exact (0.81250) ~ est (0.81250) ok 945 - q cn: exact (0.81250) <= max (0.81250) ok 946 - h id: est (0.66667) = fast (0.66667) ok 947 - h cn: est (0.77778) = fast (0.77778) ok 948 - h id: est (0.71429) = fast (0.71429) ok 949 - h cn: est (0.85714) = fast (0.85714) ok 950 - dnaEbsub_ecoli.wutblastn ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1 ok 952 - q id: est (0.36386) = fast (0.36386) ok 953 - q cn: est (0.53735) = fast (0.53735) ok 954 - h id: est (0.36562) = fast (0.36562) ok 955 - h cn: est (0.53995) = fast (0.53995) ok 956 - HUMBETGLOA.tblastx ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1 ok 958 - q id: est (0.42308) = fast (0.42308) ok 959 - q cn: est (0.61538) = fast (0.61538) ok 960 - h id: est (0.42308) = fast (0.42308) ok 961 - h cn: est (0.61538) = fast (0.61538) ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1 ok 963 - q id: est (0.47059) = fast (0.47059) ok 964 - q cn: est (0.76471) = fast (0.76471) ok 965 - h id: est (0.47059) = fast (0.47059) ok 966 - h cn: est (0.76471) = fast (0.76471) ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1 ok 968 - q id: est (0.36000) = fast (0.36000) ok 969 - q cn: est (0.56000) = fast (0.56000) ok 970 - h id: est (0.36000) = fast (0.36000) ok 971 - h cn: est (0.56000) = fast (0.56000) ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1 ok 973 - q id: est (0.29268) = fast (0.29268) ok 974 - q cn: est (0.58537) = fast (0.58537) ok 975 - h id: est (0.29268) = fast (0.29268) ok 976 - h cn: est (0.58537) = fast (0.58537) ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1 ok 978 - q id: est (0.38889) = fast (0.38889) ok 979 - q cn: est (0.55556) = fast (0.55556) ok 980 - h id: est (0.38889) = fast (0.38889) ok 981 - h cn: est (0.55556) = fast (0.55556) ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1 ok 983 - q id: est (0.43590) = fast (0.43590) ok 984 - q cn: est (0.51282) = fast (0.51282) ok 985 - h id: est (0.43590) = fast (0.43590) ok 986 - h cn: est (0.51282) = fast (0.51282) ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1 ok 988 - q id: est (0.35714) = fast (0.35714) ok 989 - q cn: est (0.42857) = fast (0.42857) ok 990 - h id: est (0.35714) = fast (0.35714) ok 991 - h cn: est (0.42857) = fast (0.42857) ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1 ok 993 - q id: est (0.33333) = fast (0.33333) ok 994 - q cn: est (0.66667) = fast (0.66667) ok 995 - h id: est (0.33333) = fast (0.33333) ok 996 - h cn: est (0.66667) = fast (0.66667) ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2 ok 998 - q id: exact (0.40541) ~ est (0.40541) ok 999 - q id: exact (0.40541) <= max (0.40541) ok 1000 - q cn: exact (0.56757) ~ est (0.56757) ok 1001 - q cn: exact (0.56757) <= max (0.56757) ok 1002 - h id: est (0.36364) = fast (0.36364) ok 1003 - h cn: est (0.63636) = fast (0.63636) ok 1004 - h id: est (0.42308) = fast (0.42308) ok 1005 - h cn: est (0.53846) = fast (0.53846) ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1 ok 1007 - q id: est (0.29167) = fast (0.29167) ok 1008 - q cn: est (0.39583) = fast (0.39583) ok 1009 - h id: est (0.29167) = fast (0.29167) ok 1010 - h cn: est (0.39583) = fast (0.39583) ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1 ok 1012 - q id: est (0.60000) = fast (0.60000) ok 1013 - q cn: est (0.65000) = fast (0.65000) ok 1014 - h id: est (0.60000) = fast (0.60000) ok 1015 - h cn: est (0.65000) = fast (0.65000) ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1 ok 1017 - q id: est (0.50000) = fast (0.50000) ok 1018 - q cn: est (0.68182) = fast (0.68182) ok 1019 - h id: est (0.50000) = fast (0.50000) ok 1020 - h cn: est (0.68182) = fast (0.68182) ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1 ok 1022 - q id: est (0.29630) = fast (0.29630) ok 1023 - q cn: est (0.48148) = fast (0.48148) ok 1024 - h id: est (0.29630) = fast (0.29630) ok 1025 - h cn: est (0.48148) = fast (0.48148) ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1 ok 1027 - q id: est (0.47826) = fast (0.47826) ok 1028 - q cn: est (0.52174) = fast (0.52174) ok 1029 - h id: est (0.47826) = fast (0.47826) ok 1030 - h cn: est (0.52174) = fast (0.52174) ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1 ok 1032 - q id: est (0.47368) = fast (0.47368) ok 1033 - q cn: est (0.63158) = fast (0.63158) ok 1034 - h id: est (0.47368) = fast (0.47368) ok 1035 - h cn: est (0.63158) = fast (0.63158) ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1 ok 1037 - q id: est (0.44444) = fast (0.44444) ok 1038 - q cn: est (0.55556) = fast (0.55556) ok 1039 - h id: est (0.44444) = fast (0.44444) ok 1040 - h cn: est (0.55556) = fast (0.55556) ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1 ok 1042 - q id: est (0.47059) = fast (0.47059) ok 1043 - q cn: est (0.70588) = fast (0.70588) ok 1044 - h id: est (0.47059) = fast (0.47059) ok 1045 - h cn: est (0.70588) = fast (0.70588) ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1 ok 1047 - q id: est (0.38889) = fast (0.38889) ok 1048 - q cn: est (0.66667) = fast (0.66667) ok 1049 - h id: est (0.38889) = fast (0.38889) ok 1050 - h cn: est (0.66667) = fast (0.66667) ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1 ok 1052 - q id: est (0.27660) = fast (0.27660) ok 1053 - q cn: est (0.48936) = fast (0.48936) ok 1054 - h id: est (0.27660) = fast (0.27660) ok 1055 - h cn: est (0.48936) = fast (0.48936) ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1 ok 1057 - q id: est (0.40000) = fast (0.40000) ok 1058 - q cn: est (0.60000) = fast (0.60000) ok 1059 - h id: est (0.40000) = fast (0.40000) ok 1060 - h cn: est (0.60000) = fast (0.60000) ok 1061 - dnaEbsub_ecoli.wutblastx ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12 ok 1063 - q id: exact (0.40224) ~ est (0.40912) ok 1064 - q id: exact (0.40224) <= max (0.42628) ok 1065 - q cn: exact (0.58494) ~ est (0.58968) ok 1066 - q cn: exact (0.58494) <= max (0.62179) ok 1067 - q id: est (0.25352) = fast (0.25352) ok 1068 - q cn: est (0.47887) = fast (0.47887) ok 1069 - q id: est (0.37500) = fast (0.37500) ok 1070 - q cn: est (0.62500) = fast (0.62500) ok 1071 - q id: exact (0.44118) ~ est (0.44118) ok 1072 - q id: exact (0.44118) <= max (0.44118) ok 1073 - q cn: exact (0.54412) ~ est (0.54412) ok 1074 - q cn: exact (0.54412) <= max (0.54412) ok 1075 - h id: est (0.25352) = fast (0.25352) ok 1076 - h cn: est (0.47887) = fast (0.47887) ok 1077 - h id: exact (0.39848) ~ est (0.40304) ok 1078 - h id: exact (0.39848) <= max (0.40355) ok 1079 - h cn: exact (0.58376) ~ est (0.58889) ok 1080 - h cn: exact (0.58376) <= max (0.58883) ok 1081 - h id: exact (0.44118) ~ est (0.44118) ok 1082 - h id: exact (0.44118) <= max (0.44118) ok 1083 - h cn: exact (0.54412) ~ est (0.54412) ok 1084 - h cn: exact (0.54412) <= max (0.54412) ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2 ok 1086 - q id: exact (0.41818) ~ est (0.41818) ok 1087 - q id: exact (0.41818) <= max (0.41818) ok 1088 - q cn: exact (0.52727) ~ est (0.52727) ok 1089 - q cn: exact (0.52727) <= max (0.52727) ok 1090 - h id: est (0.53333) = fast (0.53333) ok 1091 - h cn: est (0.66667) = fast (0.66667) ok 1092 - h id: est (0.37500) = fast (0.37500) ok 1093 - h cn: est (0.47500) = fast (0.47500) ok 1094 - bug2942: query m0: range correct ok 1095 - bug2942: query m1: range correct ok 1096 - bug2942: query m2: range correct ok 1097 - bug2942: subject all : range correct ok 1098 - get_tiled_alns ok 1099 - got all alns ok 1100 ok 1101 - aln and qfeat lengths correspond ok 1102 - q length correct ok 1103 ok 1104 - features on q and s correspond ok 1105 - aln and hfeat lengths correspond ok 1106 - s length correct ok 1107 ok 1108 - aln and qfeat lengths correspond ok 1109 - q length correct ok 1110 ok 1111 - features on q and s correspond ok 1112 - aln and hfeat lengths correspond ok 1113 - s length correct ok 1114 ok 1115 - aln and qfeat lengths correspond ok 1116 - q length correct ok 1117 ok 1118 - features on q and s correspond ok 1119 - aln and hfeat lengths correspond ok 1120 - s length correct ok 1121 ok 1122 - aln and qfeat lengths correspond ok 1123 - q length correct ok 1124 ok 1125 - features on q and s correspond ok 1126 - aln and hfeat lengths correspond ok 1127 - s length correct ok 1128 ok 1129 - aln and qfeat lengths correspond ok 1130 - q length correct ok 1131 ok 1132 - features on q and s correspond ok 1133 - aln and hfeat lengths correspond ok 1134 - s length correct ok 1135 ok 1136 - aln and qfeat lengths correspond ok 1137 - q length correct ok 1138 ok 1139 - features on q and s correspond ok 1140 - aln and hfeat lengths correspond ok 1141 - s length correct ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 193. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 193. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 193. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 193. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 193. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 193. t/SearchIO/Writer/GbrowseGFF.t ............... 1..4 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 353. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 353. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 353. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 353. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 353. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 353. t/SearchIO/Writer/HSPTableWriter.t ........... 1..8 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SearchIO::Writer::HSPTableWriter; ok 3 - The object isa Bio::Search::Result::ResultI ok 4 ok 5 ok 6 ok 7 - The object isa Bio::Align::AlignI ok 8 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 353. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 353. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 353. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 353. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 353. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 353. t/SearchIO/Writer/HTMLWriter.t ............... 1..8 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SearchIO::Writer::HTMLResultWriter; ok 3 - The object isa Bio::Search::Result::ResultI ok 4 ok 5 ok 6 ok 7 - The object isa Bio::Align::AlignI ok 8 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 353. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 353. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 353. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 353. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 353. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 353. t/SearchIO/Writer/HitTableWriter.t ........... 1..8 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SearchIO::Writer::HitTableWriter; ok 3 - The object isa Bio::Search::Result::ResultI ok 4 ok 5 ok 6 ok 7 - The object isa Bio::Align::AlignI ok 8 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 353. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 353. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 353. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 353. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 353. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 353. t/SearchIO/Writer/TextWriter.t ............... 1..8 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SearchIO::Writer::TextResultWriter; ok 3 - The object isa Bio::Search::Result::ResultI ok 4 ok 5 ok 6 ok 7 - The object isa Bio::Align::AlignI ok 8 ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 7. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 7. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 7. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 7. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 7. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 7. t/SearchIO/axt.t ............................. 1..19 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 245. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 245. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 245. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 245. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 245. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 245. t/SearchIO/blast.t ........................... 1..1348 ok 1 - use Bio::SearchIO; ok 2 ok 3 - database_name() ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 not ok 411 # TODO frac_identical & frac_conserved are still too wrong # Failed (TODO) test at t/SearchIO/blast.t line 584. # '0.852' # > # '0.9' not ok 412 # TODO frac_identical & frac_conserved are still too wrong # Failed (TODO) test at t/SearchIO/blast.t line 585. # '1.599' # <= # '1' ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok 453 ok 454 ok 455 ok 456 ok 457 ok 458 ok 459 ok 460 ok 461 ok 462 ok 463 ok 464 ok 465 ok 466 ok 467 ok 468 ok 469 ok 470 ok 471 ok 472 ok 473 ok 474 ok 475 ok 476 ok 477 ok 478 ok 479 ok 480 ok 481 ok 482 ok 483 ok 484 ok 485 ok 486 ok 487 ok 488 ok 489 ok 490 ok 491 ok 492 ok 493 ok 494 ok 495 ok 496 ok 497 ok 498 ok 499 ok 500 ok 501 ok 502 ok 503 ok 504 ok 505 ok 506 ok 507 ok 508 ok 509 ok 510 ok 511 ok 512 ok 513 ok 514 ok 515 ok 516 ok 517 ok 518 ok 519 ok 520 ok 521 ok 522 ok 523 ok 524 ok 525 ok 526 ok 527 ok 528 ok 529 ok 530 ok 531 ok 532 ok 533 ok 534 ok 535 ok 536 ok 537 ok 538 ok 539 ok 540 ok 541 ok 542 ok 543 ok 544 ok 545 ok 546 ok 547 ok 548 ok 549 ok 550 ok 551 ok 552 ok 553 ok 554 ok 555 ok 556 ok 557 ok 558 ok 559 ok 560 ok 561 ok 562 ok 563 ok 564 ok 565 ok 566 ok 567 ok 568 ok 569 ok 570 ok 571 ok 572 ok 573 ok 574 ok 575 ok 576 ok 577 ok 578 ok 579 ok 580 ok 581 ok 582 ok 583 ok 584 ok 585 ok 586 ok 587 ok 588 ok 589 ok 590 ok 591 ok 592 ok 593 - Multiblast query test ok 594 ok 595 - Multiblast query test ok 596 ok 597 - Multiblast query test ok 598 ok 599 - Multiblast query test ok 600 ok 601 ok 602 ok 603 ok 604 ok 605 ok 606 ok 607 ok 608 ok 609 ok 610 ok 611 ok 612 ok 613 ok 614 ok 615 ok 616 ok 617 ok 618 ok 619 ok 620 ok 621 ok 622 ok 623 ok 624 ok 625 ok 626 ok 627 ok 628 ok 629 ok 630 ok 631 ok 632 ok 633 ok 634 ok 635 ok 636 ok 637 ok 638 ok 639 ok 640 ok 641 ok 642 ok 643 ok 644 ok 645 ok 646 ok 647 ok 648 ok 649 ok 650 ok 651 ok 652 ok 653 ok 654 ok 655 ok 656 ok 657 ok 658 ok 659 ok 660 ok 661 ok 662 ok 663 ok 664 ok 665 ok 666 ok 667 ok 668 ok 669 ok 670 ok 671 ok 672 ok 673 ok 674 ok 675 ok 676 ok 677 ok 678 ok 679 ok 680 ok 681 ok 682 ok 683 ok 684 ok 685 ok 686 ok 687 ok 688 ok 689 ok 690 ok 691 ok 692 ok 693 ok 694 ok 695 ok 696 ok 697 ok 698 ok 699 ok 700 ok 701 ok 702 ok 703 ok 704 ok 705 ok 706 ok 707 ok 708 ok 709 ok 710 ok 711 ok 712 ok 713 ok 714 ok 715 ok 716 ok 717 ok 718 ok 719 ok 720 ok 721 ok 722 ok 723 ok 724 ok 725 ok 726 ok 727 ok 728 ok 729 ok 730 ok 731 ok 732 ok 733 ok 734 ok 735 ok 736 ok 737 ok 738 ok 739 ok 740 ok 741 ok 742 ok 743 ok 744 ok 745 ok 746 ok 747 ok 748 ok 749 ok 750 ok 751 ok 752 ok 753 ok 754 ok 755 ok 756 ok 757 ok 758 ok 759 ok 760 ok 761 ok 762 ok 763 ok 764 ok 765 ok 766 ok 767 ok 768 ok 769 ok 770 ok 771 ok 772 ok 773 ok 774 ok 775 ok 776 ok 777 ok 778 ok 779 ok 780 ok 781 ok 782 ok 783 ok 784 ok 785 ok 786 ok 787 ok 788 ok 789 ok 790 ok 791 ok 792 ok 793 ok 794 ok 795 ok 796 ok 797 ok 798 ok 799 ok 800 ok 801 ok 802 ok 803 ok 804 ok 805 ok 806 ok 807 ok 808 ok 809 ok 810 ok 811 ok 812 ok 813 ok 814 ok 815 ok 816 ok 817 ok 818 ok 819 ok 820 ok 821 ok 822 ok 823 ok 824 ok 825 ok 826 ok 827 ok 828 ok 829 ok 830 ok 831 ok 832 ok 833 ok 834 ok 835 ok 836 ok 837 ok 838 ok 839 ok 840 ok 841 ok 842 ok 843 ok 844 ok 845 ok 846 ok 847 ok 848 ok 849 ok 850 ok 851 ok 852 ok 853 ok 854 ok 855 ok 856 ok 857 ok 858 ok 859 ok 860 ok 861 ok 862 ok 863 ok 864 ok 865 ok 866 ok 867 ok 868 ok 869 ok 870 ok 871 ok 872 ok 873 ok 874 ok 875 ok 876 ok 877 ok 878 ok 879 - The object isa Bio::Search::Result::ResultI ok 880 ok 881 ok 882 ok 883 ok 884 ok 885 ok 886 ok 887 ok 888 ok 889 ok 890 ok 891 ok 892 ok 893 ok 894 ok 895 ok 896 ok 897 ok 898 ok 899 - The object isa Bio::Search::Result::ResultI ok 900 ok 901 ok 902 ok 903 ok 904 ok 905 ok 906 ok 907 ok 908 ok 909 ok 910 ok 911 ok 912 ok 913 ok 914 ok 915 ok 916 ok 917 ok 918 ok 919 ok 920 ok 921 ok 922 ok 923 - The object isa Bio::Search::Result::ResultI ok 924 ok 925 ok 926 ok 927 ok 928 ok 929 ok 930 ok 931 ok 932 ok 933 ok 934 ok 935 ok 936 ok 937 ok 938 ok 939 ok 940 ok 941 ok 942 ok 943 ok 944 ok 945 ok 946 ok 947 - The object isa Bio::Search::Result::ResultI ok 948 ok 949 ok 950 ok 951 ok 952 ok 953 ok 954 ok 955 ok 956 ok 957 ok 958 ok 959 ok 960 ok 961 ok 962 ok 963 ok 964 ok 965 ok 966 ok 967 ok 968 ok 969 ok 970 ok 971 ok 972 - The object isa Bio::Search::Result::ResultI ok 973 ok 974 ok 975 ok 976 ok 977 ok 978 ok 979 ok 980 ok 981 ok 982 ok 983 ok 984 ok 985 ok 986 ok 987 ok 988 ok 989 ok 990 ok 991 ok 992 ok 993 ok 994 ok 995 ok 996 ok 997 ok 998 ok 999 ok 1000 - The object isa Bio::Search::Result::ResultI ok 1001 ok 1002 ok 1003 ok 1004 ok 1005 ok 1006 ok 1007 ok 1008 ok 1009 ok 1010 ok 1011 ok 1012 ok 1013 ok 1014 ok 1015 ok 1016 ok 1017 ok 1018 ok 1019 ok 1020 ok 1021 ok 1022 ok 1023 ok 1024 ok 1025 ok 1026 ok 1027 ok 1028 ok 1029 - The object isa Bio::Search::Result::ResultI ok 1030 ok 1031 ok 1032 ok 1033 ok 1034 ok 1035 ok 1036 ok 1037 ok 1038 ok 1039 ok 1040 ok 1041 ok 1042 ok 1043 ok 1044 ok 1045 ok 1046 ok 1047 ok 1048 - blastxml for f.blastxml ok 1049 - fasta for f.fy ok 1050 - exonerate for f.exonerate ok 1051 - blast for f.tblx ok 1052 - fasta for f.fx ok 1053 - fasta for f.osearch ok 1054 - blast for filename.bls ok 1055 - exonerate for f.exon ok 1056 - fasta for f.SSEARCH.m9 ok 1057 - blast for filename.blast ok 1058 - fasta for f.m9 ok 1059 - blast for f.blx ok 1060 - blastxml for f.xml ok 1061 - fasta for f.fasta ok 1062 - fasta for f.fa ok 1063 - blast for fast.bls ok 1064 - fasta for f.ssearch ok 1065 - fasta for f.psearch ok 1066 ok 1067 ok 1068 ok 1069 ok 1070 ok 1071 ok 1072 ok 1073 ok 1074 ok 1075 ok 1076 ok 1077 ok 1078 ok 1079 ok 1080 ok 1081 - full hit name ok 1082 - hit accession ok 1083 ok 1084 ok 1085 - query start ok 1086 - query start ok 1087 ok 1088 ok 1089 ok 1090 ok 1091 ok 1092 ok 1093 ok 1094 ok 1095 ok 1096 ok 1097 ok 1098 ok 1099 ok 1100 ok 1101 ok 1102 ok 1103 ok 1104 ok 1105 ok 1106 ok 1107 ok 1108 ok 1109 ok 1110 ok 1111 ok 1112 ok 1113 ok 1114 ok 1115 ok 1116 ok 1117 ok 1118 ok 1119 ok 1120 ok 1121 ok 1122 ok 1123 ok 1124 ok 1125 ok 1126 ok 1127 ok 1128 ok 1129 ok 1130 ok 1131 ok 1132 ok 1133 ok 1134 ok 1135 ok 1136 ok 1137 ok 1138 ok 1139 ok 1140 ok 1141 ok 1142 ok 1143 ok 1144 ok 1145 ok 1146 ok 1147 ok 1148 ok 1149 ok 1150 ok 1151 ok 1152 ok 1153 ok 1154 ok 1155 ok 1156 ok 1157 ok 1158 ok 1159 ok 1160 ok 1161 ok 1162 ok 1163 ok 1164 ok 1165 ok 1166 ok 1167 ok 1168 ok 1169 ok 1170 ok 1171 ok 1172 ok 1173 ok 1174 ok 1175 ok 1176 ok 1177 ok 1178 ok 1179 ok 1180 ok 1181 ok 1182 ok 1183 ok 1184 ok 1185 ok 1186 ok 1187 ok 1188 ok 1189 ok 1190 ok 1191 ok 1192 ok 1193 ok 1194 ok 1195 ok 1196 ok 1197 ok 1198 ok 1199 ok 1200 ok 1201 ok 1202 ok 1203 ok 1204 ok 1205 ok 1206 ok 1207 ok 1208 ok 1209 ok 1210 ok 1211 ok 1212 ok 1213 ok 1214 ok 1215 ok 1216 ok 1217 ok 1218 ok 1219 ok 1220 ok 1221 ok 1222 ok 1223 ok 1224 ok 1225 ok 1226 ok 1227 ok 1228 ok 1229 ok 1230 ok 1231 ok 1232 ok 1233 ok 1234 ok 1235 ok 1236 ok 1237 ok 1238 ok 1239 ok 1240 ok 1241 ok 1242 ok 1243 ok 1244 ok 1245 ok 1246 ok 1247 ok 1248 ok 1249 ok 1250 ok 1251 ok 1252 ok 1253 ok 1254 ok 1255 ok 1256 ok 1257 ok 1258 ok 1259 ok 1260 ok 1261 ok 1262 ok 1263 ok 1264 ok 1265 ok 1266 ok 1267 ok 1268 ok 1269 ok 1270 ok 1271 ok 1272 ok 1273 ok 1274 ok 1275 ok 1276 ok 1277 ok 1278 ok 1279 ok 1280 ok 1281 ok 1282 ok 1283 ok 1284 ok 1285 ok 1286 ok 1287 ok 1288 ok 1289 ok 1290 ok 1291 ok 1292 ok 1293 ok 1294 ok 1295 ok 1296 ok 1297 ok 1298 ok 1299 ok 1300 ok 1301 ok 1302 ok 1303 ok 1304 ok 1305 ok 1306 ok 1307 ok 1308 ok 1309 ok 1310 ok 1311 ok 1312 ok 1313 ok 1314 ok 1315 ok 1316 ok 1317 ok 1318 ok 1319 ok 1320 ok 1321 ok 1322 ok 1323 ok 1324 ok 1325 ok 1326 ok 1327 ok 1328 ok 1329 ok 1330 ok 1331 ok 1332 ok 1333 ok 1334 ok 1335 ok 1336 ok 1337 ok 1338 ok 1339 ok 1340 ok 1341 ok 1342 ok 1343 ok 1344 ok 1345 ok 1346 ok 1347 ok 1348 ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 46. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 46. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 46. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 46. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 46. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 46. t/SearchIO/blast_pull.t ...................... 1..289 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 - database_name() ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 not ok 191 # TODO frac_identical failing! # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. # got: '0.946' # expected: '0.943' ok 192 ok 193 ok 194 ok 195 ok 196 - Multiblast query test ok 197 - Multiblast query test ok 198 - Multiblast query test ok 199 - Multiblast query test ok 200 ok 201 ok 202 ok 203 - full hit name ok 204 - hit accession ok 205 ok 206 - query start ok 207 - query start ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127. Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204. Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228. Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248. Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268. Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288. Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308. Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333. Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355. Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385. Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400. Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430. Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458. Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494. Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517. Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538. Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564. Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576. Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605. Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652. Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694. Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740. Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786. Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849. Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887. Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948. Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025. Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093. Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150. Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226. Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274. Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310. Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364. Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400. Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442. Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473. Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535. Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574. Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590. Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618. Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666. Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683. Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701. Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732. Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772. Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807. Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 420. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 420. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 420. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 420. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 420. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 420. t/SearchIO/blasttable.t ...................... 1..165 ok 1 - use Bio::SearchIO; ok 2 - use Bio::Search::SearchUtils; ok 3 - The object isa Bio::Search::Result::ResultI ok 4 ok 5 ok 6 - hit1_bits ok 7 - hit1_name ok 8 - hsp1_bits ok 9 - hsp1_gaps ok 10 - hsp1_he ok 11 - hsp1_hs ok 12 - hsp1_hstr ok 13 - hsp1_qe ok 14 - hsp1_qs ok 15 - hsp1_qstr ok 16 - hsp2_bits ok 17 - hsp2_gaps ok 18 - hsp2_he ok 19 - hsp2_hs ok 20 - hsp2_hstr ok 21 - hsp2_qe ok 22 - hsp2_qs ok 23 - hsp2_qstr ok 24 - hsp3_bits ok 25 - hsp3_gaps ok 26 - hsp3_he ok 27 - hsp3_hs ok 28 - hsp3_hstr ok 29 - hsp3_qe ok 30 - hsp3_qs ok 31 - hsp3_qstr ok 32 - hsp4_bits ok 33 - hsp4_gaps ok 34 - hsp4_he ok 35 - hsp4_hs ok 36 - hsp4_hstr ok 37 - hsp4_qe ok 38 - hsp4_qs ok 39 - hsp4_qstr ok 40 - hsp5_bits ok 41 - hsp5_gaps ok 42 - hsp5_he ok 43 - hsp5_hs ok 44 - hsp5_hstr ok 45 - hsp5_qe ok 46 - hsp5_qs ok 47 - hsp5_qstr ok 48 - hsp6_bits ok 49 - hsp6_gaps ok 50 - hsp6_he ok 51 - hsp6_hs ok 52 - hsp6_hstr ok 53 - hsp6_qe ok 54 - hsp6_qs ok 55 - hsp6_qstr ok 56 - hsp7_bits ok 57 - hsp7_gaps ok 58 - hsp7_he ok 59 - hsp7_hs ok 60 - hsp7_hstr ok 61 - hsp7_qe ok 62 - hsp7_qs ok 63 - hsp7_qstr ok 64 - hsp8_bits ok 65 - hsp8_gaps ok 66 - hsp8_he ok 67 - hsp8_hs ok 68 - hsp8_hstr ok 69 - hsp8_qe ok 70 - hsp8_qs ok 71 - hsp8_qstr ok 72 - query_name ok 73 - The object isa Bio::Search::Result::ResultI ok 74 ok 75 ok 76 - hit1_bits ok 77 - hit1_name ok 78 - hsp1_bits ok 79 - hsp1_gaps ok 80 - hsp1_he ok 81 - hsp1_hs ok 82 - hsp1_hstr ok 83 - hsp1_qe ok 84 - hsp1_qs ok 85 - hsp1_qstr ok 86 - hsp2_bits ok 87 - hsp2_gaps ok 88 - hsp2_he ok 89 - hsp2_hs ok 90 - hsp2_hstr ok 91 - hsp2_qe ok 92 - hsp2_qs ok 93 - hsp2_qstr ok 94 - hsp3_bits ok 95 - hsp3_gaps ok 96 - hsp3_he ok 97 - hsp3_hs ok 98 - hsp3_hstr ok 99 - hsp3_qe ok 100 - hsp3_qs ok 101 - hsp3_qstr ok 102 - hsp4_bits ok 103 - hsp4_gaps ok 104 - hsp4_he ok 105 - hsp4_hs ok 106 - hsp4_hstr ok 107 - hsp4_qe ok 108 - hsp4_qs ok 109 - hsp4_qstr ok 110 - hsp5_bits ok 111 - hsp5_gaps ok 112 - hsp5_he ok 113 - hsp5_hs ok 114 - hsp5_hstr ok 115 - hsp5_qe ok 116 - hsp5_qs ok 117 - hsp5_qstr ok 118 - hsp6_bits ok 119 - hsp6_gaps ok 120 - hsp6_he ok 121 - hsp6_hs ok 122 - hsp6_hstr ok 123 - hsp6_qe ok 124 - hsp6_qs ok 125 - hsp6_qstr ok 126 - hsp7_bits ok 127 - hsp7_gaps ok 128 - hsp7_he ok 129 - hsp7_hs ok 130 - hsp7_hstr ok 131 - hsp7_qe ok 132 - hsp7_qs ok 133 - hsp7_qstr ok 134 - hsp8_bits ok 135 - hsp8_gaps ok 136 - hsp8_he ok 137 - hsp8_hs ok 138 - hsp8_hstr ok 139 - hsp8_qe ok 140 - hsp8_qs ok 141 - hsp8_qstr ok 142 - query_name ok 143 ok 144 ok 145 ok 146 ok 147 - hit score ok 148 - hit raw_score ok 149 - The object isa Bio::SeqFeatureI ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 - The object isa Bio::SeqFeatureI ok 159 ok 160 ok 161 ok 162 - The object isa Bio::SeqFeatureI ok 163 ok 164 ok 165 ok Subroutine start_document redefined at Bio\SearchIO\XML\BlastHandler.pm line 186. Subroutine end_document redefined at Bio\SearchIO\XML\BlastHandler.pm line 203. Subroutine start_element redefined at Bio\SearchIO\XML\BlastHandler.pm line 223. Subroutine end_element redefined at Bio\SearchIO\XML\BlastHandler.pm line 246. Subroutine characters redefined at Bio\SearchIO\XML\BlastHandler.pm line 303. Subroutine eventHandler redefined at Bio\SearchIO\XML\BlastHandler.pm line 309. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190. Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175, line 617. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264, line 617. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284, line 617. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311, line 617. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337, line 617. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357, line 617. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378, line 617. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399, line 617. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420, line 617. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442, line 617. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465, line 617. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487, line 617. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508, line 617. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523, line 617. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540, line 617. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555, line 617. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574, line 617. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599, line 617. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616, line 617. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629, line 617. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646, line 617. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663, line 617. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680, line 617. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700, line 617. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728, line 617. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747, line 617. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763, line 617. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777, line 617. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794, line 617. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815, line 617. t/SearchIO/blastxml.t ........................ 1..391 ok 1 - use Bio::SearchIO; ok 2 ok 3 - The object isa Bio::Search::Result::ResultI ok 4 - database_name() ok 5 - query_name() ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 - database_name() ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 - query name on HSP ok 61 - query desc on HSP ok 62 - hitname ok 63 - hitdesc ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 - The object isa Bio::Search::Hit::HitI ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 - query name on HSP ok 169 - query desc on HSP ok 170 - hitname ok 171 - hitdesc ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 - query name on HSP ok 215 - query desc on HSP ok 216 - hitname ok 217 - hitdesc ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok Subroutine new redefined at Bio\Search\HSP\GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio\Search\HSP\GenericHSP.pm line 216. Subroutine algorithm redefined at Bio\Search\HSP\GenericHSP.pm line 241. Subroutine pvalue redefined at Bio\Search\HSP\GenericHSP.pm line 263. Subroutine evalue redefined at Bio\Search\HSP\GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio\Search\HSP\GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio\Search\HSP\GenericHSP.pm line 350. Subroutine gaps redefined at Bio\Search\HSP\GenericHSP.pm line 383. Subroutine query_string redefined at Bio\Search\HSP\GenericHSP.pm line 413. Subroutine hit_string redefined at Bio\Search\HSP\GenericHSP.pm line 437. Subroutine homology_string redefined at Bio\Search\HSP\GenericHSP.pm line 463. Subroutine length redefined at Bio\Search\HSP\GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio\Search\HSP\GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio\Search\HSP\GenericHSP.pm line 538. Subroutine frame redefined at Bio\Search\HSP\GenericHSP.pm line 578. Subroutine get_aln redefined at Bio\Search\HSP\GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio\Search\HSP\GenericHSP.pm line 679. Subroutine num_identical redefined at Bio\Search\HSP\GenericHSP.pm line 703. Subroutine rank redefined at Bio\Search\HSP\GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio\Search\HSP\GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio\Search\HSP\GenericHSP.pm line 873. Subroutine query redefined at Bio\Search\HSP\GenericHSP.pm line 897. Subroutine feature1 redefined at Bio\Search\HSP\GenericHSP.pm line 905. Subroutine hit redefined at Bio\Search\HSP\GenericHSP.pm line 928. Subroutine feature2 redefined at Bio\Search\HSP\GenericHSP.pm line 936. Subroutine significance redefined at Bio\Search\HSP\GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio\Search\HSP\GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio\Search\HSP\GenericHSP.pm line 1176. Subroutine n redefined at Bio\Search\HSP\GenericHSP.pm line 1197. Subroutine range redefined at Bio\Search\HSP\GenericHSP.pm line 1210. Subroutine links redefined at Bio\Search\HSP\GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio\Search\HSP\GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio\Search\HSP\GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio\Search\HSP\GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio\Search\HSP\GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio\Search\HSP\GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio\Search\HSP\GenericHSP.pm line 1690. Subroutine new redefined at Bio\Search\Hit\GenericHit.pm line 127. Subroutine add_hsp redefined at Bio\Search\Hit\GenericHit.pm line 204. Subroutine hsp_factory redefined at Bio\Search\Hit\GenericHit.pm line 228. Subroutine name redefined at Bio\Search\Hit\GenericHit.pm line 248. Subroutine accession redefined at Bio\Search\Hit\GenericHit.pm line 268. Subroutine description redefined at Bio\Search\Hit\GenericHit.pm line 288. Subroutine length redefined at Bio\Search\Hit\GenericHit.pm line 308. Subroutine algorithm redefined at Bio\Search\Hit\GenericHit.pm line 333. Subroutine raw_score redefined at Bio\Search\Hit\GenericHit.pm line 355. Subroutine score redefined at Bio\Search\Hit\GenericHit.pm line 385. Subroutine significance redefined at Bio\Search\Hit\GenericHit.pm line 400. Subroutine bits redefined at Bio\Search\Hit\GenericHit.pm line 430. Subroutine next_hsp redefined at Bio\Search\Hit\GenericHit.pm line 458. Subroutine hsps redefined at Bio\Search\Hit\GenericHit.pm line 494. Subroutine num_hsps redefined at Bio\Search\Hit\GenericHit.pm line 517. Subroutine rewind redefined at Bio\Search\Hit\GenericHit.pm line 538. Subroutine ambiguous_aln redefined at Bio\Search\Hit\GenericHit.pm line 564. Subroutine overlap redefined at Bio\Search\Hit\GenericHit.pm line 576. Subroutine n redefined at Bio\Search\Hit\GenericHit.pm line 605. Subroutine p redefined at Bio\Search\Hit\GenericHit.pm line 652. Subroutine hsp redefined at Bio\Search\Hit\GenericHit.pm line 694. Subroutine logical_length redefined at Bio\Search\Hit\GenericHit.pm line 740. Subroutine length_aln redefined at Bio\Search\Hit\GenericHit.pm line 786. Subroutine gaps redefined at Bio\Search\Hit\GenericHit.pm line 849. Subroutine matches redefined at Bio\Search\Hit\GenericHit.pm line 887. Subroutine start redefined at Bio\Search\Hit\GenericHit.pm line 948. Subroutine end redefined at Bio\Search\Hit\GenericHit.pm line 1025. Subroutine range redefined at Bio\Search\Hit\GenericHit.pm line 1093. Subroutine frac_identical redefined at Bio\Search\Hit\GenericHit.pm line 1150. Subroutine frac_conserved redefined at Bio\Search\Hit\GenericHit.pm line 1226. Subroutine frac_aligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1274. Subroutine frac_aligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1310. Subroutine num_unaligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1364. Subroutine num_unaligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1400. Subroutine seq_inds redefined at Bio\Search\Hit\GenericHit.pm line 1442. Subroutine strand redefined at Bio\Search\Hit\GenericHit.pm line 1473. Subroutine frame redefined at Bio\Search\Hit\GenericHit.pm line 1535. Subroutine rank redefined at Bio\Search\Hit\GenericHit.pm line 1574. Subroutine locus redefined at Bio\Search\Hit\GenericHit.pm line 1590. Subroutine each_accession_number redefined at Bio\Search\Hit\GenericHit.pm line 1618. Subroutine tiled_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1666. Subroutine query_length redefined at Bio\Search\Hit\GenericHit.pm line 1683. Subroutine ncbi_gi redefined at Bio\Search\Hit\GenericHit.pm line 1701. Subroutine sort_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1732. Subroutine iteration redefined at Bio\Search\Hit\GenericHit.pm line 1772. Subroutine found_again redefined at Bio\Search\Hit\GenericHit.pm line 1807. Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1333. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1341. Subroutine new redefined at Bio\Search\Result\GenericResult.pm line 175. Subroutine algorithm redefined at Bio\Search\Result\GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio\Search\Result\GenericResult.pm line 284. Subroutine next_hit redefined at Bio\Search\Result\GenericResult.pm line 311. Subroutine query_name redefined at Bio\Search\Result\GenericResult.pm line 337. Subroutine query_accession redefined at Bio\Search\Result\GenericResult.pm line 357. Subroutine query_gi redefined at Bio\Search\Result\GenericResult.pm line 378. Subroutine query_length redefined at Bio\Search\Result\GenericResult.pm line 399. Subroutine query_description redefined at Bio\Search\Result\GenericResult.pm line 420. Subroutine database_name redefined at Bio\Search\Result\GenericResult.pm line 442. Subroutine database_letters redefined at Bio\Search\Result\GenericResult.pm line 465. Subroutine database_entries redefined at Bio\Search\Result\GenericResult.pm line 487. Subroutine get_parameter redefined at Bio\Search\Result\GenericResult.pm line 508. Subroutine available_parameters redefined at Bio\Search\Result\GenericResult.pm line 523. Subroutine get_statistic redefined at Bio\Search\Result\GenericResult.pm line 540. Subroutine available_statistics redefined at Bio\Search\Result\GenericResult.pm line 555. Subroutine add_hit redefined at Bio\Search\Result\GenericResult.pm line 574. Subroutine hit_factory redefined at Bio\Search\Result\GenericResult.pm line 599. Subroutine rewind redefined at Bio\Search\Result\GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio\Search\Result\GenericResult.pm line 629. Subroutine add_parameter redefined at Bio\Search\Result\GenericResult.pm line 646. Subroutine add_statistic redefined at Bio\Search\Result\GenericResult.pm line 663. Subroutine num_hits redefined at Bio\Search\Result\GenericResult.pm line 680. Subroutine hits redefined at Bio\Search\Result\GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio\Search\Result\GenericResult.pm line 728. Subroutine program_reference redefined at Bio\Search\Result\GenericResult.pm line 747. Subroutine rid redefined at Bio\Search\Result\GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio\Search\Result\GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio\Search\Result\GenericResult.pm line 794. Subroutine to_string redefined at Bio\Search\Result\GenericResult.pm line 815. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 41. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 41. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 41. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 41. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 41. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 41. t/SearchIO/cross_match.t ..................... 1..15 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 28. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 28. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 28. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 28. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 28. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 28. t/SearchIO/erpin.t ........................... 1..91 ok 1 - use Bio::SearchIO; ok 2 - The object isa Bio::Search::Result::ResultI ok 3 - Result ERPIN ok 4 - Result ERPIN reference ok 5 - Result ERPIN version ok 6 - Result parameters ok 7 - Result statistics ok 8 - Result entries ok 9 - Result letters ok 10 - Result database_name ok 11 - Result num_hits ok 12 - Result program_reference ok 13 - Result query_accession ok 14 - Result query_description ok 15 - Result query_name ok 16 - The object isa Bio::Search::Hit::HitI ok 17 - Hit accession ok 18 - Hit GI ok 19 - Hit algorithm ok 20 - Hit bits ok 21 - Hit description ok 22 - Hit length ok 23 - Hit locus ok 24 - Hit n ok 25 - Hit name ok 26 - Hit num_hsps ok 27 - Hit overlap ok 28 - Hit query_length ok 29 - Hit rank ok 30 - Hit raw_score ok 31 - Hit score ok 32 ok 33 - The object isa Bio::Search::HSP::HSPI ok 34 - HSP algorithm ok 35 ok 36 - The object isa Bio::SeqFeature::Similarity ok 37 - The object isa Bio::SeqFeature::Similarity ok 38 - HSP frame ok 39 - HSP gaps ok 40 - HSP hit isa Bio::SeqFeature::Similarity ok 41 - HSP hit_string ok 42 - HSP homology_string ok 43 - HSP hsp_group ok 44 - HSP hsp_length ok 45 - HSP length ok 46 - HSP links ok 47 - HSP query isa Bio::SeqFeature::Similarity ok 48 - HSP query_string ok 49 - HSP range ok 50 - HSP rank ok 51 ok 52 - HSP expect ok 53 - The object isa Bio::LocatableSeq ok 54 - HSP seq_str ok 55 - HSP start ok 56 - HSP custom_score ok 57 - HSP meta ok 58 ok 59 ok 60 - HSP strand ok 61 ok 62 ok 63 - ERPIN get_aln warning ok 64 - The object isa Bio::Search::HSP::HSPI ok 65 - HSP algorithm ok 66 ok 67 - The object isa Bio::SeqFeature::Similarity ok 68 - The object isa Bio::SeqFeature::Similarity ok 69 - HSP frame ok 70 - HSP gaps ok 71 - HSP hit isa Bio::SeqFeature::Similarity ok 72 - HSP hit_string ok 73 - HSP homology_string ok 74 - HSP query_string ok 75 - HSP hsp_group ok 76 - HSP hsp_length ok 77 - HSP length ok 78 - HSP links ok 79 - The object isa Bio::SeqFeature::Similarity ok 80 - HSP range ok 81 - HSP rank ok 82 ok 83 - HSP end ok 84 - HSP expect ok 85 - The object isa Bio::LocatableSeq ok 86 - HSP seq_str ok 87 - HSP start ok 88 - HSP custom_score ok 89 ok 90 ok 91 - HSP strand ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 42. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 42. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 42. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 42. