PATH=C:\PlatSDK\Bin\Win64\x86\AMD64;C:\PlatSDK\Bin;C:\PlatSDK\Bin\WinNT;C:\cygwin\bin;C:\cpanfly-5.16\var\megalib\bin;C:\Perl64-5.16\site\bin;C:\Perl64-5.16\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:\instantclient_11_2;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 2013-12-18T03:13:49 ActivePerl-1600 CPAN-2.00 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~1.16/var/libs/bin;C:\PlatSDK\Bin\Win64\x86\AMD64;C:\PlatSDK\Bin;C:\PlatSDK\Bin\WinNT;C:\cygwin\bin;C:\CPANFL~1.16\var\megalib\bin;C:\Perl64-5.16\site\bin;C:\Perl64-5.16\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:\INSTAN~1;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 Reading 'C:\cpanfly-5.16\var\cpan\Metadata' Database was generated on Wed, 18 Dec 2013 09:53:03 GMT Running make for C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz Fetching with LWP: http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz Fetching with LWP: http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/CHECKSUMS Checksum for C:\cpanfly-5.16\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.923.tar.gz ok BioPerl-1.6.923 BioPerl-1.6.923/.travis.yml BioPerl-1.6.923/AUTHORS BioPerl-1.6.923/BioPerl.pm BioPerl-1.6.923/BUGS BioPerl-1.6.923/Build.PL BioPerl-1.6.923/Changes BioPerl-1.6.923/DEPENDENCIES BioPerl-1.6.923/DEPRECATED BioPerl-1.6.923/INSTALL BioPerl-1.6.923/INSTALL.SKIP BioPerl-1.6.923/INSTALL.WIN BioPerl-1.6.923/LICENSE BioPerl-1.6.923/MANIFEST BioPerl-1.6.923/META.json BioPerl-1.6.923/META.yml BioPerl-1.6.923/README BioPerl-1.6.923/README.md BioPerl-1.6.923/Bio BioPerl-1.6.923/Bio/AlignIO.pm BioPerl-1.6.923/Bio/AnalysisI.pm BioPerl-1.6.923/Bio/AnalysisParserI.pm BioPerl-1.6.923/Bio/AnalysisResultI.pm BioPerl-1.6.923/Bio/AnnotatableI.pm BioPerl-1.6.923/Bio/AnnotationCollectionI.pm BioPerl-1.6.923/Bio/AnnotationI.pm BioPerl-1.6.923/Bio/ClusterI.pm BioPerl-1.6.923/Bio/ClusterIO.pm BioPerl-1.6.923/Bio/DasI.pm BioPerl-1.6.923/Bio/DBLinkContainerI.pm BioPerl-1.6.923/Bio/DescribableI.pm BioPerl-1.6.923/Bio/FeatureHolderI.pm BioPerl-1.6.923/Bio/HandlerBaseI.pm BioPerl-1.6.923/Bio/IdCollectionI.pm BioPerl-1.6.923/Bio/IdentifiableI.pm BioPerl-1.6.923/Bio/LocatableSeq.pm BioPerl-1.6.923/Bio/LocationI.pm BioPerl-1.6.923/Bio/MapIO.pm BioPerl-1.6.923/Bio/NexmlIO.pm BioPerl-1.6.923/Bio/OntologyIO.pm BioPerl-1.6.923/Bio/ParameterBaseI.pm BioPerl-1.6.923/Bio/Perl.pm BioPerl-1.6.923/Bio/PhyloNetwork.pm BioPerl-1.6.923/Bio/PrimarySeq.pm BioPerl-1.6.923/Bio/PrimarySeqI.pm BioPerl-1.6.923/Bio/PullParserI.pm BioPerl-1.6.923/Bio/Range.pm BioPerl-1.6.923/Bio/RangeI.pm BioPerl-1.6.923/Bio/SearchDist.pm BioPerl-1.6.923/Bio/SearchIO.pm BioPerl-1.6.923/Bio/Seq.pm BioPerl-1.6.923/Bio/SeqAnalysisParserI.pm BioPerl-1.6.923/Bio/SeqFeatureI.pm BioPerl-1.6.923/Bio/SeqI.pm BioPerl-1.6.923/Bio/SeqIO.pm BioPerl-1.6.923/Bio/SeqUtils.pm BioPerl-1.6.923/Bio/SimpleAlign.pm BioPerl-1.6.923/Bio/SimpleAnalysisI.pm BioPerl-1.6.923/Bio/Species.pm BioPerl-1.6.923/Bio/Taxon.pm BioPerl-1.6.923/Bio/Taxonomy.pm BioPerl-1.6.923/Bio/TreeIO.pm BioPerl-1.6.923/Bio/UpdateableSeqI.pm BioPerl-1.6.923/Bio/WebAgent.pm BioPerl-1.6.923/Bio/Align BioPerl-1.6.923/Bio/Align/AlignI.pm BioPerl-1.6.923/Bio/Align/DNAStatistics.pm BioPerl-1.6.923/Bio/Align/Graphics.pm BioPerl-1.6.923/Bio/Align/PairwiseStatistics.pm BioPerl-1.6.923/Bio/Align/ProteinStatistics.pm BioPerl-1.6.923/Bio/Align/StatisticsI.pm BioPerl-1.6.923/Bio/Align/Utilities.pm BioPerl-1.6.923/Bio/AlignIO BioPerl-1.6.923/Bio/AlignIO/arp.pm BioPerl-1.6.923/Bio/AlignIO/bl2seq.pm BioPerl-1.6.923/Bio/AlignIO/clustalw.pm BioPerl-1.6.923/Bio/AlignIO/emboss.pm BioPerl-1.6.923/Bio/AlignIO/fasta.pm BioPerl-1.6.923/Bio/AlignIO/largemultifasta.pm BioPerl-1.6.923/Bio/AlignIO/maf.pm BioPerl-1.6.923/Bio/AlignIO/mase.pm BioPerl-1.6.923/Bio/AlignIO/mega.pm BioPerl-1.6.923/Bio/AlignIO/meme.pm BioPerl-1.6.923/Bio/AlignIO/metafasta.pm BioPerl-1.6.923/Bio/AlignIO/msf.pm BioPerl-1.6.923/Bio/AlignIO/nexml.pm BioPerl-1.6.923/Bio/AlignIO/nexus.pm BioPerl-1.6.923/Bio/AlignIO/pfam.pm BioPerl-1.6.923/Bio/AlignIO/phylip.pm BioPerl-1.6.923/Bio/AlignIO/po.pm BioPerl-1.6.923/Bio/AlignIO/proda.pm BioPerl-1.6.923/Bio/AlignIO/prodom.pm BioPerl-1.6.923/Bio/AlignIO/psi.pm BioPerl-1.6.923/Bio/AlignIO/selex.pm BioPerl-1.6.923/Bio/AlignIO/stockholm.pm BioPerl-1.6.923/Bio/AlignIO/xmfa.pm BioPerl-1.6.923/Bio/AlignIO/Handler BioPerl-1.6.923/Bio/AlignIO/Handler/GenericAlignHandler.pm BioPerl-1.6.923/Bio/Annotation BioPerl-1.6.923/Bio/Annotation/AnnotationFactory.pm BioPerl-1.6.923/Bio/Annotation/Collection.pm BioPerl-1.6.923/Bio/Annotation/Comment.pm BioPerl-1.6.923/Bio/Annotation/DBLink.pm BioPerl-1.6.923/Bio/Annotation/OntologyTerm.pm BioPerl-1.6.923/Bio/Annotation/Reference.pm BioPerl-1.6.923/Bio/Annotation/Relation.pm BioPerl-1.6.923/Bio/Annotation/SimpleValue.pm BioPerl-1.6.923/Bio/Annotation/StructuredValue.pm BioPerl-1.6.923/Bio/Annotation/TagTree.pm BioPerl-1.6.923/Bio/Annotation/Target.pm BioPerl-1.6.923/Bio/Annotation/Tree.pm BioPerl-1.6.923/Bio/Annotation/TypeManager.pm BioPerl-1.6.923/Bio/Assembly BioPerl-1.6.923/Bio/Assembly/Contig.pm BioPerl-1.6.923/Bio/Assembly/ContigAnalysis.pm BioPerl-1.6.923/Bio/Assembly/IO.pm