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 42. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 42. t/SearchIO/exonerate.t ....................... 1..51 ok 1 - use Bio::SearchIO; ok 2 ok 3 # skip no query length available in default output ok 4 ok 5 # skip no hit length available in default output ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 # skip no query length available in default output ok 26 ok 27 # skip no hit length available in default output ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - query_name ok 47 ok 48 - query_name ok 49 ok 50 - query_name ok 51 ok Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 2549. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 2549. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 2549. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 2549. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 2549. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 2549. t/SearchIO/fasta.t ........................... 1..301 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 - TFASTXY ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 - num_identical() ok 289 - num_conserved() ok 290 - bug 2937 and FASTA version 3.5 ok 291 - algorithm version ok 292 - query name ok 293 - query description ok 294 - query length ok 295 - algorithm ok 296 - num_identical() ok 297 - num_conserved() ok 298 - hsp->strand(hit) ok 299 - hsp->hit->strand ok 300 - hsp->strand(query) ok 301 - hsp->query->strand ok Subroutine new redefined at Bio\Search\HSP\GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio\Search\HSP\GenericHSP.pm line 216. Subroutine algorithm redefined at Bio\Search\HSP\GenericHSP.pm line 241. Subroutine pvalue redefined at Bio\Search\HSP\GenericHSP.pm line 263. Subroutine evalue redefined at Bio\Search\HSP\GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio\Search\HSP\GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio\Search\HSP\GenericHSP.pm line 350. Subroutine gaps redefined at Bio\Search\HSP\GenericHSP.pm line 383. Subroutine query_string redefined at Bio\Search\HSP\GenericHSP.pm line 413. Subroutine hit_string redefined at Bio\Search\HSP\GenericHSP.pm line 437. Subroutine homology_string redefined at Bio\Search\HSP\GenericHSP.pm line 463. Subroutine length redefined at Bio\Search\HSP\GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio\Search\HSP\GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio\Search\HSP\GenericHSP.pm line 538. Subroutine frame redefined at Bio\Search\HSP\GenericHSP.pm line 578. Subroutine get_aln redefined at Bio\Search\HSP\GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio\Search\HSP\GenericHSP.pm line 679. Subroutine num_identical redefined at Bio\Search\HSP\GenericHSP.pm line 703. Subroutine rank redefined at Bio\Search\HSP\GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio\Search\HSP\GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio\Search\HSP\GenericHSP.pm line 873. Subroutine query redefined at Bio\Search\HSP\GenericHSP.pm line 897. Subroutine feature1 redefined at Bio\Search\HSP\GenericHSP.pm line 905. Subroutine hit redefined at Bio\Search\HSP\GenericHSP.pm line 928. Subroutine feature2 redefined at Bio\Search\HSP\GenericHSP.pm line 936. Subroutine significance redefined at Bio\Search\HSP\GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio\Search\HSP\GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio\Search\HSP\GenericHSP.pm line 1176. Subroutine n redefined at Bio\Search\HSP\GenericHSP.pm line 1197. Subroutine range redefined at Bio\Search\HSP\GenericHSP.pm line 1210. Subroutine links redefined at Bio\Search\HSP\GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio\Search\HSP\GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio\Search\HSP\GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio\Search\HSP\GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio\Search\HSP\GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio\Search\HSP\GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio\Search\HSP\GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio\Search\HSP\GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio\Search\HSP\GenericHSP.pm line 1690. Subroutine new redefined at Bio\Search\Hit\GenericHit.pm line 127. Subroutine add_hsp redefined at Bio\Search\Hit\GenericHit.pm line 204. Subroutine hsp_factory redefined at Bio\Search\Hit\GenericHit.pm line 228. Subroutine name redefined at Bio\Search\Hit\GenericHit.pm line 248. Subroutine accession redefined at Bio\Search\Hit\GenericHit.pm line 268. Subroutine description redefined at Bio\Search\Hit\GenericHit.pm line 288. Subroutine length redefined at Bio\Search\Hit\GenericHit.pm line 308. Subroutine algorithm redefined at Bio\Search\Hit\GenericHit.pm line 333. Subroutine raw_score redefined at Bio\Search\Hit\GenericHit.pm line 355. Subroutine score redefined at Bio\Search\Hit\GenericHit.pm line 385. Subroutine significance redefined at Bio\Search\Hit\GenericHit.pm line 400. Subroutine bits redefined at Bio\Search\Hit\GenericHit.pm line 430. Subroutine next_hsp redefined at Bio\Search\Hit\GenericHit.pm line 458. Subroutine hsps redefined at Bio\Search\Hit\GenericHit.pm line 494. Subroutine num_hsps redefined at Bio\Search\Hit\GenericHit.pm line 517. Subroutine rewind redefined at Bio\Search\Hit\GenericHit.pm line 538. Subroutine ambiguous_aln redefined at Bio\Search\Hit\GenericHit.pm line 564. Subroutine overlap redefined at Bio\Search\Hit\GenericHit.pm line 576. Subroutine n redefined at Bio\Search\Hit\GenericHit.pm line 605. Subroutine p redefined at Bio\Search\Hit\GenericHit.pm line 652. Subroutine hsp redefined at Bio\Search\Hit\GenericHit.pm line 694. Subroutine logical_length redefined at Bio\Search\Hit\GenericHit.pm line 740. Subroutine length_aln redefined at Bio\Search\Hit\GenericHit.pm line 786. Subroutine gaps redefined at Bio\Search\Hit\GenericHit.pm line 849. Subroutine matches redefined at Bio\Search\Hit\GenericHit.pm line 887. Subroutine start redefined at Bio\Search\Hit\GenericHit.pm line 948. Subroutine end redefined at Bio\Search\Hit\GenericHit.pm line 1025. Subroutine range redefined at Bio\Search\Hit\GenericHit.pm line 1093. Subroutine frac_identical redefined at Bio\Search\Hit\GenericHit.pm line 1150. Subroutine frac_conserved redefined at Bio\Search\Hit\GenericHit.pm line 1226. Subroutine frac_aligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1274. Subroutine frac_aligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1310. Subroutine num_unaligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1364. Subroutine num_unaligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1400. Subroutine seq_inds redefined at Bio\Search\Hit\GenericHit.pm line 1442. Subroutine strand redefined at Bio\Search\Hit\GenericHit.pm line 1473. Subroutine frame redefined at Bio\Search\Hit\GenericHit.pm line 1535. Subroutine rank redefined at Bio\Search\Hit\GenericHit.pm line 1574. Subroutine locus redefined at Bio\Search\Hit\GenericHit.pm line 1590. Subroutine each_accession_number redefined at Bio\Search\Hit\GenericHit.pm line 1618. Subroutine tiled_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1666. Subroutine query_length redefined at Bio\Search\Hit\GenericHit.pm line 1683. Subroutine ncbi_gi redefined at Bio\Search\Hit\GenericHit.pm line 1701. Subroutine sort_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1732. Subroutine iteration redefined at Bio\Search\Hit\GenericHit.pm line 1772. Subroutine found_again redefined at Bio\Search\Hit\GenericHit.pm line 1807. Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1333. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1341. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 313. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 313. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 313. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 313. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 313. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 313. t/SearchIO/gmap_f9.t ......................... 1..54 ok 1 - use Bio::SearchIO; ok 2 - Did we get a Result? isa Bio::Search::Result::GenericResult ok 3 - Did we get the expected number of hits? ok 4 - Did we get the expected algorithm? ok 5 - Did we get the expected query_name? ok 6 - Did we get a Hit? isa Bio::Search::Hit::GenericHit ok 7 - The object isa Bio::Search::Hit::HitI ok 8 - Check the name ok 9 - Check the hit length ok 10 - Check the number of hsps ok 11 - Check the query length ok 12 - The object isa Bio::Search::HSP::HSPI ok 13 - Check the algorithm ok 14 - Count gaps in the query ok 15 - Count gaps in the hit ok 16 - Length of the query ok 17 - Length of the hit ok 18 - Query sequence ok 19 - Hit sequence ok 20 - Check query start ok 21 - Check query end ok 22 - Check query end ok 23 - Check the homology string ok 24 - Check seq_inds ok 25 - Check hit start ok 26 - Check hit end ok 27 - Check hit end ok 28 - Did we get a Result? isa Bio::Search::Result::GenericResult ok 29 - Did we get the expected number of hits? ok 30 - Did we get the expected algorithm? ok 31 - Did we get the expected query_name? ok 32 - The object isa Bio::Search::Hit::HitI ok 33 - Check the name ok 34 - Check the hit length ok 35 - Check the number of hsps ok 36 - Check the query length ok 37 - The object isa Bio::Search::HSP::HSPI ok 38 - Check the algorithm ok 39 - Count gaps in the query ok 40 - Count gaps in the hit ok 41 - Length of the query ok 42 - Length of the hit ok 43 - Query sequence ok 44 - Hit sequence ok 45 - Check query start ok 46 - Check query end ok 47 - Check query end ok 48 - Check the homology string ok 49 - Check seq_inds ok 50 - Check hit start ok 51 - Check hit end ok 52 - Check hit end ok 53 - Can we loop over multiple results properly (expecting 58)? ok 54 - simple query_name now caught, bug 3021 ok Subroutine new redefined at Bio/SearchIO/hmmer.pm line 90. Subroutine _initialize redefined at Bio/SearchIO/hmmer.pm line 142. Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 41. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 41. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 41. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 41. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 41. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 41. t/SearchIO/hmmer.t ........................... 1..295 ok 1 - use Bio::SearchIO; ok 2 - Check for the correct result reference type ok 3 - Check algorithm ok 4 - Check algorithm version ok 5 - Check hmm_name ok 6 - Check sequence_file ok 7 - Check query_name ok 8 - Check query_description ok 9 - Check num_hits ok 10 - Check hit name ok 11 - Check hit raw_score ok 12 - Check hit significance ok 13 - Check for the correct hit reference type ok 14 - Check num_hsps ok 15 - Check for hit hmmfrom value ok 16 - Check for hit hmm to value ok 17 - Check for query alifrom value ok 18 - Check for query ali to value ok 19 - Check for hsp score ok 20 - Check for hsp c-Evalue ok 21 - Check for query string ok 22 - Check for number of gaps in query ok 23 - Check for hit string ok 24 - Check for homology string ok 25 - Check if homology string and hit string have an equal lenght ok 26 - Check if query string and homology string have an equal lenght ok 27 - Check for hit hmmfrom value ok 28 - Check for hit hmm to value ok 29 - Check for query alifrom value ok 30 - Check for query ali to value ok 31 - Check for hsp score ok 32 - Check for hsp c-Evalue ok 33 - Check for query string ok 34 - Check for number of gaps in query ok 35 - Check for hit string ok 36 - Check for homology string ok 37 - Check if homology string and hit string have an equal lenght ok 38 - Check if query string and homology string have an equal lenght ok 39 - Check for the correct result reference type ok 40 - Check algorithm ok 41 - Check algorithm version ok 42 - Check hmm_name ok 43 - Check sequence_file ok 44 - Check database_name ok 45 - Check query_name ok 46 - Check query_description ok 47 - Check num_hits ok 48 - Check hit name ok 49 - Check for hit description ok 50 - Check hit significance ok 51 - Check hit raw_score ok 52 - Check for hsp score ok 53 - Check for hsp c-Evalue ok 54 - Check for query alifrom value ok 55 - Check for query ali to value ok 56 - Check for hit hmmfrom value ok 57 - Check for hit hmm to value ok 58 - Check for query seq_id ok 59 - Check for hit seq_id ok 60 - Check for the correct result reference type ok 61 - Check algorithm ok 62 - Check algorithm version ok 63 - Check hmm_name ok 64 - Check sequence_file ok 65 - Check query_name ok 66 - Check query_description ok 67 - Check num_hits ok 68 - Check hit name ok 69 - Check for hit description ok 70 - Check hit significance ok 71 - Check hit raw_score ok 72 - Check for hsp score ok 73 - Check for hsp evalue ok 74 - Check for query alifrom value ok 75 - Check for query ali to value ok 76 - Check for hit hmmfrom value ok 77 - Check for hit hmm to value ok 78 - Check for query seq_id ok 79 - Check for hit seq_id ok 80 - Check for hiy string ok 81 - Check for query string ok 82 - Check for homology string ok 83 - Check for nomatch indices in query ok 84 - Check for nomatch indices in hit ok 85 - Check for gap indices in query ok 86 - Check for gap indices in hit ok 87 - Check for the correct result reference type ok 88 - Check algorithm ok 89 - Check algorithm version ok 90 - Check hmm_name ok 91 - Check database_name ok 92 - Check sequence_file ok 93 - Check query_name ok 94 - Check query_accession ok 95 - Check query_description ok 96 - Check num_hits ok 97 - Check hit name ok 98 - Check for hit description ok 99 - Check hit significance ok 100 - Check hit raw_score ok 101 - Check for hsp score ok 102 - Check for hsp evalue ok 103 - Check for query alifrom value ok 104 - Check for query ali to value ok 105 - Check for hit hmmfrom value ok 106 - Check for hit hmm to value ok 107 - Check for query seq_id ok 108 - Check for hit seq_id ok 109 - Check for hiy string ok 110 - Check for homology string ok 111 - Check for query string ok 112 - Check hit name ok 113 - Check for hit description ok 114 - Check hit significance ok 115 - Check hit raw_score ok 116 - Check for hsp seq_str ok 117 - Check for the correct result reference type ok 118 - Check algorithm ok 119 - Check algorithm version ok 120 - Check hmm_name ok 121 - Check sequence_file ok 122 - Check query_name ok 123 - Check query_length ok 124 - Check query_description ok 125 - Check num_hits ok 126 - Check for the correct hit reference type ok 127 - Check hit name ok 128 - Check for hit description ok 129 - Check hit raw_score ok 130 - Check hit significance ok 131 - Check num_hsps ok 132 - Check for correct hsp reference type ok 133 - Check for hit hmmfrom value ok 134 - Check for hit hmm to value ok 135 - Check for query alifrom value ok 136 - Check for query ali to value ok 137 - Check for hsp score ok 138 - Check for hsp c-Evalue ok 139 - Check for query string ok 140 - Check for hit string ok 141 - Check for homology string ok 142 - Check for the correct result reference type ok 143 - Check algorithm ok 144 - Check algorithm version ok 145 - Check hmm_name ok 146 - Check sequence_file ok 147 - Check query_name ok 148 - Check query_length ok 149 - Check query_description ok 150 - Check num_hits ok 151 - Check for the correct result reference type ok 152 - Check algorithm ok 153 - Check algorithm version ok 154 - Check hmm_name ok 155 - Check sequence_file ok 156 - Check query_name ok 157 - Check query_length ok 158 - Check query_description ok 159 - Check num_hits ok 160 - Check for the correct hit reference type ok 161 - Check hit name ok 162 - Check for hit description ok 163 - Check hit raw_score ok 164 - Check hit significance ok 165 - Check num_hsps ok 166 - Check for correct hsp reference type ok 167 - Check for hit envfrom value ok 168 - Check for hit env to value ok 169 - Check for query hmmfrom value ok 170 - Check for query hmm to value ok 171 - Check for hsp score ok 172 - Check for hsp c-Evalue ok 173 - Check for correct hsp reference type ok 174 - Check for hit envfrom value ok 175 - Check for hit env to value ok 176 - Check for query hmmfrom value ok 177 - Check for query hmm to value ok 178 - Check for hsp score ok 179 - Check for hsp c-Evalue ok 180 - Check for correct hsp reference type ok 181 - Check for hit envfrom value ok 182 - Check for hit env to value ok 183 - Check for query hmmfrom value ok 184 - Check for query hmm to value ok 185 - Check for hsp score ok 186 - Check for hsp c-Evalue ok 187 - Check for correct hsp reference type ok 188 - Check for hit envfrom value ok 189 - Check for hit env to value ok 190 - Check for query hmmfrom value ok 191 - Check for query hmm to value ok 192 - Check for hsp score ok 193 - Check for hsp c-Evalue ok 194 - Check for correct hsp reference type ok 195 - Check for hit envfrom value ok 196 - Check for hit env to value ok 197 - Check for query hmmfrom value ok 198 - Check for query hmm to value ok 199 - Check for hsp score ok 200 - Check for hsp c-Evalue ok 201 - Check for correct hsp reference type ok 202 - Check for hit envfrom value ok 203 - Check for hit env to value ok 204 - Check for query hmmfrom value ok 205 - Check for query hmm to value ok 206 - Check for hsp score ok 207 - Check for hsp c-Evalue ok 208 - Check for the correct hit reference type ok 209 - Check hit name ok 210 - Check for hit description ok 211 - Check hit raw_score ok 212 - Check hit significance ok 213 - Check num_hsps ok 214 - Check for correct hsp reference type ok 215 - Check for hit envfrom value ok 216 - Check for hit env to value ok 217 - Check for query hmmfrom value ok 218 - Check for query hmm to value ok 219 - Check for hsp score ok 220 - Check for hsp c-Evalue ok 221 - Check for correct hsp reference type ok 222 - Check for hit envfrom value ok 223 - Check for hit env to value ok 224 - Check for query hmmfrom value ok 225 - Check for query hmm to value ok 226 - Check for hsp score ok 227 - Check for hsp c-Evalue ok 228 - Check for correct hsp reference type ok 229 - Check for hit envfrom value ok 230 - Check for hit env to value ok 231 - Check for query hmmfrom value ok 232 - Check for query hmm to value ok 233 - Check for hsp score ok 234 - Check for hsp c-Evalue ok 235 - Check for the correct result reference type ok 236 - Check algorithm ok 237 - Check algorithm version ok 238 - Check hmm_name ok 239 - Check sequence_file ok 240 - Check query_name ok 241 - Check query_length ok 242 - Check query_description ok 243 - Check num_hits ok 244 - Check for the correct hit reference type ok 245 - Check hit name ok 246 - Check for hit description ok 247 - Check hit raw_score ok 248 - Check hit significance ok 249 - Check num_hsps ok 250 - Check for correct hsp reference type ok 251 - Check hit sequence ok 252 - Check query sequence ok 253 - Check for correct hsp reference type ok 254 - Check hit sequence ok 255 - Check query sequence ok 256 - Check for the correct hit reference type ok 257 - Check hit name ok 258 - Check for hit description ok 259 - Check hit raw_score ok 260 - Check hit significance ok 261 - Check num_hsps ok 262 - Check for correct hsp reference type ok 263 - Check hit sequence ok 264 - Check query sequence ok 265 - Check for correct hsp reference type ok 266 - Check hit sequence ok 267 - Check query sequence ok 268 - Check for the correct hit reference type ok 269 - Check hit name ok 270 - Check for hit description ok 271 - Check hit raw_score ok 272 - Check hit significance ok 273 - Check num_hsps ok 274 - Check for correct hsp reference type ok 275 - Check hit sequence ok 276 - Check query sequence ok 277 - Check for correct hsp reference type ok 278 - Check hit sequence ok 279 - Check query sequence ok 280 - Check if loading hmmpfam output via the hmm2 parser directly works ok 281 - Check for the correct result reference type ok 282 - Check if loading hmmsearch2 output via the hmm2 parser directly works ok 283 - Check for the correct result reference type ok 284 - Check if loading hmmscan output via the hmm3 parser directly works ok 285 - Check for the correct result reference type ok 286 - Check if loading hmmsearch3 output via the hmm3 parser directly works ok 287 - Check for the correct result reference type ok 288 - Check if selecting the correct hmmpfam parser using -version works ok 289 - Check for the correct result reference type ok 290 - Check if selecting the correct hmmsearch2 parser using -version works ok 291 - Check for the correct result reference type ok 292 - Check if selecting the correct hmmscan parser using -version works ok 293 - Check for the correct result reference type ok 294 - Check if selecting the correct hmmsearch3 parser using -version works ok 295 - Check for the correct result reference type ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 14. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 14. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 14. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 14. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 14. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 14. t/SearchIO/hmmer_pull.t ...................... 1..290 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 80. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 80. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 80. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 80. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 80. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 80. t/SearchIO/infernal.t ........................ 1..412 ok 1 - use Bio::SearchIO; ok 2 - The object isa Bio::Search::Result::ResultI ok 3 - Result ok 4 - Result reference ok 5 - Result version ok 6 - Result parameters ok 7 - Result statistics ok 8 - Result entries ok 9 - Result letters ok 10 - Result database_name ok 11 - Result num_hits ok 12 - Result program_reference ok 13 - Result query_accession ok 14 - Result query_description ok 15 - Result query_length ok 16 - Result query_name ok 17 - The object isa Bio::Search::Hit::HitI ok 18 - Hit GI ok 19 - Hit accession ok 20 - Hit algorithm ok 21 - Hit bits ok 22 - Hit description ok 23 - Hit locus ok 24 - Hit n ok 25 - Hit name ok 26 - Hit num_hsps ok 27 - Hit length_aln() not implemented ok 28 - Hit num_unaligned_hit() not implemented ok 29 - Hit num_unaligned_query() not implemented ok 30 - Hit num_unaligned_sbjct() not implemented ok 31 - Hit start not implemented ok 32 - Hit end not implemented ok 33 - Hit strand not implemented ok 34 - Hit logical_length not implemented ok 35 - Hit frac_aligned_hit not implemented ok 36 - Hit frac_aligned_query not implemented ok 37 - Hit frac_conserved not implemented ok 38 - Hit frac_identical not implemented ok 39 - Hit matches not implemented ok 40 - Hit gaps not implemented ok 41 - Hit frame not implemented ok 42 - Hit range not implemented ok 43 - Hit seq_inds not implemented ok 44 - Hit length ok 45 - Hit overlap ok 46 - Hit query_length ok 47 - Hit rank ok 48 - Hit raw_score ok 49 - Hit score ok 50 - Hit p ok 51 ok 52 - The object isa Bio::Search::HSP::HSPI ok 53 - HSP algorithm ok 54 ok 55 - The object isa Bio::SeqFeature::Similarity ok 56 - The object isa Bio::SeqFeature::Similarity ok 57 ok 58 ok 59 - HSP frame ok 60 - HSP gaps ok 61 - Hit length ok 62 - The object isa Bio::Align::AlignI ok 63 - HSP hit isa Bio::SeqFeature::Similarity ok 64 - HSP hit_string ok 65 - HSP homology_string ok 66 - HSP hsp_group ok 67 - HSP hsp_length ok 68 - HSP length ok 69 - HSP links ok 70 - HSP n ok 71 - HSP pvalue ok 72 - HSP query isa Bio::SeqFeature::Similarity ok 73 - HSP query_string ok 74 - HSP range ok 75 - HSP rank ok 76 ok 77 - HSP end ok 78 - HSP expect ok 79 - HSP seq_inds not implemented ok 80 - HSP matches not implemented ok 81 - HSP frac_conserved not implemented ok 82 - HSP frac_identical not implemented ok 83 - HSP num_conserved not implemented ok 84 - HSP num_identical not implemented ok 85 - HSP percent_identity not implemented ok 86 - HSP cigar_string not implemented ok 87 - HSP cigar_string not implemented ok 88 - The object isa Bio::LocatableSeq ok 89 - HSP seq_str ok 90 - HSP start ok 91 - HSP custom_score ok 92 - HSP meta ok 93 - HSP strand ok 94 - The object isa Bio::Search::HSP::HSPI ok 95 - HSP algorithm ok 96 ok 97 - The object isa Bio::SeqFeature::Similarity ok 98 - The object isa Bio::SeqFeature::Similarity ok 99 - HSP frame ok 100 - HSP gaps ok 101 - The object isa Bio::Align::AlignI ok 102 - HSP hit isa Bio::SeqFeature::Similarity ok 103 - HSP hit_string ok 104 - HSP homology_string ok 105 - HSP hsp_group ok 106 - HSP hsp_length ok 107 - HSP length ok 108 - HSP links ok 109 - HSP n ok 110 - HSP pvalue ok 111 - HSP query isa Bio::SeqFeature::Similarity ok 112 - HSP query_string ok 113 - HSP range ok 114 - HSP rank ok 115 ok 116 - HSP end ok 117 - HSP expect ok 118 - The object isa Bio::LocatableSeq ok 119 - HSP seq_str ok 120 - HSP start ok 121 - HSP custom_score ok 122 - HSP meta ok 123 - HSP strand ok 124 - The object isa Bio::Search::Result::ResultI ok 125 - Result CMSEARCH ok 126 - Result CMSEARCH reference ok 127 - Result CMSEARCH version ok 128 - Result parameters ok 129 - Result statistics ok 130 - Result entries ok 131 - Result letters ok 132 - Result database_name ok 133 - Result num_hits ok 134 - Result program_reference ok 135 - Result query_accession ok 136 - Result query_description ok 137 - Result query_length ok 138 - Result query_name ok 139 - The object isa Bio::Search::Hit::HitI ok 140 - Hit GI ok 141 - Hit accession ok 142 - Hit algorithm ok 143 - Hit bits ok 144 - Hit description ok 145 - Hit locus ok 146 - Hit n ok 147 - Hit name ok 148 - Hit num_hsps ok 149 - No p values ok 150 - Hit length ok 151 - Hit overlap ok 152 - Hit query_length ok 153 - Hit rank ok 154 - Hit raw_score ok 155 - Hit score ok 156 ok 157 - The object isa Bio::Search::HSP::HSPI ok 158 - HSP algorithm ok 159 ok 160 - The object isa Bio::SeqFeature::Similarity ok 161 - The object isa Bio::SeqFeature::Similarity ok 162 ok 163 ok 164 - HSP frame ok 165 - HSP gaps ok 166 - Hit length ok 167 - The object isa Bio::Align::AlignI ok 168 - HSP hit isa Bio::SeqFeature::Similarity ok 169 - HSP hit_string ok 170 - HSP homology_string ok 171 - HSP hsp_group ok 172 - HSP hsp_length ok 173 - HSP length ok 174 - HSP links ok 175 - HSP n ok 176 - HSP pvalue ok 177 - HSP query isa Bio::SeqFeature::Similarity ok 178 - HSP query_string ok 179 - HSP range ok 180 - HSP rank ok 181 ok 182 - HSP end ok 183 - HSP expect ok 184 - The object isa Bio::LocatableSeq ok 185 - HSP seq_str ok 186 - HSP start ok 187 - HSP custom_score ok 188 - HSP meta ok 189 - HSP strand ok 190 - The object isa Bio::Search::HSP::HSPI ok 191 - HSP algorithm ok 192 ok 193 - The object isa Bio::SeqFeature::Similarity ok 194 - The object isa Bio::SeqFeature::Similarity ok 195 - HSP frame ok 196 - HSP gaps ok 197 - The object isa Bio::Align::AlignI ok 198 - HSP hit isa Bio::SeqFeature::Similarity ok 199 - HSP hit_string ok 200 - HSP homology_string ok 201 - HSP hsp_group ok 202 - HSP hsp_length ok 203 - HSP length ok 204 - HSP links ok 205 - HSP n ok 206 - HSP pvalue ok 207 - HSP query isa Bio::SeqFeature::Similarity ok 208 - HSP query_string ok 209 - HSP range ok 210 - HSP rank ok 211 ok 212 - HSP end ok 213 - HSP expect ok 214 - The object isa Bio::LocatableSeq ok 215 - HSP seq_str ok 216 - HSP start ok 217 - HSP custom_score ok 218 - HSP meta ok 219 - HSP strand ok 220 - The object isa Bio::Search::Hit::HitI ok 221 - Hit accession ok 222 - Hit GI ok 223 - Hit algorithm ok 224 - Hit bits ok 225 - Hit description ok 226 - Hit length ok 227 - Hit locus ok 228 - Hit n ok 229 - Hit name ok 230 - Hit num_hsps ok 231 - Hit overlap ok 232 - Hit query_length ok 233 - Hit rank ok 234 - Hit raw_score ok 235 - Hit score ok 236 ok 237 - The object isa Bio::Search::HSP::HSPI ok 238 - HSP algorithm ok 239 ok 240 - The object isa Bio::SeqFeature::Similarity ok 241 - The object isa Bio::SeqFeature::Similarity ok 242 - HSP frame ok 243 - HSP gaps ok 244 - The object isa Bio::Align::AlignI ok 245 - HSP hit isa Bio::SeqFeature::Similarity ok 246 - HSP hit_string ok 247 - HSP homology_string ok 248 - HSP hsp_group ok 249 - HSP hsp_length ok 250 - HSP length ok 251 - HSP links ok 252 - HSP n ok 253 - HSP query isa Bio::SeqFeature::Similarity ok 254 - HSP query_string ok 255 - HSP range ok 256 - HSP rank ok 257 ok 258 - HSP end ok 259 - HSP expect ok 260 - The object isa Bio::LocatableSeq ok 261 - HSP seq_str ok 262 - HSP start ok 263 - HSP custom_score ok 264 - HSP meta ok 265 - HSP strand ok 266 - HSP meta gap bug ok 267 - HSP meta ok 268 - HSP meta ok 269 ok 270 ok 271 - The object isa Bio::Search::Result::ResultI ok 272 - Result CMSEARCH ok 273 - Result CMSEARCH reference ok 274 - Result CMSEARCH version ok 275 - Result parameters ok 276 - Result statistics ok 277 - Result entries ok 278 - Result letters ok 279 - Result database_name ok 280 - Result num_hits ok 281 - Result program_reference ok 282 - Result query_accession ok 283 - Result query_description ok 284 - Result query_length ok 285 - Result query_name ok 286 - The object isa Bio::Search::Hit::HitI ok 287 - Hit GI ok 288 - Hit accession ok 289 - Hit algorithm ok 290 - Hit bits ok 291 - Hit description ok 292 - Hit locus ok 293 - Hit n ok 294 - Hit name ok 295 - Hit num_hsps ok 296 - No p values ok 297 - Hit length ok 298 - Hit overlap ok 299 - Hit query_length ok 300 - Hit rank ok 301 - Hit raw_score ok 302 - Hit score ok 303 ok 304 - The object isa Bio::Search::HSP::HSPI ok 305 - HSP algorithm ok 306 ok 307 - The object isa Bio::SeqFeature::Similarity ok 308 - The object isa Bio::SeqFeature::Similarity ok 309 ok 310 ok 311 - HSP frame ok 312 - HSP gaps ok 313 - Hit length ok 314 - The object isa Bio::Align::AlignI ok 315 - HSP hit isa Bio::SeqFeature::Similarity ok 316 - HSP hit_string ok 317 - HSP homology_string ok 318 - HSP hsp_group ok 319 - HSP hsp_length ok 320 - HSP length ok 321 - HSP links ok 322 - HSP n ok 323 - HSP pvalue ok 324 - HSP query isa Bio::SeqFeature::Similarity ok 325 - HSP query_string ok 326 - HSP range ok 327 - HSP rank ok 328 ok 329 - HSP end ok 330 - HSP expect ok 331 - The object isa Bio::LocatableSeq ok 332 - HSP seq_str ok 333 - HSP start ok 334 - HSP custom_score ok 335 - HSP meta ok 336 - HSP strand ok 337 - The object isa Bio::Search::HSP::HSPI ok 338 - HSP algorithm ok 339 ok 340 - The object isa Bio::SeqFeature::Similarity ok 341 - The object isa Bio::SeqFeature::Similarity ok 342 - HSP frame ok 343 - HSP gaps ok 344 - The object isa Bio::Align::AlignI ok 345 - HSP hit isa Bio::SeqFeature::Similarity ok 346 - HSP hit_string ok 347 - HSP homology_string ok 348 - HSP hsp_group ok 349 - HSP hsp_length ok 350 - HSP length ok 351 - HSP links ok 352 - HSP n ok 353 - HSP pvalue ok 354 - HSP query isa Bio::SeqFeature::Similarity ok 355 - HSP query_string ok 356 - HSP range ok 357 - HSP rank ok 358 ok 359 - HSP end ok 360 - HSP expect ok 361 - The object isa Bio::LocatableSeq ok 362 - HSP seq_str ok 363 - HSP start ok 364 - HSP custom_score ok 365 - HSP meta ok 366 - HSP strand ok 367 - The object isa Bio::Search::Hit::HitI ok 368 - Hit accession ok 369 - Hit GI ok 370 - Hit algorithm ok 371 - Hit bits ok 372 - Hit description ok 373 - Hit length ok 374 - Hit locus ok 375 - Hit n ok 376 - Hit name ok 377 - Hit num_hsps ok 378 - Hit overlap ok 379 - Hit query_length ok 380 - Hit rank ok 381 - Hit raw_score ok 382 - Hit score ok 383 ok 384 - The object isa Bio::Search::HSP::HSPI ok 385 - HSP algorithm ok 386 ok 387 - The object isa Bio::SeqFeature::Similarity ok 388 - The object isa Bio::SeqFeature::Similarity ok 389 - HSP frame ok 390 - HSP gaps ok 391 - The object isa Bio::Align::AlignI ok 392 - HSP hit isa Bio::SeqFeature::Similarity ok 393 - HSP hit_string ok 394 - HSP homology_string ok 395 - HSP hsp_group ok 396 - HSP hsp_length ok 397 - HSP length ok 398 - HSP links ok 399 - HSP n ok 400 - HSP query isa Bio::SeqFeature::Similarity ok 401 - HSP query_string ok 402 - HSP range ok 403 - HSP rank ok 404 ok 405 - HSP end ok 406 - HSP expect ok 407 - The object isa Bio::LocatableSeq ok 408 - HSP seq_str ok 409 - HSP start ok 410 - HSP custom_score ok 411 - HSP meta ok 412 - HSP strand ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 21. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 21. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 21. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 21. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 21. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 21. t/SearchIO/megablast.t ....................... 1..31 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 4. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 4. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 4. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 4. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 4. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 4. t/SearchIO/psl.t ............................. 1..53 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 - next_hsp should be undef ok 51 - next_hit should be undef not ok 52 - next_result should be undef # TODO next_result should really return undef, not empty string # Failed (TODO) test 'next_result should be undef' # at t/SearchIO/psl.t line 97. # got: '' # expected: undef ok 53 ok Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 199. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 199. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 199. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 199. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 199. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 199. t/SearchIO/rnamotif.t ........................ 1..60 ok 1 - use Bio::SearchIO; ok 2 - The object isa Bio::Search::Result::ResultI ok 3 - Result RNAMOTIF ok 4 - Result RNAMOTIF reference ok 5 - Result RNAMOTIF version ok 6 - Result entries ok 7 - Result letters ok 8 - Result database_name ok 9 - Result num_hits ok 10 - Result program_reference ok 11 - Result query_accession ok 12 - Result query_description ok 13 - Result query_length ok 14 - Result query_name ok 15 - The object isa Bio::Search::Hit::HitI ok 16 - Hit accession ok 17 - Hit GI ok 18 - Hit algorithm ok 19 - Hit description ok 20 - Hit length ok 21 - Hit locus ok 22 - Hit n ok 23 - Hit name ok 24 - Hit num_hsps ok 25 - Hit overlap ok 26 - Hit rank ok 27 - Hit raw_score ok 28 - Hit score ok 29 ok 30 - The object isa Bio::Search::HSP::HSPI ok 31 - HSP algorithm ok 32 ok 33 - The object isa Bio::SeqFeature::Similarity ok 34 - The object isa Bio::SeqFeature::Similarity ok 35 - HSP frame ok 36 - HSP gaps ok 37 - RNAMotif get_aln warning ok 38 - HSP hit isa Bio::SeqFeature::Similarity ok 39 - HSP hit_string ok 40 - HSP homology_string ok 41 - HSP hsp_group ok 42 - HSP hsp_length ok 43 - HSP length ok 44 - HSP links ok 45 - HSP n ok 46 - HSP query isa Bio::SeqFeature::Similarity ok 47 - HSP query_string ok 48 - HSP range ok 49 - HSP rank ok 50 ok 51 - HSP end ok 52 - HSP expect ok 53 - The object isa Bio::LocatableSeq ok 54 - HSP seq_str ok 55 - HSP start ok 56 - HSP custom_score ok 57 - HSP meta ok 58 - HSP strand ok 59 ok 60 ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 6. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 6. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 6. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 6. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 6. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 6. t/SearchIO/sim4.t ............................ 1..102 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175. Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264. Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284. Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311. Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337. Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357. Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378. Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399. Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420. Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442. Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465. Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487. Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508. Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523. Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540. Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555. Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574. Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599. Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616. Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629. Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646. Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663. Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680. Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700. Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728. Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747. Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763. Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777. Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794. Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815. Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 175. Subroutine _logical_length redefined at Bio/Search/HSP/GenericHSP.pm line 216. Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 241. Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 263. Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 282. Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 308. Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 350. Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 383. Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 413. Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 437. Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 463. Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 493. Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 525. Subroutine percent_identity redefined at Bio/Search/HSP/GenericHSP.pm line 538. Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 578. Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 622. Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 679. Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 703. Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 726. Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 778. Subroutine ambiguous_seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 873. Subroutine query redefined at Bio/Search/HSP/GenericHSP.pm line 897. Subroutine feature1 redefined at Bio/Search/HSP/GenericHSP.pm line 905. Subroutine hit redefined at Bio/Search/HSP/GenericHSP.pm line 928. Subroutine feature2 redefined at Bio/Search/HSP/GenericHSP.pm line 936. Subroutine significance redefined at Bio/Search/HSP/GenericHSP.pm line 962. Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line 1020. Subroutine _calculate_seq_offsets redefined at Bio/Search/HSP/GenericHSP.pm line 1176. Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1197. Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1210. Subroutine links redefined at Bio/Search/HSP/GenericHSP.pm line 1241. Subroutine hsp_group redefined at Bio/Search/HSP/GenericHSP.pm line 1260. Subroutine hit_features redefined at Bio/Search/HSP/GenericHSP.pm line 1280. Subroutine cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1337. Subroutine generate_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1359. Subroutine _sub_cigar_string redefined at Bio/Search/HSP/GenericHSP.pm line 1391. Subroutine _pre_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1408. Subroutine _query_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1448. Subroutine _subject_seq_feature redefined at Bio/Search/HSP/GenericHSP.pm line 1526. Subroutine _pre_similar_stats redefined at Bio/Search/HSP/GenericHSP.pm line 1597. Subroutine _pre_frac redefined at Bio/Search/HSP/GenericHSP.pm line 1625. Subroutine _pre_gaps redefined at Bio/Search/HSP/GenericHSP.pm line 1660. Subroutine _pre_pi redefined at Bio/Search/HSP/GenericHSP.pm line 1690. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 13. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 13. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 13. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 13. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 13. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 13. t/SearchIO/waba.t ............................ 1..64 ok 1 - use Bio::SearchIO; ok 2 - The object isa Bio::SearchIO ok 3 - query_name ok 4 - query database ok 5 - database name ok 6 - name ok 7 - hsps ok 8 - total length ok 9 - start ok 10 - end ok 11 - strand ok 12 - start ok 13 - end ok 14 - strand ok 15 - query string ok 16 - hit_string ok 17 - hmmstate string ok 18 ok 19 ok 20 ok 21 - total length ok 22 - start ok 23 - end ok 24 - strand ok 25 - start ok 26 - end ok 27 - strand ok 28 - query string ok 29 - hit_string ok 30 - hmmstate string ok 31 ok 32 ok 33 ok 34 - total length ok 35 - start ok 36 - end ok 37 - strand ok 38 - start ok 39 - end ok 40 - strand ok 41 - query string ok 42 - hit_string ok 43 - hmmstate string ok 44 ok 45 ok 46 ok 47 - query_name ok 48 - query database ok 49 - database name ok 50 - name ok 51 - hsps ok 52 - total length ok 53 - start ok 54 - end ok 55 - strand ok 56 - start ok 57 - end ok 58 - strand ok 59 - query string ok 60 - hit_string ok 61 - hmmstate string ok 62 ok 63 ok 64 ok Subroutine new redefined at Bio\SeqFeature\Generic.pm line 153, chunk 2. Subroutine set_attributes redefined at Bio\SeqFeature\Generic.pm line 195, chunk 2. Subroutine direct_new redefined at Bio\SeqFeature\Generic.pm line 265, chunk 2. Subroutine location redefined at Bio\SeqFeature\Generic.pm line 286, chunk 2. Subroutine start redefined at Bio\SeqFeature\Generic.pm line 316, chunk 2. Subroutine end redefined at Bio\SeqFeature\Generic.pm line 333, chunk 2. Subroutine length redefined at Bio\SeqFeature\Generic.pm line 350, chunk 2. Subroutine strand redefined at Bio\SeqFeature\Generic.pm line 367, chunk 2. Subroutine score redefined at Bio\SeqFeature\Generic.pm line 384, chunk 2. Subroutine frame redefined at Bio\SeqFeature\Generic.pm line 418, chunk 2. Subroutine primary_tag redefined at Bio\SeqFeature\Generic.pm line 446, chunk 2. Subroutine source_tag redefined at Bio\SeqFeature\Generic.pm line 465, chunk 2. Subroutine has_tag redefined at Bio\SeqFeature\Generic.pm line 483, chunk 2. Subroutine add_tag_value redefined at Bio\SeqFeature\Generic.pm line 498, chunk 2. Subroutine get_tag_values redefined at Bio\SeqFeature\Generic.pm line 518, chunk 2. Subroutine get_all_tags redefined at Bio\SeqFeature\Generic.pm line 544, chunk 2. Subroutine remove_tag redefined at Bio\SeqFeature\Generic.pm line 560, chunk 2. Subroutine attach_seq redefined at Bio\SeqFeature\Generic.pm line 585, chunk 2. Subroutine seq redefined at Bio\SeqFeature\Generic.pm line 614, chunk 2. Subroutine entire_seq redefined at Bio\SeqFeature\Generic.pm line 656, chunk 2. Subroutine seq_id redefined at Bio\SeqFeature\Generic.pm line 679, chunk 2. Subroutine display_name redefined at Bio\SeqFeature\Generic.pm line 696, chunk 2. Subroutine annotation redefined at Bio\SeqFeature\Generic.pm line 720, chunk 2. Subroutine get_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 751, chunk 2. Subroutine add_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 775, chunk 2. Subroutine remove_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 814, chunk 2. Subroutine gff_format redefined at Bio\SeqFeature\Generic.pm line 846, chunk 2. Subroutine gff_string redefined at Bio\SeqFeature\Generic.pm line 876, chunk 2. Subroutine slurp_gff_file redefined at Bio\SeqFeature\Generic.pm line 899, chunk 2. Subroutine _from_gff_string redefined at Bio\SeqFeature\Generic.pm line 936, chunk 2. Subroutine _expand_region redefined at Bio\SeqFeature\Generic.pm line 958, chunk 2. Subroutine _parse redefined at Bio\SeqFeature\Generic.pm line 989, chunk 2. Subroutine _tag_value redefined at Bio\SeqFeature\Generic.pm line 1006, chunk 2. Subroutine seqname redefined at Bio\SeqFeature\Generic.pm line 1022, chunk 2. Subroutine display_id redefined at Bio\SeqFeature\Generic.pm line 1028, chunk 2. Subroutine each_tag_value redefined at Bio\SeqFeature\Generic.pm line 1035, chunk 2. Subroutine all_tags redefined at Bio\SeqFeature\Generic.pm line 1036, chunk 2. Subroutine cleanup_generic redefined at Bio\SeqFeature\Generic.pm line 1047, chunk 2. Subroutine Bio::SeqFeature::Generic::sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1040, chunk 2. Subroutine Bio::SeqFeature::Generic::add_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1041, chunk 2. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 1042, chunk 2. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1044, chunk 2. Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, line 3. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, line 3. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, line 3. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, line 3. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, line 3. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, line 3. t/SearchIO/wise.t ............................ 1..20 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok t/Seq/DBLink.t ............................... 1..131 ok 1 - use Bio::SeqIO; ok 2 - "swissprot:K1C9_HUMAN" ok 3 - no double colon ok 4 - no trailing colon ok 5 - no double space ok 6 - dblink value is splittable ok 7 - "GenBank:Z29074.1" ok 8 - no double colon ok 9 - no trailing colon ok 10 - no double space ok 11 - dblink value is splittable ok 12 - "GenPept:CAA82315.1" ok 13 - no double colon ok 14 - no trailing colon ok 15 - no double space ok 16 - dblink value is splittable ok 17 - "GenBank:S69510.1" ok 18 - no double colon ok 19 - no trailing colon ok 20 - no double space ok 21 - dblink value is splittable ok 22 - "GenPept:AAC60619.1" ok 23 - no double colon ok 24 - no trailing colon ok 25 - no double space ok 26 - dblink value is splittable ok 27 - "GenBank:X75015.1" ok 28 - no double colon ok 29 - no trailing colon ok 30 - no double space ok 31 - dblink value is splittable ok 32 - "GenPept:CAA52924.1" ok 33 - no double colon ok 34 - no trailing colon ok 35 - no double space ok 36 - dblink value is splittable ok 37 - "GenBank:AB001594.1" ok 38 - no double colon ok 39 - no trailing colon ok 40 - no double space ok 41 - dblink value is splittable ok 42 - "GenPept:BAA19418.1" ok 43 - no double colon ok 44 - no trailing colon ok 45 - no double space ok 46 - dblink value is splittable ok 47 - "GenBank:I37984" ok 48 - no double colon ok 49 - no trailing colon ok 50 - no double space ok 51 - dblink value is splittable ok 52 - "HSSP:P08670" ok 53 - no double colon ok 54 - no trailing colon ok 55 - no double space ok 56 - dblink value is splittable ok 57 - "IntAct:P35527" ok 58 - no double colon ok 59 - no trailing colon ok 60 - no double space ok 61 - dblink value is splittable ok 62 - "Ensembl:ENSG00000171403" ok 63 - no double colon ok 64 - no trailing colon ok 65 - no double space ok 66 - dblink value is splittable ok 67 - "KEGG:hsa:3857" ok 68 - no double colon ok 69 - no trailing colon ok 70 - no double space ok 71 - dblink value is splittable ok 72 - "HGNC:6447" ok 73 - no double colon ok 74 - no trailing colon ok 75 - no double space ok 76 - dblink value is splittable ok 77 - "MIM:144200" ok 78 - no double colon ok 79 - no trailing colon ok 80 - no double space ok 81 - dblink value is splittable ok 82 - "MIM:607606" ok 83 - no double colon ok 84 - no trailing colon ok 85 - no double space ok 86 - dblink value is splittable ok 87 - "ArrayExpress:P35527" ok 88 - no double colon ok 89 - no trailing colon ok 90 - no double space ok 91 - dblink value is splittable ok 92 - "GO:0005200" ok 93 - no double colon ok 94 - no trailing colon ok 95 - no double space ok 96 - dblink value is splittable ok 97 - "GO:0008544" ok 98 - no double colon ok 99 - no trailing colon ok 100 - no double space ok 101 - dblink value is splittable ok 102 - "InterPro:IPR011000" ok 103 - no double colon ok 104 - no trailing colon ok 105 - no double space ok 106 - dblink value is splittable ok 107 - "InterPro:IPR001664" ok 108 - no double colon ok 109 - no trailing colon ok 110 - no double space ok 111 - dblink value is splittable ok 112 - "InterPro:IPR002957" ok 113 - no double colon ok 114 - no trailing colon ok 115 - no double space ok 116 - dblink value is splittable ok 117 - "Pfam:PF00038" ok 118 - no double colon ok 119 - no trailing colon ok 120 - no double space ok 121 - dblink value is splittable ok 122 - "PRINTS:PR01248" ok 123 - no double colon ok 124 - no trailing colon ok 125 - no double space ok 126 - dblink value is splittable ok 127 - "PROSITE:PS00226" ok 128 - no double colon ok 129 - no trailing colon ok 130 - no double space ok 131 - dblink value is splittable ok t/Seq/EncodedSeq.t ........................... 1..37 ok 1 - use Bio::Seq::EncodedSeq; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Location::Simple ok 12 ok 13 ok 14 - The object isa Bio::Location::Simple ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok t/Seq/LargeLocatableSeq.t .................... 1..8 ok 1 - use Bio::Seq::LargeLocatableSeq; ok 2 ok 3 - The object isa Bio::Seq::LargeSeqI ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Seq/LargePSeq.t ............................ 1..30 ok 1 - use Bio::Seq::LargePrimarySeq; ok 2 - use Bio::Seq::LargeSeq; ok 3 - use Bio::Location::Simple; ok 4 - use Bio::Location::Fuzzy; ok 5 - use Bio::Location::Split; ok 6 - use Bio::SeqIO; ok 7 ok 8 ok 9 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT ok 10 - Subseq is GGGGT ok 11 ok 12 ok 13 ok 14 - trunc seq was GGGGTGAA ok 15 ok 16 ok 17 ok 18 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT ok 19 ok 20 - output via Bio::SeqIO::fasta ok 21 - Subseq is GGGGT ok 22 - trunc seq was GGGGTGAA ok 23 ok 24 ok 25 ok 26 - Sequence is ATGGGGTGGGGT ok 27 - Subseq is GGGGT ok 28 - trunc seq was GGGGT ok 29 ok 30 ok t/Seq/LocatableSeq.t ......................... 1..118 ok 1 - use Bio::LocatableSeq; ok 2 - use Bio::AlignIO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - The object isa Bio::Location::Simple ok 13 ok 14 ok 15 - The object isa Bio::Location::Simple ok 16 ok 17 ok 18 ok 19 not ok 20 # TODO Need to fix columns before start of seq w/ start > 1 # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. # got: 'Bio::Location::Simple=HASH(0x500c678)' # expected: undef ok 21 ok 22 - The object isa Bio::AlignIO ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 - The object isa Bio::Location::Simple ok 50 ok 51 ok 52 - The object isa Bio::Location::Simple ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 - * is counted in length ok 106 - * is counted in length, but end is wrong ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 not ok 117 # TODO Bio::LocatableSeq global variables have scoping issues # Failed (TODO) test at t/Seq/LocatableSeq.t line 301. # got: '\-\.=~' # expected: '-\?' not ok 118 # TODO Bio::LocatableSeq global variables have scoping issues # Failed (TODO) test at t/Seq/LocatableSeq.t line 303. # got: '19' # expected: anything else ok t/Seq/MetaSeq.t .............................. 1..128 ok 1 - use Bio::Seq::Meta; ok 2 - use Bio::Seq::Meta::Array; ok 3 - use Bio::SeqIO; ok 4 - use Bio::AlignIO; ok 5 - use Bio::Seq::Quality; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 - aa-bb bb ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok t/Seq/PrimaryQual.t .......................... 1..35 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Seq::Quality; ok 3 - use Bio::Seq::PrimaryQual; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok t/Seq/PrimarySeq.t ........................... 1..87 ok 1 - use Bio::PrimarySeq; ok 2 - use Bio::Location::Simple; ok 3 - use Bio::Location::Fuzzy; ok 4 - use Bio::Location::Split; ok 5 ok 6 - The object isa Bio::PrimarySeqI ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::IdentifiableI ok 15 - The object isa Bio::DescribableI ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 - The object isa Bio::PrimarySeqI ok 30 ok 31 - The object isa Bio::PrimarySeqI ok 32 ok 33 - The object isa Bio::PrimarySeqI ok 34 ok 35 - The object isa Bio::PrimarySeqI ok 36 ok 37 ok 38 - alphabet copied through revcom not ok 39 - namespace copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms # Failed (TODO) test 'namespace copied through revcom' # at t/Seq/PrimarySeq.t line 110. # got: '' # expected: 't' not ok 40 - namespace_string copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms # Failed (TODO) test 'namespace_string copied through revcom' # at t/Seq/PrimarySeq.t line 111. # got: ':X677667' # expected: 't:X677667.47' not ok 41 - is_circular copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms # Failed (TODO) test 'is_circular copied through revcom' # at t/Seq/PrimarySeq.t line 113. # got: undef # expected: '0' ok 42 - Translation: LVAST ok 43 - Translation: MVAST ok 44 - Translation: MVAST ok 45 - Translation: MVAST* ok 46 - Translation: M* ok 47 - Translation: M ok 48 ok 49 - Translation: MWP ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 - Alphabet ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 - Bug 2438 ok 78 ok 79 - Bug \#2864 ok 80 - Terminator + inside sequence ok 81 ok 82 - _find_orfs 1 ok 83 - orfs are sorted by descending length ok 84 - got correct -orf => "longest" seq ok 85 - _find_orfs 1 ok 86 - orfs are sorted by descending length ok 87 - got correct -orf => "longest" seq ok t/Seq/PrimedSeq.t ............................ 1..10 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Seq::PrimedSeq; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok t/Seq/Quality.t .............................. 1..85 ok 1 - use Bio::Seq::Quality; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 - Bug 2845 ok 73 ok 74 - Bug 2845 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok t/Seq/Seq.t .................................. 1..72 ok 1 - use Bio::Seq; ok 2 - use Bio::Seq::RichSeq; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::Species; ok 5 - use Bio::Annotation::SimpleValue; ok 6 ok 7 ok 8 ok 9 ok 10 - truncated sequence length ok 11 - truncated sequence string ok 12 ok 13 ok 14 - alphabet ok 15 - id ok 16 - accession number ok 17 - subseq ok 18 - The object isa Bio::IdentifiableI ok 19 - The object isa Bio::DescribableI ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 - translated sequence ok 34 - translated sequence with explicit unambiguous codons ok 35 - translated sequence with unknown unambiguous codons ok 36 - translated sequence with unknown unambiguous codons, completed ok 37 - translated sequence with unambiguous codons ok 38 - translated sequence with unambiguous codons ok 39 - translated sequence with unknown unambiguous codons, completed ok 40 - translated sequence with unambiguous codons ok 41 - translated sequence with unknown unambiguous codons, completed ok 42 - translated sequence with stop ok 43 - translated sequence ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 - Bug \#2864 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok t/Seq/WithQuality.t .......................... 1..22 ok 1 - use Bio::Seq::SeqWithQuality; ok 2 - use Bio::PrimarySeq; ok 3 - use Bio::Seq::PrimaryQual; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 - The object isa Bio::Seq::PrimaryQual ok 20 - The object isa Bio::PrimarySeq ok 21 ok 22 ok Subroutine new redefined at Bio\Seq.pm line 482. Subroutine seq redefined at Bio\Seq.pm line 568. Subroutine validate_seq redefined at Bio\Seq.pm line 595. Subroutine length redefined at Bio\Seq.pm line 610. Subroutine subseq redefined at Bio\Seq.pm line 634. Subroutine display_id redefined at Bio\Seq.pm line 664. Subroutine accession_number redefined at Bio\Seq.pm line 692. Subroutine desc redefined at Bio\Seq.pm line 708. Subroutine primary_id redefined at Bio\Seq.pm line 735. Subroutine can_call_new redefined at Bio\Seq.pm line 775. Subroutine alphabet redefined at Bio\Seq.pm line 797. Subroutine is_circular redefined at Bio\Seq.pm line 813. Subroutine object_id redefined at Bio\Seq.pm line 836. Subroutine version redefined at Bio\Seq.pm line 853. Subroutine authority redefined at Bio\Seq.pm line 870. Subroutine namespace redefined at Bio\Seq.pm line 887. Subroutine display_name redefined at Bio\Seq.pm line 910. Subroutine description redefined at Bio\Seq.pm line 930. Subroutine annotation redefined at Bio\Seq.pm line 952. Subroutine get_Annotations redefined at Bio\Seq.pm line 977. Subroutine add_Annotation redefined at Bio\Seq.pm line 1002. Subroutine remove_Annotations redefined at Bio\Seq.pm line 1017. Subroutine get_num_of_annotations redefined at Bio\Seq.pm line 1030. Subroutine num_Annotations redefined at Bio\Seq.pm line 1031. Subroutine get_SeqFeatures redefined at Bio\Seq.pm line 1064. Subroutine feature_count redefined at Bio\Seq.pm line 1111. Subroutine add_SeqFeature redefined at Bio\Seq.pm line 1136. Subroutine remove_SeqFeatures redefined at Bio\Seq.pm line 1170. Subroutine id redefined at Bio\Seq.pm line 1243. Subroutine primary_seq redefined at Bio\Seq.pm line 1266. Subroutine species redefined at Bio\Seq.pm line 1299. Subroutine DESTROY redefined at Bio\Seq.pm line 1313. Subroutine all_SeqFeatures redefined at Bio\Seq.pm line 1328. Subroutine accession redefined at Bio\Seq.pm line 1332. Subroutine Bio::Seq::flush_SeqFeature redefined at Bio\Seq.pm line 1321. Subroutine Bio::Seq::flush_SeqFeatures redefined at Bio\Seq.pm line 1322. Subroutine Bio::Seq::top_SeqFeatures redefined at Bio\Seq.pm line 1325. t/SeqEvolution.t ............................. 1..39 ok 1 - use Bio::SeqEvolution::Factory; ok 2 - use Bio::PrimarySeq; ok 3 ok 4 - The object isa Bio::SeqEvolution::DNAPoint ok 5 ok 6 - The object isa Bio::SeqEvolution::DNAPoint ok 7 ok 8 - The object isa Bio::SeqEvolution::DNAPoint ok 9 ok 10 ok 11 - get rate() ok 12 - get and set rate() ok 13 - identity() ok 14 - identity() ok 15 - pam() ok 16 - pam() ok 17 - mutation_count() ok 18 - mutation_count() ok 19 - seq_type() ok 20 - seq_type() ok 21 - next_seq() ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 - each_mutation() ok 28 ok 29 ok 30 - get_alignment_identity() ok 31 ok 32 ok 33 - get_mutation_counter() ok 34 - get_sequence_counter() ok 35 - reset_sequence_counter() ok 36 - get_sequence_counter() == 0 ok 37 ok 38 ok 39 - The object isa Bio::SimpleAlign ok t/SeqFeature/Clone.t ......................... 1..17 ok 1 - clone() ok 2 - start() clone set ok 3 - start() clone get ok 4 - start() original unchanged ok 5 - clone() with arguments ok 6 - start() orig get ok 7 - end() orig get ok 8 - start() clone get ok 9 - end() clone get ok 10 - start() clone set ok 11 - start() clone get ok 12 - start() original unchanged ok 13 - location() Bio::Location::Split ok 14 - clone() ok 15 - start() clone set ok 16 - start() clone get ok 17 - start() original unchanged ok t/SeqFeature/FeatureIO.t ..................... 1..47 ok 1 - use Bio::FeatureIO; ok 2 ok 3 not ok 4 # TODO How did this ever work?!? # Failed (TODO) test at t/SeqFeature/FeatureIO.t line 43. # got: 'TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC' # expected: 'Test1' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 not ok 13 # TODO How did this ever work?!? # Failed (TODO) test at t/SeqFeature/FeatureIO.t line 103. # got: 'GATTACAGATTACA' # expected: 'Test1' ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 not ok 24 # TODO How did this ever work?!? # Failed (TODO) test at t/SeqFeature/FeatureIO.t line 173. # got: 'GATTACAGATTACA' # expected: 'Test1' ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 - vecscreen_simple gets the correct features ok 46 ok 47 ok Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85. Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122. Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138. Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154. Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170. Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190. Subroutine new redefined at Bio\SeqFeature\Generic.pm line 153. Subroutine set_attributes redefined at Bio\SeqFeature\Generic.pm line 195. Subroutine direct_new redefined at Bio\SeqFeature\Generic.pm line 265. Subroutine location redefined at Bio\SeqFeature\Generic.pm line 286. Subroutine start redefined at Bio\SeqFeature\Generic.pm line 316. Subroutine end redefined at Bio\SeqFeature\Generic.pm line 333. Subroutine length redefined at Bio\SeqFeature\Generic.pm line 350. Subroutine strand redefined at Bio\SeqFeature\Generic.pm line 367. Subroutine score redefined at Bio\SeqFeature\Generic.pm line 384. Subroutine frame redefined at Bio\SeqFeature\Generic.pm line 418. Subroutine primary_tag redefined at Bio\SeqFeature\Generic.pm line 446. Subroutine source_tag redefined at Bio\SeqFeature\Generic.pm line 465. Subroutine has_tag redefined at Bio\SeqFeature\Generic.pm line 483. Subroutine add_tag_value redefined at Bio\SeqFeature\Generic.pm line 498. Subroutine get_tag_values redefined at Bio\SeqFeature\Generic.pm line 518. Subroutine get_all_tags redefined at Bio\SeqFeature\Generic.pm line 544. Subroutine remove_tag redefined at Bio\SeqFeature\Generic.pm line 560. Subroutine attach_seq redefined at Bio\SeqFeature\Generic.pm line 585. Subroutine seq redefined at Bio\SeqFeature\Generic.pm line 614. Subroutine entire_seq redefined at Bio\SeqFeature\Generic.pm line 656. Subroutine seq_id redefined at Bio\SeqFeature\Generic.pm line 679. Subroutine display_name redefined at Bio\SeqFeature\Generic.pm line 696. Subroutine annotation redefined at Bio\SeqFeature\Generic.pm line 720. Subroutine get_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 751. Subroutine add_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 775. Subroutine remove_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 814. Subroutine gff_format redefined at Bio\SeqFeature\Generic.pm line 846. Subroutine gff_string redefined at Bio\SeqFeature\Generic.pm line 876. Subroutine slurp_gff_file redefined at Bio\SeqFeature\Generic.pm line 899. Subroutine _from_gff_string redefined at Bio\SeqFeature\Generic.pm line 936. Subroutine _expand_region redefined at Bio\SeqFeature\Generic.pm line 958. Subroutine _parse redefined at Bio\SeqFeature\Generic.pm line 989. Subroutine _tag_value redefined at Bio\SeqFeature\Generic.pm line 1006. Subroutine seqname redefined at Bio\SeqFeature\Generic.pm line 1022. Subroutine display_id redefined at Bio\SeqFeature\Generic.pm line 1028. Subroutine each_tag_value redefined at Bio\SeqFeature\Generic.pm line 1035. Subroutine all_tags redefined at Bio\SeqFeature\Generic.pm line 1036. Subroutine cleanup_generic redefined at Bio\SeqFeature\Generic.pm line 1047. Subroutine Bio::SeqFeature::Generic::sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1040. Subroutine Bio::SeqFeature::Generic::add_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1041. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 1042. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1044. t/SeqFeature/Location.t ...................... 1..103 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Location::Split; ok 3 - use Bio::Location::Fuzzy; ok 4 - use Bio::SeqFeature::Generic; ok 5 - use Bio::SeqFeature::SimilarityPair; ok 6 - use Bio::SeqFeature::FeaturePair; ok 7 - The object isa Bio::LocationI ok 8 - The object isa Bio::RangeI ok 9 - Bio::Location::Simple tests ok 10 ok 11 ok 12 ok 13 ok 14 - Bio::SeqFeature::Generic isa Bio::SeqFeatureI ok 15 - The object isa Bio::RangeI ok 16 ok 17 ok 18 - Bio::SeqFeature::FeaturePair tests ok 19 ok 20 ok 21 ok 22 - Bio::SeqFeature::Generic tests ok 23 ok 24 - Bio::Location::Fuzzy tests ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 - Bio::Location::Split tests ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 - Bugfix 1074 ok 56 ok 57 ok 58 ok 59 - Positive length ok 60 ok 61 - seq_id() on Bio::Location::Split ok 62 ok 63 ok 64 - The object isa Bio::LocationI ok 65 - The object isa Bio::RangeI ok 66 - Bio::Location::Simple EXACT ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 - Bio::Location::Simple IN-BETWEEN ok 73 ok 74 ok 75 ok 76 ok 77 - Testing error handling ok 78 ok 79 ok 80 ok 81 - use Bio::Location::WidestCoordPolicy; ok 82 - use Bio::Location::NarrowestCoordPolicy; ok 83 - use Bio::Location::AvWithinCoordPolicy; ok 84 - Default coodinate policy ok 85 ok 86 ok 87 ok 88 - The object isa Bio::Location::WidestCoordPolicy ok 89 - Narrowest coodinate policy ok 90 ok 91 ok 92 ok 93 - The object isa Bio::Location::NarrowestCoordPolicy ok 94 - Average coodinate policy ok 95 ok 96 ok 97 ok 98 - The object isa Bio::Location::AvWithinCoordPolicy ok 99 - Widest coodinate policy ok 100 ok 101 ok 102 ok 103 - The object isa Bio::Location::WidestCoordPolicy ok t/SeqFeature/LocationFactory.t ............... 1..272 ok 1 - use Bio::Factory::FTLocationFactory; ok 2 - The object isa Bio::Factory::LocationFactoryI ok 3 - Bio::Location::Simple ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - Location String: J00194:100..202 ok 13 ok 14 - Bio::Location::Fuzzy ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 - Location String: 1..? ok 24 ok 25 - Bio::Location::Fuzzy ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 - Location String: (122.133)..(204.221) ok 35 ok 36 - Bio::Location::Fuzzy ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 - Location String: (102.110) ok 46 ok 47 - Bio::Location::Simple ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 - Location String: 340..565 ok 57 ok 58 - Bio::Location::Split ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 - Location String: join(12..78,134..202) ok 68 ok 69 - Bio::Location::Fuzzy ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 - Location String: ?..? ok 79 ok 80 - Bio::Location::Fuzzy ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 - Location String: <345..500 ok 90 ok 91 - Bio::Location::Fuzzy ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 - Location String: ?22..?64 ok 101 ok 102 - Bio::Location::Simple ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 - Location String: J00194:100..202 ok 112 ok 113 - Bio::Location::Simple ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 - Location String: 467 ok 123 ok 124 - Bio::Location::Fuzzy ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 - Location String: (23.45)..600 ok 134 ok 135 - Bio::Location::Simple ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 - Location String: 123^124 ok 145 ok 146 - Bio::Location::Fuzzy ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 - Location String: <1..? ok 156 ok 157 - Bio::Location::Fuzzy ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 - Location String: 145^177 ok 167 ok 168 - Bio::Location::Fuzzy ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 - Location String: 22..?64 ok 178 ok 179 - Bio::Location::Fuzzy ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 - Location String: complement(34..(122.126)) ok 189 ok 190 - Bio::Location::Split ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 - Location String: complement(join(4918..5163,2691..4571)) ok 200 ok 201 - Bio::Location::Split ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599) ok 211 ok 212 - Bio::Location::Fuzzy ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 - Location String: ?..>393 ok 222 ok 223 - Bio::Location::Fuzzy ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 - Location String: ?2465..2774 ok 233 ok 234 - Bio::Location::Fuzzy ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 - Location String: (122.133)..(204.221) ok 244 ok 245 - Bio::Location::Fuzzy ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 - Location String: ?..536 ok 255 ok 256 - Bio::Location::Fuzzy ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 - Location String: <1..888 ok 266 ok 267 - join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294))) ok 268 - join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081))) ok 269 - join(20464..20694,21548..22763,complement(join(314652..314672,232596..232990,231520..231669))) ok 270 - join(20464..20694,21548..22763,join(complement(231520..231669),complement(232596..232990),complement(314652..314672))) ok 271 - join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000) ok 272 - order(S67862.1:72..75,join(S67863.1:1..788,1..19)) ok t/SeqFeature/Primer.t ........................ 1..18 ok 1 - use Bio::SeqFeature::Primer; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/SeqFeature/Range.t ......................... 1..49 ok 1 - use Bio::Range; ok 2 - BioRange object isa Bio::Range ok 3 ok 4 - BioRange object isa Bio::Range ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 - BioRange object isa Bio::Range ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 - BioRange object isa Bio::Range ok 26 - BioRange object isa Bio::Range ok 27 - BioRange object isa Bio::Range ok 28 - 1 & -1 ok 29 - 1 & 1 true ok 30 - 1 & 0 true ok 31 - 1 & -1 false ok 32 - 1 & 1 true ok 33 - 1 & 0 false ok 34 - 1 & -1 false ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 - Bio::Range object isa Bio::Range ok 46 ok 47 ok 48 ok 49 ok t/SeqFeature/RangeI.t ........................ 1..45 ok 1 - use Bio::SeqFeature::Generic; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 - subtract() of split features ok 40 - 0 start ok 41 - 0 end ok 42 - 1 start ok 43 - 1 end ok 44 - 2 start ok 45 - 2 end ok t/SeqFeature/SeqAnalysisParser.t ............. 1..14 ok 1 - use Bio::Factory::SeqAnalysisParserFactory; ok 2 - use Bio::SeqIO; ok 3 - The object isa Bio::SeqIO ok 4 - The object isa Bio::PrimarySeqI ok 5 - The object isa Bio::SeqAnalysisParserI ok 6 ok 7 ok 8 ok 9 - The object isa Bio::PrimarySeqI ok 10 - The object isa Bio::SeqAnalysisParserI ok 11 ok 12 ok 13 - The object isa Bio::SeqAnalysisParserI ok 14 ok t/SeqFeature/SeqFeatAnnotated.t .............. skipped: Network tests have not been requested t/SeqFeature/SeqFeatCollection.t ............. skipped: The optional module DB_File (or dependencies thereof) was not installed Subroutine new redefined at Bio\SeqFeature\Generic.pm line 153. Subroutine set_attributes redefined at Bio\SeqFeature\Generic.pm line 195. Subroutine direct_new redefined at Bio\SeqFeature\Generic.pm line 265. Subroutine location redefined at Bio\SeqFeature\Generic.pm line 286. Subroutine start redefined at Bio\SeqFeature\Generic.pm line 316. Subroutine end redefined at Bio\SeqFeature\Generic.pm line 333. Subroutine length redefined at Bio\SeqFeature\Generic.pm line 350. Subroutine strand redefined at Bio\SeqFeature\Generic.pm line 367. Subroutine score redefined at Bio\SeqFeature\Generic.pm line 384. Subroutine frame redefined at Bio\SeqFeature\Generic.pm line 418. Subroutine primary_tag redefined at Bio\SeqFeature\Generic.pm line 446. Subroutine source_tag redefined at Bio\SeqFeature\Generic.pm line 465. Subroutine has_tag redefined at Bio\SeqFeature\Generic.pm line 483. Subroutine add_tag_value redefined at Bio\SeqFeature\Generic.pm line 498. Subroutine get_tag_values redefined at Bio\SeqFeature\Generic.pm line 518. Subroutine get_all_tags redefined at Bio\SeqFeature\Generic.pm line 544. Subroutine remove_tag redefined at Bio\SeqFeature\Generic.pm line 560. Subroutine attach_seq redefined at Bio\SeqFeature\Generic.pm line 585. Subroutine seq redefined at Bio\SeqFeature\Generic.pm line 614. Subroutine entire_seq redefined at Bio\SeqFeature\Generic.pm line 656. Subroutine seq_id redefined at Bio\SeqFeature\Generic.pm line 679. Subroutine display_name redefined at Bio\SeqFeature\Generic.pm line 696. Subroutine annotation redefined at Bio\SeqFeature\Generic.pm line 720. Subroutine get_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 751. Subroutine add_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 775. Subroutine remove_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 814. Subroutine gff_format redefined at Bio\SeqFeature\Generic.pm line 846. Subroutine gff_string redefined at Bio\SeqFeature\Generic.pm line 876. Subroutine slurp_gff_file redefined at Bio\SeqFeature\Generic.pm line 899. Subroutine _from_gff_string redefined at Bio\SeqFeature\Generic.pm line 936. Subroutine _expand_region redefined at Bio\SeqFeature\Generic.pm line 958. Subroutine _parse redefined at Bio\SeqFeature\Generic.pm line 989. Subroutine _tag_value redefined at Bio\SeqFeature\Generic.pm line 1006. Subroutine seqname redefined at Bio\SeqFeature\Generic.pm line 1022. Subroutine display_id redefined at Bio\SeqFeature\Generic.pm line 1028. Subroutine each_tag_value redefined at Bio\SeqFeature\Generic.pm line 1035. Subroutine all_tags redefined at Bio\SeqFeature\Generic.pm line 1036. Subroutine cleanup_generic redefined at Bio\SeqFeature\Generic.pm line 1047. Subroutine Bio::SeqFeature::Generic::sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1040. Subroutine Bio::SeqFeature::Generic::add_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1041. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeatures redefined at Bio\SeqFeature\Generic.pm line 1042. Subroutine Bio::SeqFeature::Generic::flush_sub_SeqFeature redefined at Bio\SeqFeature\Generic.pm line 1044. t/SeqFeature/SeqFeature.t .................... 1..249 ok 1 - use Bio::Seq; ok 2 - use Bio::SeqIO; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::SeqFeature::FeaturePair; ok 5 - use Bio::SeqFeature::Computation; ok 6 - use Bio::SeqFeature::Gene::Transcript; ok 7 - use Bio::SeqFeature::Gene::UTR; ok 8 - use Bio::SeqFeature::Gene::Exon; ok 9 - use Bio::SeqFeature::Gene::Poly_A_site; ok 10 - use Bio::SeqFeature::Gene::GeneStructure; ok 11 - use Bio::Location::Fuzzy; ok 12 - start of feature location ok 13 - end of feature location ok 14 - primary tag ok 15 - source tag ok 16 - undef phase by default ok 17 - phase accessor returns ok 18 - phase is persistent ok 19 ok 20 - set phase from constructor ok 21 ok 22 - feature1 of pair stored ok 23 - feature2 of pair stored ok 24 - feature start ok 25 - feature end ok 26 - primary tag ok 27 - source tag ok 28 - hstart ok 29 - hend ok 30 - hprimary tag ok 31 - hsource tag ok 32 - inverted end ok 33 ok 34 - seq string ok 35 - sf1 end ok 36 - sf1 start ok 37 ok 38 - sf2 ok 39 ok 40 - computation id ok 41 - score value ok 42 ok 43 ok 44 - sft[0] is exon ok 45 ok 46 - computation id ok 47 ok 48 - score value ok 49 - sfeat start for EXPAND-ED feature (bug \#947) ok 50 - sfeat end for EXPAND-ED feature (bug \#947) ok 51 ok 52 - can create feature starting and ending at 0 ok 53 ok 54 - can create feature starting and ending at 0 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 - mRNA spliced length ok 75 - has 2 UTRs ok 76 ok 77 ok 78 ok 79 ok 80 - The object isa Bio::SeqIO ok 81 - The object isa Bio::Seq ok 82 # skip Network tests have not been requested ok 83 # skip Network tests have not been requested ok 84 # skip Network tests have not been requested ok 85 # skip Network tests have not been requested ok 86 # skip Network tests have not been requested ok 87 - The object isa Bio::SeqIO ok 88 - The object isa Bio::Seq ok 89 # skip Network tests have not been requested ok 90 # skip Network tests have not been requested ok 91 - The object isa Bio::SeqIO ok 92 - spliced seq translation matches expected ok 93 - spliced seq translation matches expected ok 94 - spliced seq translation matches expected ok 95 - spliced seq translation matches expected ok 96 - spliced seq translation matches expected ok 97 - spliced seq translation matches expected ok 98 - spliced seq translation matches expected ok 99 - spliced seq translation matches expected ok 100 - spliced seq translation matches expected ok 101 - spliced seq translation matches expected ok 102 - spliced seq translation matches expected ok 103 - spliced seq translation matches expected ok 104 - spliced seq translation matches expected ok 105 - spliced seq translation matches expected ok 106 - spliced seq translation matches expected ok 107 - spliced seq translation matches expected ok 108 - spliced seq translation matches expected ok 109 - spliced seq translation matches expected ok 110 - spliced seq translation matches expected ok 111 - spliced seq translation matches expected ok 112 - spliced seq translation matches expected ok 113 - spliced seq translation matches expected ok 114 - spliced seq translation matches expected ok 115 - spliced seq translation matches expected ok 116 - spliced seq translation matches expected ok 117 - spliced seq translation matches expected ok 118 - spliced seq translation matches expected ok 119 - spliced seq translation matches expected ok 120 - spliced seq translation matches expected ok 121 - spliced seq translation matches expected ok 122 - spliced seq translation matches expected ok 123 - spliced seq translation matches expected ok 124 - spliced seq translation matches expected ok 125 - spliced seq translation matches expected ok 126 - spliced seq translation matches expected ok 127 - spliced seq translation matches expected ok 128 - spliced seq translation matches expected ok 129 - spliced seq translation matches expected ok 130 - spliced seq translation matches expected ok 131 - spliced seq translation matches expected ok 132 - spliced seq translation matches expected ok 133 - spliced seq translation matches expected ok 134 - spliced seq translation matches expected ok 135 - spliced seq translation matches expected ok 136 - spliced seq translation matches expected ok 137 - spliced seq translation matches expected ok 138 - spliced seq translation matches expected ok 139 - spliced seq translation matches expected ok 140 - spliced seq translation matches expected ok 141 - spliced seq translation matches expected ok 142 - spliced seq translation matches expected ok 143 - spliced seq translation matches expected ok 144 - spliced seq translation matches expected ok 145 - spliced seq translation matches expected ok 146 - spliced seq translation matches expected ok 147 - spliced seq translation matches expected ok 148 - spliced seq translation matches expected ok 149 - spliced seq translation matches expected ok 150 - spliced seq translation matches expected ok 151 - spliced seq translation matches expected ok 152 - spliced seq translation matches expected ok 153 - spliced seq translation matches expected ok 154 - spliced seq translation matches expected ok 155 - spliced seq translation matches expected ok 156 - spliced seq translation matches expected ok 157 - spliced seq translation matches expected ok 158 - spliced seq translation matches expected ok 159 - spliced seq translation matches expected ok 160 - spliced seq translation matches expected ok 161 - spliced seq translation matches expected ok 162 - spliced seq translation matches expected ok 163 - spliced seq translation matches expected ok 164 - spliced seq translation matches expected ok 165 - spliced seq translation matches expected ok 166 - spliced seq translation matches expected ok 167 - spliced seq translation matches expected ok 168 - spliced seq translation matches expected ok 169 - spliced seq translation matches expected ok 170 - spliced seq translation matches expected ok 171 - spliced seq translation matches expected ok 172 - spliced seq translation matches expected ok 173 - spliced seq translation matches expected ok 174 - spliced seq translation matches expected ok 175 - spliced seq translation matches expected ok 176 - spliced seq translation matches expected ok 177 - spliced seq translation matches expected ok 178 - spliced seq translation matches expected ok 179 - spliced seq translation matches expected ok 180 - spliced seq translation matches expected ok 181 - spliced seq translation matches expected ok 182 - spliced seq translation matches expected ok 183 - spliced seq translation matches expected ok 184 - spliced seq translation matches expected ok 185 - spliced seq translation matches expected ok 186 - spliced seq translation matches expected ok 187 - spliced seq translation matches expected ok 188 - spliced seq translation matches expected ok 189 - spliced seq translation matches expected ok 190 - spliced seq translation matches expected ok 191 - spliced seq translation matches expected ok 192 - spliced seq translation matches expected ok 193 - spliced seq translation matches expected ok 194 - spliced seq translation matches expected ok 195 - spliced seq translation matches expected ok 196 - spliced seq translation matches expected ok 197 - spliced seq translation matches expected ok 198 - spliced seq translation matches expected ok 199 - spliced seq translation matches expected ok 200 - spliced seq translation matches expected ok 201 - spliced seq translation matches expected ok 202 - spliced seq translation matches expected ok 203 - spliced seq translation matches expected ok 204 - spliced seq translation matches expected ok 205 - spliced seq translation matches expected ok 206 - spliced seq translation matches expected ok 207 - spliced seq translation matches expected ok 208 - spliced seq translation matches expected ok 209 ok 210 - phase check ok 211 ok 212 - phase check ok 213 ok 214 - phase check ok 215 ok 216 - phase check ok 217 ok 218 - phase check ok 219 - tags found ok 220 - get_tagset_values tag values found ok 221 - get_tagset_values tag values for multiple tags found ok 222 - get_tag_values tag values found ok 223 - get_tag_values lives with tag ok 224 - get_tagset_values no tag values found ok 225 - get_tagset_values lives with no tag ok 226 - get_tag_values throws with no tag ok 227 - Phi-X174 genome is circular ok 228 - only 3 split locations ok 229 - The object isa Bio::Location::SplitLocationI ok 230 - feature string ok 231 - first ten nucleotides ok 232 - strand not ok 233 - start # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'start' # at t/SeqFeature/SeqFeature.t line 421. # got: '1' # expected: '3981' not ok 234 - end # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'end' # at t/SeqFeature/SeqFeature.t line 422. # got: '5386' # expected: '136' not ok 235 - expected length # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'expected length' # at t/SeqFeature/SeqFeature.t line 423. # got: '5386' # expected: '1542' ok 236 - The object isa Bio::Location::SplitLocationI ok 237 - feature string ok 238 - first ten nucleotides ok 239 - strand not ok 240 - start # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'start' # at t/SeqFeature/SeqFeature.t line 421. # got: '1' # expected: '4497' not ok 241 - end # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'end' # at t/SeqFeature/SeqFeature.t line 422. # got: '5386' # expected: '136' not ok 242 - expected length # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'expected length' # at t/SeqFeature/SeqFeature.t line 423. # got: '5386' # expected: '1026' ok 243 - The object isa Bio::Location::SplitLocationI ok 244 - feature string ok 245 - first ten nucleotides ok 246 - strand not ok 247 - start # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'start' # at t/SeqFeature/SeqFeature.t line 421. # got: '1' # expected: '5075' not ok 248 - end # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'end' # at t/SeqFeature/SeqFeature.t line 422. # got: '5386' # expected: '136' not ok 249 - expected length # TODO Need to define how to deal with start, end length for circular sequences # Failed (TODO) test 'expected length' # at t/SeqFeature/SeqFeature.t line 423. # got: '5386' # expected: '363' ok t/SeqFeature/SeqFeaturePrimer.t .............. 1..8 ok 1 - use Bio::SeqFeature::Primer; ok 2 - The object isa Bio::SeqFeature::Primer ok 3 - The object isa Bio::SeqFeature::Primer ok 4 - The object isa Bio::Seq ok 5 ok 6 ok 7 ok 8 ok t/SeqFeature/Unflattener.t ................... 1..10 ok 1 - use Bio::SeqIO; ok 2 - use Bio::SeqFeature::Tools::Unflattener; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok t/SeqFeature/Unflattener2.t .................. 1..12 ok 1 - use Bio::SeqIO; ok 2 - use Bio::SeqFeature::Tools::Unflattener; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok t/SeqIO/Handler.t ............................ 1..561 ok 1 - use Bio::SeqIO; ok 2 - AI129902 ok 3 ok 4 ok 5 ok 6 - NT_021877 ok 7 ok 8 ok 9 ok 10 ok 11 - BAB68554 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 - operator overloading in AnnotationI is deprecated ok 22 - NC_006346 ok 23 ok 24 ok 25 - U71225 ok 26 ok 27 - AB077698 ok 28 ok 29 - DQ018368 ok 30 - D10483 ok 31 ok 32 ok 33 ok 34 - bug 1487 ok 35 ok 36 - bug 1647 ok 37 ok 38 ok 39 - bug 1673 ok 40 ok 41 ok 42 ok 43 - AF165282 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 - species parsing incorrect for genbank ok 53 - genus duplicated in genbank parsing ok 54 ok 55 ok 56 - species parsing incorrect for genbank ok 57 - genus duplicated in genbank parsing ok 58 ok 59 ok 60 - species parsing incorrect for genbank ok 61 - genus duplicated in genbank parsing ok 62 ok 63 - streaming ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 - Total number of sequences in test file ok 70 ok 71 - Fuzzy in ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 - Fuzzy out ok 84 - BK000016 ok 85 ok 86 - BK000016 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 - BK000016 ok 102 - roundtrip ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 - revcomp split location ok 121 - Bug 1925 ok 122 ok 123 ok 124 - wgs ok 125 ok 126 - wgs_scafld ok 127 ok 128 - wgs_scafld ok 129 ok 130 ok 131 - BC000007 ok 132 - BK000016-tpa.gbk ok 133 - ay116458.gb ok 134 - ay149291.gb ok 135 - NC_006346.gb ok 136 - ay007676.gb ok 137 - dq519393.gb ok 138 ok 139 - swissprot:K1C9_HUMAN ok 140 ok 141 - swissprot ok 142 ok 143 - GenBank:Z29074.1 ok 144 ok 145 - GenBank ok 146 ok 147 - GenPept:CAA82315.1 ok 148 ok 149 - GenPept ok 150 ok 151 - GenBank:S69510.1 ok 152 ok 153 - GenBank ok 154 ok 155 - GenPept:AAC60619.1 ok 156 ok 157 - GenPept ok 158 ok 159 - GenBank:X75015.1 ok 160 ok 161 - GenBank ok 162 ok 163 - GenPept:CAA52924.1 ok 164 ok 165 - GenPept ok 166 ok 167 - GenBank:AB001594.1 ok 168 ok 169 - GenBank ok 170 ok 171 - GenPept:BAA19418.1 ok 172 ok 173 - GenPept ok 174 ok 175 - GenBank:I37984 ok 176 ok 177 - GenBank ok 178 ok 179 - HSSP:P08670 ok 180 ok 181 - HSSP ok 182 ok 183 - IntAct:P35527 ok 184 ok 185 - IntAct ok 186 ok 187 - Ensembl:ENSG00000171403 ok 188 ok 189 - Ensembl ok 190 ok 191 - KEGG:hsa:3857 ok 192 ok 193 - KEGG ok 194 ok 195 - HGNC:6447 ok 196 ok 197 - HGNC ok 198 ok 199 - MIM:144200 ok 200 ok 201 - MIM ok 202 ok 203 - MIM:607606 ok 204 ok 205 - MIM ok 206 ok 207 - ArrayExpress:P35527 ok 208 ok 209 - ArrayExpress ok 210 ok 211 - GO:0005200 ok 212 ok 213 - GO ok 214 ok 215 - GO:0008544 ok 216 ok 217 - GO ok 218 ok 219 - InterPro:IPR011000 ok 220 ok 221 - InterPro ok 222 ok 223 - InterPro:IPR001664 ok 224 ok 225 - InterPro ok 226 ok 227 - InterPro:IPR002957 ok 228 ok 229 - InterPro ok 230 ok 231 - Pfam:PF00038 ok 232 ok 233 - Pfam ok 234 ok 235 - PRINTS:PR01248 ok 236 ok 237 - PRINTS ok 238 ok 239 - PROSITE:PS00226 ok 240 ok 241 - PROSITE ok 242 ok 243 - Bug 2195 ok 244 - Bug 2195 ok 245 - The object isa Bio::Annotation::SimpleValue ok 246 ok 247 - The object isa Bio::Annotation::SimpleValue ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 - success reading Embl with ^ location and badly split double quotes ok 274 ok 275 ok 276 - success writing Embl format with ^ < and > locations ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 - genus duplication test ok 310 ok 311 ok 312 - The object isa Bio::SeqIO ok 313 - The object isa Bio::Species ok 314 ok 315 ok 316 - operator overloading in AnnotationI is deprecated ok 317 ok 318 - dates ok 319 - dates ok 320 - dates ok 321 ok 322 - The object isa Bio::Seq::RichSeqI ok 323 ok 324 ok 325 ok 326 - operator overloading in AnnotationI is deprecated ok 327 ok 328 ok 329 ok 330 ok 331 - id is ROA1_HUMAN ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 - operator overloading in AnnotationI is deprecated ok 340 ok 341 ok 342 ok 343 - The object isa Bio::Seq::RichSeqI ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 - operator overloading in AnnotationI is deprecated ok 354 ok 355 ok 356 ok 357 - GC1QBP ok 358 - HABP1 ok 359 - SF2P32 ok 360 - C1QBP ok 361 ok 362 - The object isa Bio::Seq::RichSeqI ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 - F54H12.1 ok 370 - The object isa Bio::Seq::RichSeqI ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 - The object isa Bio::Seq::RichSeqI ok 383 ok 384 ok 385 ok 386 ok 387 - The object isa Bio::Seq::RichSeqI ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 - The object isa Bio::Seq::RichSeqI ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 ok 411 ok 412 ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok 453 ok 454 ok 455 ok 456 ok 457 ok 458 ok 459 ok 460 ok 461 ok 462 ok 463 ok 464 ok 465 ok 466 ok 467 ok 468 ok 469 ok 470 ok 471 ok 472 ok 473 ok 474 ok 475 ok 476 ok 477 ok 478 ok 479 ok 480 ok 481 ok 482 ok 483 ok 484 ok 485 - The object isa Bio::Species ok 486 ok 487 ok 488 ok 489 ok 490 ok 491 ok 492 ok 493 ok 494 ok 495 ok 496 ok 497 ok 498 ok 499 ok 500 ok 501 ok 502 ok 503 ok 504 ok 505 ok 506 ok 507 ok 508 ok 509 ok 510 ok 511 ok 512 ok 513 ok 514 ok 515 ok 516 ok 517 - The object isa Bio::Species ok 518 ok 519 ok 520 - operator overloading in AnnotationI is deprecated ok 521 ok 522 ok 523 ok 524 ok 525 ok 526 ok 527 ok 528 ok 529 ok 530 ok 531 ok 532 ok 533 ok 534 ok 535 ok 536 ok 537 ok 538 ok 539 ok 540 ok 541 ok 542 ok 543 ok 544 ok 545 ok 546 ok 547 ok 548 ok 549 ok 550 ok 551 - P39765 ok 552 ok 553 ok 554 ok 555 ok 556 ok 557 ok 558 ok 559 ok 560 ok 561 - operator overloading in AnnotationI is deprecated ok t/SeqIO/MultiFile.t .......................... 1..3 ok 1 - use Bio::SeqIO::MultiFile; ok 2 ok 3 ok t/SeqIO/Multiple_fasta.t ..................... 1..9 ok 1 - use Bio::SeqIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - all sequences in the file ok t/SeqIO/SeqBuilder.t ......................... 1..101 ok 1 - use Bio::SeqIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - The object isa Bio::Factory::ObjectBuilderI ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok t/SeqIO/SeqIO.t .............................. 1..45 ok 1 - use Bio::SeqIO; ok 2 ok 3 - ID for format gcg ok 4 ok 5 ok 6 ok 7 ok 8 - ID for format fasta ok 9 ok 10 ok 11 ok 12 - accession.version ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 - ID for format pir ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 - ID for format tab ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - ID for format ace ok 32 ok 33 ok 34 ok 35 ok 36 - use Algorithm::Diff; ok 37 - use IO::ScalarArray; ok 38 - use IO::String; ok 39 ok 40 ok 41 not ok 42 - Must pass a file or file handle # TODO file/fh-based tests should be in Bio::Root::IO, see issue #3204 # Failed (TODO) test 'Must pass a file or file handle' # at t/SeqIO/SeqIO.t line 120. # expecting: Regexp ((?-xism:No file, fh, or string argument provided)) # found: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: Could not guess format from file/fh # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::SeqIO::new Bio/SeqIO.pm:389 # STACK: Test::Exception::throws_ok t/SeqIO/SeqIO.t:119 # STACK: t/SeqIO/SeqIO.t:120 # ----------------------------------------------------------- # ) ok 43 - Must pass a file or file handle ok 44 - Must pass a file or file handle ok 45 - Must pass a real file ok t/SeqIO/Splicedseq.t ......................... 1..14 ok 1 - use Bio::SeqIO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - get_SeqFeatures() ok 12 - protein sequence ok 13 - nucleotide sequence - correct CDS range ok 14 - nucleotide length ok t/SeqIO/abi.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/ace.t ................................ 1..7 ok 1 - use Bio::SeqIO; ok 2 - number of sequence objects ok 3 - unescaping of characters, Name; 4% strewn with \ various / escaped characters ok 4 - alphabets detected ok 5 - alphabets detected ok 6 - writing sequence ok 7 - test output ok t/SeqIO/agave.t .............................. 1..8 ok 1 - use Bio::SeqIO::agave; not ok 2 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 3 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 4 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 5 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 6 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 7 # TODO & SKIP No tests for agave format -- no sample file to test against not ok 8 # TODO & SKIP No tests for agave format -- no sample file to test against ok t/SeqIO/alf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/asciitree.t .......................... 1..2 ok 1 - use Bio::SeqIO; ok 2 - File exists, has contents on MSWin32 ok Subroutine next_seq redefined at Bio\SeqIO\bsml.pm line 187. Subroutine GETFLOPPIES redefined at Bio\SeqIO\bsml.pm line 428. Subroutine FLOPPYVALS redefined at Bio\SeqIO\bsml.pm line 444. Subroutine FIRSTDATA redefined at Bio\SeqIO\bsml.pm line 464. Subroutine STRIP redefined at Bio\SeqIO\bsml.pm line 481. Subroutine to_bsml redefined at Bio\SeqIO\bsml.pm line 547. Subroutine write_seq redefined at Bio\SeqIO\bsml.pm line 846. Subroutine _parse_location redefined at Bio\SeqIO\bsml.pm line 894. Subroutine _parse_bsml_feature redefined at Bio\SeqIO\bsml.pm line 947. Subroutine _parse_bsml_location redefined at Bio\SeqIO\bsml.pm line 1026. Subroutine _parse_reference redefined at Bio\SeqIO\bsml.pm line 1083. Subroutine _parse_annotation redefined at Bio\SeqIO\bsml.pm line 1149. Subroutine _parse_annotation_old redefined at Bio\SeqIO\bsml.pm line 1221. Subroutine _add_page redefined at Bio\SeqIO\bsml.pm line 1266. Subroutine _addel redefined at Bio\SeqIO\bsml.pm line 1305. Subroutine _show_dna redefined at Bio\SeqIO\bsml.pm line 1329. Subroutine _initialize redefined at Bio\SeqIO\bsml.pm line 1349. Subroutine _parseparams redefined at Bio\SeqIO\bsml.pm line 1388. Subroutine _parse_xml redefined at Bio\SeqIO\bsml.pm line 1415. Subroutine DESTROY redefined at Bio\SeqIO\bsml.pm line 1428. t/SeqIO/bsml.t ............................... 1..16 ok 1 - use XML::DOM; ok 2 - use Bio::SeqIO::bsml; ok 3 - The object isa Bio::Seq::RichSeqI ok 4 - got correct number of refs ok 5 - display_id ok 6 - molecule ok 7 - is_circular ok 8 - dates ok 9 - accession_number ok 10 - seq_version ok 11 - got correct number of SeqFeatures ok 12 - feature start ok 13 - feature end ok 14 - get_tag_values db_xref ok 15 - get_Annotations reference ok 16 - get_Annotations dblink ok t/SeqIO/bsml_sax.t ........................... 1..15 ok 1 - use Bio::SeqIO; ok 2 - The object isa Bio::Seq::RichSeqI ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok t/SeqIO/chadoxml.t ........................... 1..8 ok 1 - use Bio::SeqIO::chadoxml; not ok 2 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 3 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 4 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 5 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 6 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 7 # TODO & SKIP No tests for chadoxml format -- no sample file to test against not ok 8 # TODO & SKIP No tests for chadoxml format -- no sample file to test against ok t/SeqIO/chaos.t .............................. 1..8 ok 1 - use Bio::SeqIO::chaos; not ok 2 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 3 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 4 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 5 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 6 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 7 # TODO & SKIP No tests for chaos format -- no sample file to test against not ok 8 # TODO & SKIP No tests for chaos format -- no sample file to test against ok t/SeqIO/chaosxml.t ........................... 1..2 ok 1 - use Bio::SeqIO; ok 2 ok t/SeqIO/ctf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed Subroutine _initialize redefined at Bio\SeqIO\embl.pm line 154. Subroutine next_seq redefined at Bio\SeqIO\embl.pm line 179. Subroutine _write_ID_line redefined at Bio\SeqIO\embl.pm line 494. Subroutine _is_valid_division redefined at Bio\SeqIO\embl.pm line 571. Subroutine _is_valid_molecule_type redefined at Bio\SeqIO\embl.pm line 604. Subroutine write_seq redefined at Bio\SeqIO\embl.pm line 637. Subroutine _print_EMBL_FTHelper redefined at Bio\SeqIO\embl.pm line 935. Subroutine _read_EMBL_Contig redefined at Bio\SeqIO\embl.pm line 999. Subroutine _read_EMBL_References redefined at Bio\SeqIO\embl.pm line 1030. Subroutine _read_EMBL_Species redefined at Bio\SeqIO\embl.pm line 1098. Subroutine _read_EMBL_DBLink redefined at Bio\SeqIO\embl.pm line 1205. Subroutine _read_EMBL_TaxID_DBLink redefined at Bio\SeqIO\embl.pm line 1239. Subroutine _filehandle redefined at Bio\SeqIO\embl.pm line 1272. Subroutine _read_FTHelper_EMBL redefined at Bio\SeqIO\embl.pm line 1293. Subroutine _write_line_EMBL redefined at Bio\SeqIO\embl.pm line 1418. Subroutine _write_line_EMBL_regex redefined at Bio\SeqIO\embl.pm line 1454. Subroutine _post_sort redefined at Bio\SeqIO\embl.pm line 1506. Subroutine _show_dna redefined at Bio\SeqIO\embl.pm line 1527. Subroutine _id_generation_func redefined at Bio\SeqIO\embl.pm line 1548. Subroutine _ac_generation_func redefined at Bio\SeqIO\embl.pm line 1569. Subroutine _sv_generation_func redefined at Bio\SeqIO\embl.pm line 1590. Subroutine _kw_generation_func redefined at Bio\SeqIO\embl.pm line 1611. t/SeqIO/embl.t ............................... 1..95 ok 1 - use Bio::SeqIO::embl; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 - success reading Embl with ^ location and badly split double quotes ok 25 ok 26 - success writing Embl format with ^ < and > locations ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 - genus duplication test ok 55 ok 56 ok 57 ok 58 ok 59 - CDS - accession on PA line ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 - CDS - OX tagname ok 68 - CDS - OX database ok 69 - CDS - OX primary_id ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 - Check if product was parsed correctly ok 86 - Parse long qualifier ok 87 ok 88 - TaxID set correctly ok 89 - The read sequence has a species object ok 90 - NCBI TaxID has roundtripped ok 91 - Name has roundtripped ok 92 - TaxID set correctly ok 93 - The read sequence has a species object ok 94 - The taxid of the source feature overrides that of the OX line ok 95 - Name has roundtripped ok t/SeqIO/entrezgene.t ......................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed Subroutine _initialize redefined at Bio\SeqIO\excel.pm line 133. Subroutine worksheet redefined at Bio\SeqIO\excel.pm line 165. Subroutine close redefined at Bio\SeqIO\excel.pm line 194. Subroutine _worksheet redefined at Bio\SeqIO\excel.pm line 223. Subroutine _next_record redefined at Bio\SeqIO\excel.pm line 248. Subroutine _get_row_values redefined at Bio\SeqIO\excel.pm line 295. t/SeqIO/excel.t .............................. 1..4 ok 1 - use Bio::SeqIO::excel; ok 2 - The object isa Bio::SeqIO ok 3 - Bio::SeqIO::excel->can('next_seq') ok 4 - Bio::SeqIO::excel->can('write_seq') ok t/SeqIO/exp.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed Subroutine _initialize redefined at Bio\SeqIO\fasta.pm line 91. Subroutine next_seq redefined at Bio\SeqIO\fasta.pm line 111. Subroutine write_seq redefined at Bio\SeqIO\fasta.pm line 192. Subroutine width redefined at Bio\SeqIO\fasta.pm line 271. Subroutine preferred_id_type redefined at Bio\SeqIO\fasta.pm line 294. t/SeqIO/fasta.t .............................. 1..22 ok 1 - use Bio::SeqIO::fasta; ok 2 - The object isa Bio::SeqIO ok 3 - Bio::SeqIO::fasta->can('next_seq') ok 4 - Bio::SeqIO::fasta->can('write_seq') ok 5 - The object isa Bio::Seq ok 6 - sequence ok 7 - length ok 8 - primary_id ok 9 - description ok 10 - The object isa Bio::Seq ok 11 - sequence ok 12 - length ok 13 - primary_id ok 14 - description ok 15 - use Algorithm::Diff; ok 16 - use IO::ScalarArray; ok 17 - use IO::String; ok 18 - fasta format can round-trip ok 19 - dies with roa1.genbank ok 20 - dies with test.gcg ok 21 - dies with test.ace ok 22 - dies with test.raw ok Subroutine _initialize redefined at Bio\SeqIO\fastq.pm line 10. Subroutine next_seq redefined at Bio\SeqIO\fastq.pm line 27. Subroutine next_dataset redefined at Bio\SeqIO\fastq.pm line 39. Subroutine write_seq redefined at Bio\SeqIO\fastq.pm line 122. Subroutine write_fastq redefined at Bio\SeqIO\fastq.pm line 178. Subroutine write_fasta redefined at Bio\SeqIO\fastq.pm line 183. Subroutine write_qual redefined at Bio\SeqIO\fastq.pm line 191. Subroutine variant redefined at Bio\SeqIO\fastq.pm line 218. Subroutine _init_tables redefined at Bio\SeqIO\fastq.pm line 229. Subroutine validate redefined at Bio\SeqIO\fastq.pm line 267. Subroutine quality_header redefined at Bio\SeqIO\fastq.pm line 275. t/SeqIO/fastq.t .............................. 1..139 ok 1 - use Bio::SeqIO::fastq; ok 2 - use Bio::Seq::Quality; ok 3 - bug2335 parses ok 4 - correct num. seqs in bug2335 ok 5 - sample sequence obtained ok 6 - The object isa Bio::Seq::Quality ok 7 - seq() matches bug2335 ok 8 - desc() matches bug2335 ok 9 - display_id() matches bug2335 ok 10 - qual() matches bug2335 ok 11 ok 12 - evil_wrapping parses ok 13 - correct num. seqs in evil_wrapping ok 14 - sample sequence obtained ok 15 - The object isa Bio::Seq::Quality ok 16 - seq() matches evil_wrapping ok 17 - desc() matches evil_wrapping ok 18 - display_id() matches evil_wrapping ok 19 - qual() matches evil_wrapping ok 20 ok 21 - example parses ok 22 - correct num. seqs in example ok 23 - sample sequence obtained ok 24 - The object isa Bio::Seq::Quality ok 25 - seq() matches example ok 26 - desc() matches example ok 27 - display_id() matches example ok 28 - qual() matches example ok 29 ok 30 - illumina_faked parses ok 31 - correct num. seqs in illumina_faked ok 32 - sample sequence obtained ok 33 - The object isa Bio::Seq::Quality ok 34 - seq() matches illumina_faked ok 35 - desc() matches illumina_faked ok 36 - display_id() matches illumina_faked ok 37 - qual() matches illumina_faked ok 38 ok 39 - sanger_93 parses ok 40 - correct num. seqs in sanger_93 ok 41 - sample sequence obtained ok 42 - The object isa Bio::Seq::Quality ok 43 - seq() matches sanger_93 ok 44 - desc() matches sanger_93 ok 45 - display_id() matches sanger_93 ok 46 - qual() matches sanger_93 ok 47 ok 48 - sanger_faked parses ok 49 - correct num. seqs in sanger_faked ok 50 - sample sequence obtained ok 51 - The object isa Bio::Seq::Quality ok 52 - seq() matches sanger_faked ok 53 - desc() matches sanger_faked ok 54 - display_id() matches sanger_faked ok 55 - qual() matches sanger_faked ok 56 ok 57 - solexa_example parses ok 58 - correct num. seqs in solexa_example ok 59 - sample sequence obtained ok 60 - The object isa Bio::Seq::Quality ok 61 - seq() matches solexa_example ok 62 - desc() matches solexa_example ok 63 - display_id() matches solexa_example ok 64 - qual() matches solexa_example ok 65 ok 66 - solexa_faked parses ok 67 - correct num. seqs in solexa_faked ok 68 - sample sequence obtained ok 69 - The object isa Bio::Seq::Quality ok 70 - seq() matches solexa_faked ok 71 - desc() matches solexa_faked ok 72 - display_id() matches solexa_faked ok 73 - qual() matches solexa_faked ok 74 ok 75 - test1_sanger parses ok 76 - correct num. seqs in test1_sanger ok 77 - sample sequence obtained ok 78 - The object isa Bio::Seq::Quality ok 79 - seq() matches test1_sanger ok 80 - desc() matches test1_sanger ok 81 - display_id() matches test1_sanger ok 82 - qual() matches test1_sanger ok 83 ok 84 - test2_solexa parses ok 85 - correct num. seqs in test2_solexa ok 86 - sample sequence obtained ok 87 - The object isa Bio::Seq::Quality ok 88 - seq() matches test2_solexa ok 89 - desc() matches test2_solexa ok 90 - display_id() matches test2_solexa ok 91 - qual() matches test2_solexa ok 92 ok 93 - test3_illumina parses ok 94 - correct num. seqs in test3_illumina ok 95 - sample sequence obtained ok 96 - The object isa Bio::Seq::Quality ok 97 - seq() matches test3_illumina ok 98 - desc() matches test3_illumina ok 99 - display_id() matches test3_illumina ok 100 - qual() matches test3_illumina ok 101 ok 102 - tricky parses ok 103 - correct num. seqs in tricky ok 104 - sample sequence obtained ok 105 - The object isa Bio::Seq::Quality ok 106 - seq() matches tricky ok 107 - desc() matches tricky ok 108 - display_id() matches tricky ok 109 - qual() matches tricky ok 110 ok 111 - Conversion from illumina to sanger ok 112 - Conversion from illumina to illumina ok 113 - Conversion from illumina to solexa ok 114 - Conversion from sanger to sanger ok 115 - Conversion from sanger to illumina ok 116 - Conversion from sanger to solexa ok 117 - Conversion from solexa to sanger ok 118 - Conversion from solexa to illumina ok 119 - Conversion from solexa to solexa ok 120 - Exception caught for error_diff_ids ok 121 - Exception caught for error_long_qual ok 122 - Exception caught for error_no_qual ok 123 - Exception caught for error_qual_del ok 124 - Exception caught for error_qual_escape ok 125 - Exception caught for error_qual_null ok 126 - Exception caught for error_qual_space ok 127 - Exception caught for error_qual_tab ok 128 - Exception caught for error_qual_unit_sep ok 129 - Exception caught for error_qual_vtab ok 130 - Exception caught for error_short_qual ok 131 - Exception caught for error_spaces ok 132 - Exception caught for error_tabs ok 133 - Exception caught for error_trunc_at_plus ok 134 - Exception caught for error_trunc_at_qual ok 135 - Exception caught for error_trunc_at_seq ok 136 - Exception caught for error_trunc_in_plus ok 137 - Exception caught for error_trunc_in_qual ok 138 - Exception caught for error_trunc_in_seq ok 139 - Exception caught for error_trunc_in_title ok t/SeqIO/flybase_chadoxml.t ................... 1..8 ok 1 - use Bio::SeqIO::flybase_chadoxml; not ok 2 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 3 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 4 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 5 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 6 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 7 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against not ok 8 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against ok Subroutine _initialize redefined at Bio\SeqIO\game.pm line 89. Subroutine next_seq redefined at Bio\SeqIO\game.pm line 105. Subroutine write_seq redefined at Bio\SeqIO\game.pm line 130. Subroutine _getseqs redefined at Bio\SeqIO\game.pm line 148. Subroutine _hide_dna redefined at Bio\SeqIO\game.pm line 177. t/SeqIO/game.t ............................... 1..24 ok 1 - use Bio::SeqIO::game; ok 2 - The object isa Bio::SeqIO ok 3 - The object isa Bio::Seq::RichSeq ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok Subroutine _initialize redefined at Bio\SeqIO\gbxml.pm line 91. Subroutine next_seq redefined at Bio\SeqIO\gbxml.pm line 117. Subroutine start_document redefined at Bio\SeqIO\gbxml.pm line 128. Subroutine end_document redefined at Bio\SeqIO\gbxml.pm line 137. Subroutine start_element redefined at Bio\SeqIO\gbxml.pm line 143. Subroutine end_element redefined at Bio\SeqIO\gbxml.pm line 196. Subroutine characters redefined at Bio\SeqIO\gbxml.pm line 355. t/SeqIO/gbxml.t .............................. 1..14 ok 1 - use Bio::SeqIO::gbxml; ok 2 - The object isa Bio::SeqIO ok 3 - molecule ok 4 - alphabet ok 5 - primary_id ok 6 - display_id ok 7 - version ok 8 - is_circular ok 9 - description ok 10 - sequence ok 11 - classification ok 12 - feat - clone_lib ok 13 - feat - db_xref ok 14 - feat - lab_host ok Subroutine _initialize redefined at Bio\SeqIO\gcg.pm line 85. Subroutine next_seq redefined at Bio\SeqIO\gcg.pm line 105. Subroutine write_seq redefined at Bio\SeqIO\gcg.pm line 178. Subroutine GCG_checksum redefined at Bio\SeqIO\gcg.pm line 249. Subroutine _validate_checksum redefined at Bio\SeqIO\gcg.pm line 284. t/SeqIO/gcg.t ................................ 1..17 ok 1 - use Bio::SeqIO::gcg; ok 2 - The object isa Bio::SeqIO ok 3 - Bio::SeqIO::gcg->can('next_seq') ok 4 - Bio::SeqIO::gcg->can('write_seq') ok 5 - The object isa Bio::Seq ok 6 - The object isa Bio::Seq::RichSeq ok 7 - sequence ok 8 - length not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id? # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 54. # got: 'Bio::PrimarySeq=HASH(0x4d7b350)' # expected: 'roa1_drome' ok 10 - description ok 11 ok 12 - The object isa Bio::SeqI ok 13 ok 14 - use Algorithm::Diff; ok 15 - use IO::ScalarArray; ok 16 - use IO::String; ok 17 - gcg format can round-trip ok Subroutine _initialize redefined at Bio\SeqIO\genbank.pm line 229. Subroutine next_seq redefined at Bio\SeqIO\genbank.pm line 253. Subroutine write_seq redefined at Bio\SeqIO\genbank.pm line 785. Subroutine _print_GenBank_FTHelper redefined at Bio\SeqIO\genbank.pm line 1102. Subroutine _read_GenBank_References redefined at Bio\SeqIO\genbank.pm line 1147. Subroutine _add_ref_to_array redefined at Bio\SeqIO\genbank.pm line 1285. Subroutine _read_GenBank_Species redefined at Bio\SeqIO\genbank.pm line 1331. Subroutine _read_FTHelper_GenBank redefined at Bio\SeqIO\genbank.pm line 1442. Subroutine _write_line_GenBank redefined at Bio\SeqIO\genbank.pm line 1577. Subroutine _write_line_GenBank_regex redefined at Bio\SeqIO\genbank.pm line 1615. Subroutine _post_sort redefined at Bio\SeqIO\genbank.pm line 1662. Subroutine _show_dna redefined at Bio\SeqIO\genbank.pm line 1682. Subroutine _id_generation_func redefined at Bio\SeqIO\genbank.pm line 1701. Subroutine _ac_generation_func redefined at Bio\SeqIO\genbank.pm line 1720. Subroutine _sv_generation_func redefined at Bio\SeqIO\genbank.pm line 1740. Subroutine _kw_generation_func redefined at Bio\SeqIO\genbank.pm line 1761. t/SeqIO/genbank.t ............................ 1..272 ok 1 - use Bio::SeqIO::genbank; ok 2 - The object isa Bio::SeqIO ok 3 - AI129902 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - NT_021877 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 - BAB68554 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 - operator overloading in AnnotationI is deprecated ok 29 - NC_006346 ok 30 ok 31 ok 32 - U71225 ok 33 ok 34 - AB077698 ok 35 ok 36 - DQ018368 ok 37 - D10483 ok 38 ok 39 ok 40 ok 41 - bug 1487 ok 42 ok 43 - bug 1647 ok 44 ok 45 ok 46 - bug 1673 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 - AF165282 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 - species parsing incorrect for genbank ok 62 - genus duplicated in genbank parsing ok 63 ok 64 ok 65 - species parsing incorrect for genbank ok 66 - genus duplicated in genbank parsing ok 67 ok 68 ok 69 - species parsing incorrect for genbank ok 70 - genus duplicated in genbank parsing ok 71 ok 72 - streaming ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 - Total number of sequences in test file ok 79 ok 80 - Fuzzy in ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 - Fuzzy out ok 93 - BK000016 ok 94 ok 95 - BK000016 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 - BK000016 ok 111 - roundtrip ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 - revcomp split location ok 130 - Bug 1925 ok 131 ok 132 ok 133 - wgs ok 134 ok 135 - wgs_scafld ok 136 ok 137 - wgs_scafld ok 138 ok 139 ok 140 - BC000007 ok 141 - BK000016-tpa.gbk ok 142 - ay116458.gb ok 143 - ay149291.gb ok 144 - NC_006346.gb ok 145 - ay007676.gb ok 146 - dq519393.gb ok 147 ok 148 - swissprot:K1C9_HUMAN ok 149 ok 150 - swissprot ok 151 ok 152 - GenBank:Z29074.1 ok 153 ok 154 - GenBank ok 155 ok 156 - GenPept:CAA82315.1 ok 157 ok 158 - GenPept ok 159 ok 160 - GenBank:S69510.1 ok 161 ok 162 - GenBank ok 163 ok 164 - GenPept:AAC60619.1 ok 165 ok 166 - GenPept ok 167 ok 168 - GenBank:X75015.1 ok 169 ok 170 - GenBank ok 171 ok 172 - GenPept:CAA52924.1 ok 173 ok 174 - GenPept ok 175 ok 176 - GenBank:AB001594.1 ok 177 ok 178 - GenBank ok 179 ok 180 - GenPept:BAA19418.1 ok 181 ok 182 - GenPept ok 183 ok 184 - GenBank:I37984 ok 185 ok 186 - GenBank ok 187 ok 188 - HSSP:P08670 ok 189 ok 190 - HSSP ok 191 ok 192 - IntAct:P35527 ok 193 ok 194 - IntAct ok 195 ok 196 - Ensembl:ENSG00000171403 ok 197 ok 198 - Ensembl ok 199 ok 200 - KEGG:hsa:3857 ok 201 ok 202 - KEGG ok 203 ok 204 - HGNC:6447 ok 205 ok 206 - HGNC ok 207 ok 208 - MIM:144200 ok 209 ok 210 - MIM ok 211 ok 212 - MIM:607606 ok 213 ok 214 - MIM ok 215 ok 216 - ArrayExpress:P35527 ok 217 ok 218 - ArrayExpress ok 219 ok 220 - GO:0005200 ok 221 ok 222 - GO ok 223 ok 224 - GO:0008544 ok 225 ok 226 - GO ok 227 ok 228 - InterPro:IPR011000 ok 229 ok 230 - InterPro ok 231 ok 232 - InterPro:IPR001664 ok 233 ok 234 - InterPro ok 235 ok 236 - InterPro:IPR002957 ok 237 ok 238 - InterPro ok 239 ok 240 - Pfam:PF00038 ok 241 ok 242 - Pfam ok 243 ok 244 - PRINTS:PR01248 ok 245 ok 246 - PRINTS ok 247 ok 248 - PROSITE:PS00226 ok 249 ok 250 - PROSITE ok 251 ok 252 - Bug 2195 ok 253 - Bug 2195 ok 254 - The object isa Bio::Annotation::SimpleValue ok 255 ok 256 - The object isa Bio::Annotation::SimpleValue ok 257 ok 258 - P39765 ok 259 - P39765 ok 260 - P39765 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 - operator overloading in AnnotationI is deprecated ok 271 ok 272 ok Subroutine next_seq redefined at Bio\SeqIO\interpro.pm line 105. Subroutine _initialize redefined at Bio\SeqIO\interpro.pm line 218. Subroutine _sequence_factory redefined at Bio\SeqIO\interpro.pm line 255. Subroutine _xml_parser redefined at Bio\SeqIO\interpro.pm line 273. Subroutine _parse_xml redefined at Bio\SeqIO\interpro.pm line 291. Subroutine _dom redefined at Bio\SeqIO\interpro.pm line 307. t/SeqIO/interpro.t ........................... 1..20 ok 1 - use Bio::SeqIO::interpro; ok 2 - The object isa Bio::SeqIO ok 3 - seq obj is defined ok 4 - The object isa Bio::Seq::RichSeq ok 5 - right number of SeqFeatures ok 6 - The object isa Bio::SeqFeature::Generic ok 7 - display_name() ok 8 - seq object is defined ok 9 - right number of SeqFeatures ok 10 - there is no next_seq (correctly) ok 11 - bug 1908 ok 12 - right number of SeqFeatures ok 13 - primary_tag() ok 14 - display_name() ok 15 - location->end() ok 16 - right number of dblinks ok 17 - first primary_id ok 18 - second primary_id ok 19 - right number of dblinks ok 20 - primary_id via dblinks ok Subroutine _initialize redefined at Bio\SeqIO\kegg.pm line 149. Subroutine next_seq redefined at Bio\SeqIO\kegg.pm line 172. Subroutine write_seq redefined at Bio\SeqIO\kegg.pm line 323. t/SeqIO/kegg.t ............................... 1..16 ok 1 - use Bio::SeqIO::kegg; ok 2 - The object isa Bio::SeqIO ok 3 ok 4 - The object isa Bio::Seq::RichSeq ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok Subroutine _initialize redefined at Bio\SeqIO\largefasta.pm line 93. Subroutine next_seq redefined at Bio\SeqIO\largefasta.pm line 113. Subroutine write_seq redefined at Bio\SeqIO\largefasta.pm line 155. t/SeqIO/largefasta.t ......................... 1..16 ok 1 - use Bio::SeqIO::largefasta; ok 2 - The object isa Bio::SeqIO ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok Subroutine next_seq redefined at Bio\SeqIO\lasergene.pm line 101. Subroutine write_seq redefined at Bio\SeqIO\lasergene.pm line 160. t/SeqIO/lasergene.t .......................... 1..13 ok 1 - use Bio::SeqIO::lasergene; ok 2 ok 3 - The object isa Bio::SeqIO ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok Subroutine _initialize redefined at Bio\SeqIO\locuslink.pm line 273. Subroutine search_pattern redefined at Bio\SeqIO\locuslink.pm line 306. Subroutine read_species redefined at Bio\SeqIO\locuslink.pm line 327. Subroutine read_dblink redefined at Bio\SeqIO\locuslink.pm line 340. Subroutine read_reference redefined at Bio\SeqIO\locuslink.pm line 358. Subroutine add_annotation redefined at Bio\SeqIO\locuslink.pm line 373. Subroutine add_annotation_ref redefined at Bio\SeqIO\locuslink.pm line 396. Subroutine make_unique redefined at Bio\SeqIO\locuslink.pm line 410. Subroutine next_seq redefined at Bio\SeqIO\locuslink.pm line 427. Subroutine show_obj redefined at Bio\SeqIO\locuslink.pm line 580. t/SeqIO/locuslink.t .......................... 1..26 ok 1 - use Bio::SeqIO::locuslink; ok 2 - use Bio::SeqFeature::Generic; ok 3 - use Bio::SeqFeature::AnnotationAdaptor; ok 4 ok 5 - The object isa Bio::SeqIO ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok Subroutine _initialize redefined at Bio\SeqIO\mbsout.pm line 102. Subroutine _read_start redefined at Bio\SeqIO\mbsout.pm line 164. Subroutine get_segsites redefined at Bio\SeqIO\mbsout.pm line 246. Subroutine get_current_run_segsites redefined at Bio\SeqIO\mbsout.pm line 266. Subroutine get_pop_mut_param_per_site redefined at Bio\SeqIO\mbsout.pm line 281. Subroutine get_pop_recomb_param_per_site redefined at Bio\SeqIO\mbsout.pm line 296. Subroutine get_nsites redefined at Bio\SeqIO\mbsout.pm line 311. Subroutine get_selpos redefined at Bio\SeqIO\mbsout.pm line 326. Subroutine get_nreps redefined at Bio\SeqIO\mbsout.pm line 341. Subroutine get_nfiles redefined at Bio\SeqIO\mbsout.pm line 356. Subroutine get_traj_filename redefined at Bio\SeqIO\mbsout.pm line 371. Subroutine get_runs redefined at Bio\SeqIO\mbsout.pm line 386. Subroutine get_Positions redefined at Bio\SeqIO\mbsout.pm line 401. Subroutine get_tot_run_haps redefined at Bio\SeqIO\mbsout.pm line 416. Subroutine get_mbs_info_line redefined at Bio\SeqIO\mbsout.pm line 431. Subroutine get_tot_haps redefined at Bio\SeqIO\mbsout.pm line 446. Subroutine get_next_run_num redefined at Bio\SeqIO\mbsout.pm line 463. Subroutine get_last_haps_run_num redefined at Bio\SeqIO\mbsout.pm line 480. Subroutine get_last_read_hap_num redefined at Bio\SeqIO\mbsout.pm line 497. Subroutine outgroup redefined at Bio\SeqIO\mbsout.pm line 520. Subroutine get_next_seq redefined at Bio\SeqIO\mbsout.pm line 539. Subroutine get_next_hap redefined at Bio\SeqIO\mbsout.pm line 589. Subroutine get_next_run redefined at Bio\SeqIO\mbsout.pm line 622. Subroutine get_base_conversion_table redefined at Bio\SeqIO\mbsout.pm line 671. Subroutine _get_next_clean_hap redefined at Bio\SeqIO\mbsout.pm line 680. Subroutine _load_run_info redefined at Bio\SeqIO\mbsout.pm line 728. t/SeqIO/mbsout.t ............................. 1..74 ok 1 - use Bio::SeqIO::mbsout; ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3 ok 3 - The object isa Bio::SeqIO::mbsout ok 4 - The object isa Bio::SeqIO::mbsout ok 5 - Get NSITES ok 6 - Get TRAJ_FILENAME ok 7 - Get SELPOS ok 8 - Get TOT_RUN_HAPS ok 9 - Get MBS_INFO_LINE ok 10 - Get NFILES ok 11 - Get POP_MUT_PARAM_PER_SITE ok 12 - Get POP_RECOMB_PARAM_PER_SITE ok 13 - Get NEXT_RUN_NUM ok 14 - Get CURRENT_RUN_SEGSITES ok 15 - Get RUNS ok 16 - Get LAST_READ_HAP_NUM ok 17 - Get NREPS ok 18 - Get POSITIONS ok 19 - Get SEGSITES ok 20 - Get next_hap at beginning of run ok 21 - Get next_hap after beginning of run ok 22 - Get next_pop after beginning of pop ok 23 - Get next_hap ok 24 - Get next_hap ok 25 - Get next_run after beginning of run ok 26 - Get next_run at beginning of run ok 27 - Get next_run at beginning of run ok 28 - have all lines been read? ok 29 - The object isa Bio::SeqIO::mbsout ok 30 - Get NSITES ok 31 - Get TRAJ_FILENAME ok 32 - Get SELPOS ok 33 - Get TOT_RUN_HAPS ok 34 - Get MBS_INFO_LINE ok 35 - Get NFILES ok 36 - Get POP_MUT_PARAM_PER_SITE ok 37 - Get POP_RECOMB_PARAM_PER_SITE ok 38 - Get NEXT_RUN_NUM ok 39 - Get CURRENT_RUN_SEGSITES ok 40 - Get RUNS ok 41 - Get LAST_READ_HAP_NUM ok 42 - Get NREPS ok 43 - Get POSITIONS ok 44 - Get SEGSITES ok 45 - Get next_hap at beginning of run ok 46 - Get next_hap after beginning of run ok 47 - Testing mbsout::outgroup ok 48 - Get next_run after beginning of run ok 49 - Get next_run after beginning of run ok 50 - Get next_run at beginning of run ok 51 - Get next_hap at beginning of run 2 ok 52 - Get next_run after hap ok 53 - next run should be 5. ok 54 - The object isa Bio::SeqIO::mbsout ok 55 - Get NSITES ok 56 - Get TRAJ_FILENAME ok 57 - Get SELPOS ok 58 - Get TOT_RUN_HAPS ok 59 - Get MBS_INFO_LINE ok 60 - Get NFILES ok 61 - Get POP_MUT_PARAM_PER_SITE ok 62 - Get POP_RECOMB_PARAM_PER_SITE ok 63 - Get NEXT_RUN_NUM ok 64 - Get CURRENT_RUN_SEGSITES ok 65 - Get RUNS ok 66 - Get LAST_READ_HAP_NUM ok 67 - Get NREPS ok 68 - Get POSITIONS ok 69 - Get SEGSITES ok 70 - Get next_run at end/beginning of run ok 71 - have all lines been read? ok 72 - Get next_run at eof ok 73 - Get next_hap at eof ok 74 - Get next_seq at eof ok Subroutine _initialize redefined at Bio\SeqIO\metafasta.pm line 107. Subroutine next_seq redefined at Bio\SeqIO\metafasta.pm line 127. Subroutine write_seq redefined at Bio\SeqIO\metafasta.pm line 206. Subroutine width redefined at Bio\SeqIO\metafasta.pm line 249. t/SeqIO/metafasta.t .......................... 1..6 ok 1 - use Bio::SeqIO::metafasta; ok 2 - The object isa Bio::SeqIO ok 3 ok 4 - The object isa Bio::Seq::Meta ok 5 ok 6 ok Subroutine _initialize redefined at Bio\SeqIO\msout.pm line 101. Subroutine _read_start redefined at Bio\SeqIO\msout.pm line 159. Subroutine get_segsites redefined at Bio\SeqIO\msout.pm line 224. Subroutine get_current_run_segsites redefined at Bio\SeqIO\msout.pm line 245. Subroutine get_runs redefined at Bio\SeqIO\msout.pm line 261. Subroutine get_Seeds redefined at Bio\SeqIO\msout.pm line 279. Subroutine get_Positions redefined at Bio\SeqIO\msout.pm line 297. Subroutine get_tot_run_haps redefined at Bio\SeqIO\msout.pm line 314. Subroutine get_ms_info_line redefined at Bio\SeqIO\msout.pm line 329. Subroutine get_tot_haps redefined at Bio\SeqIO\msout.pm line 345. Subroutine get_Pops redefined at Bio\SeqIO\msout.pm line 362. Subroutine get_next_run_num redefined at Bio\SeqIO\msout.pm line 379. Subroutine get_last_haps_run_num redefined at Bio\SeqIO\msout.pm line 396. Subroutine get_last_read_hap_num redefined at Bio\SeqIO\msout.pm line 413. Subroutine outgroup redefined at Bio\SeqIO\msout.pm line 433. Subroutine get_next_haps_pop_num redefined at Bio\SeqIO\msout.pm line 454. Subroutine get_next_seq redefined at Bio\SeqIO\msout.pm line 485. Subroutine next_seq redefined at Bio\SeqIO\msout.pm line 535. Subroutine get_next_hap redefined at Bio\SeqIO\msout.pm line 553. Subroutine get_next_pop redefined at Bio\SeqIO\msout.pm line 585. Subroutine get_next_run redefined at Bio\SeqIO\msout.pm line 626. Subroutine get_base_conversion_table redefined at Bio\SeqIO\msout.pm line 680. Subroutine _get_next_clean_hap redefined at Bio\SeqIO\msout.pm line 689. Subroutine _load_run_info redefined at Bio\SeqIO\msout.pm line 737. t/SeqIO/msout.t .............................. 1..85 ok 1 - use Bio::SeqIO::msout; ok 2 - Bio::SeqIO::msout is at least api version 1.1.5 ok 3 - The object isa Bio::SeqIO::msout ok 4 - Get TOT_RUN_HAPS ok 5 - Get POPS ok 6 - Get CURRENT_RUN_SEGSITES ok 7 - Get NEXT_RUN_NUM ok 8 - Get RUNS ok 9 - Get MS_INFO_LINE ok 10 - Get LAST_READ_HAP_NUM ok 11 - Get POSITIONS ok 12 - Get SEGSITES ok 13 - Get SEEDS ok 14 - Get next_hap at beginning of run ok 15 - Get next_hap after beginning of run ok 16 - Testing msout::outgroup ok 17 - Get next_pop after beginning of pop ok 18 - Get next_pop at beginning of pop ok 19 - Get next_run after beginning of run ok 20 - Get next_pop at beginning of run ok 21 - Get next_hap after pop ok 22 - Get next_run after pop and hap ok 23 - Get next_run at beginning of run ok 24 - have all lines been read? ok 25 - The object isa Bio::SeqIO::msout ok 26 - Get TOT_RUN_HAPS ok 27 - Get POPS ok 28 - Get CURRENT_RUN_SEGSITES ok 29 - Get NEXT_RUN_NUM ok 30 - Get RUNS ok 31 - Get MS_INFO_LINE ok 32 - Get LAST_READ_HAP_NUM ok 33 - Get POSITIONS ok 34 - Get SEGSITES ok 35 - Get SEEDS ok 36 - Get next_hap at beginning of run ok 37 - Get next_hap after beginning of run ok 38 - Testing msout::outgroup ok 39 - Get next_pop after beginning of pop ok 40 - Get next_pop at beginning of pop/run ok 41 - Get next_run at beginning of run ok 42 - Get next_hap at beginning of run 2 ok 43 - Get next_run after hap ok 44 - next run should be 5. ok 45 - Get last hap through next_hap ok 46 - The object isa Bio::SeqIO::msout ok 47 - The object isa Bio::SeqIO::msout ok 48 - Get TOT_RUN_HAPS ok 49 - Get POPS ok 50 - Get CURRENT_RUN_SEGSITES ok 51 - Get NEXT_RUN_NUM ok 52 - Get RUNS ok 53 - Get MS_INFO_LINE ok 54 - Get LAST_READ_HAP_NUM ok 55 - Get POSITIONS ok 56 - Get SEGSITES ok 57 - Get SEEDS ok 58 - Get next_pop at end of run ok 59 - have all lines been read? ok 60 - Get next_pop at eof ok 61 - Get next_run at eof ok 62 - Get next_hap at eof ok 63 - Get next_seq at eof ok 64 - The object isa Bio::SeqIO::msout ok 65 - Get TOT_RUN_HAPS ok 66 - Get POPS ok 67 - Get CURRENT_RUN_SEGSITES ok 68 - Get NEXT_RUN_NUM ok 69 - Get RUNS ok 70 - Get MS_INFO_LINE ok 71 - Get LAST_READ_HAP_NUM ok 72 - Get POSITIONS ok 73 - Get SEGSITES ok 74 - Get SEEDS ok 75 - Get next_hap at beginning of run ok 76 - Get next_hap after beginning of run ok 77 - Testing msout::outgroup ok 78 - Get next_pop after beginning of pop ok 79 - Get next_pop at beginning of pop ok 80 - Get next_run after beginning of run ok 81 - Get next_pop at beginning of run ok 82 - Get next_hap after pop ok 83 - Get next_run after pop and hap ok 84 - Get next_run at beginning of run ok 85 - have all lines been read? ok Timeout (max run time is 300s) C:\Perl64-5.12\bin\perl.exe exits with 37