BioPerl-1.6.923/Bio/Assembly/Scaffold.pm BioPerl-1.6.923/Bio/Assembly/ScaffoldI.pm BioPerl-1.6.923/Bio/Assembly/Singlet.pm BioPerl-1.6.923/Bio/Assembly/IO BioPerl-1.6.923/Bio/Assembly/IO/ace.pm BioPerl-1.6.923/Bio/Assembly/IO/bowtie.pm BioPerl-1.6.923/Bio/Assembly/IO/maq.pm BioPerl-1.6.923/Bio/Assembly/IO/phrap.pm BioPerl-1.6.923/Bio/Assembly/IO/sam.pm BioPerl-1.6.923/Bio/Assembly/IO/tigr.pm BioPerl-1.6.923/Bio/Assembly/Tools BioPerl-1.6.923/Bio/Assembly/Tools/ContigSpectrum.pm BioPerl-1.6.923/Bio/Cluster BioPerl-1.6.923/Bio/Cluster/ClusterFactory.pm BioPerl-1.6.923/Bio/Cluster/FamilyI.pm BioPerl-1.6.923/Bio/Cluster/SequenceFamily.pm BioPerl-1.6.923/Bio/Cluster/UniGene.pm BioPerl-1.6.923/Bio/Cluster/UniGeneI.pm BioPerl-1.6.923/Bio/ClusterIO BioPerl-1.6.923/Bio/ClusterIO/dbsnp.pm BioPerl-1.6.923/Bio/ClusterIO/unigene.pm BioPerl-1.6.923/Bio/CodonUsage BioPerl-1.6.923/Bio/CodonUsage/IO.pm BioPerl-1.6.923/Bio/CodonUsage/Table.pm BioPerl-1.6.923/Bio/Coordinate BioPerl-1.6.923/Bio/Coordinate/Chain.pm BioPerl-1.6.923/Bio/Coordinate/Collection.pm BioPerl-1.6.923/Bio/Coordinate/ExtrapolatingPair.pm BioPerl-1.6.923/Bio/Coordinate/GeneMapper.pm BioPerl-1.6.923/Bio/Coordinate/Graph.pm BioPerl-1.6.923/Bio/Coordinate/MapperI.pm BioPerl-1.6.923/Bio/Coordinate/Pair.pm BioPerl-1.6.923/Bio/Coordinate/Result.pm BioPerl-1.6.923/Bio/Coordinate/ResultI.pm BioPerl-1.6.923/Bio/Coordinate/Utils.pm BioPerl-1.6.923/Bio/Coordinate/Result BioPerl-1.6.923/Bio/Coordinate/Result/Gap.pm BioPerl-1.6.923/Bio/Coordinate/Result/Match.pm BioPerl-1.6.923/Bio/Das BioPerl-1.6.923/Bio/Das/FeatureTypeI.pm BioPerl-1.6.923/Bio/Das/SegmentI.pm BioPerl-1.6.923/Bio/DB BioPerl-1.6.923/Bio/DB/Ace.pm BioPerl-1.6.923/Bio/DB/BioFetch.pm BioPerl-1.6.923/Bio/DB/CUTG.pm BioPerl-1.6.923/Bio/DB/DBFetch.pm BioPerl-1.6.923/Bio/DB/EMBL.pm BioPerl-1.6.923/Bio/DB/EntrezGene.pm BioPerl-1.6.923/Bio/DB/Expression.pm BioPerl-1.6.923/Bio/DB/Failover.pm BioPerl-1.6.923/Bio/DB/Fasta.pm BioPerl-1.6.923/Bio/DB/FileCache.pm BioPerl-1.6.923/Bio/DB/Flat.pm BioPerl-1.6.923/Bio/DB/GenBank.pm BioPerl-1.6.923/Bio/DB/GenericWebAgent.pm BioPerl-1.6.923/Bio/DB/GenPept.pm BioPerl-1.6.923/Bio/DB/GFF.pm BioPerl-1.6.923/Bio/DB/HIV.pm BioPerl-1.6.923/Bio/DB/IndexedBase.pm BioPerl-1.6.923/Bio/DB/InMemoryCache.pm BioPerl-1.6.923/Bio/DB/LocationI.pm BioPerl-1.6.923/Bio/DB/MeSH.pm BioPerl-1.6.923/Bio/DB/NCBIHelper.pm BioPerl-1.6.923/Bio/DB/Qual.pm BioPerl-1.6.923/Bio/DB/QueryI.pm BioPerl-1.6.923/Bio/DB/RandomAccessI.pm BioPerl-1.6.923/Bio/DB/ReferenceI.pm BioPerl-1.6.923/Bio/DB/RefSeq.pm BioPerl-1.6.923/Bio/DB/Registry.pm BioPerl-1.6.923/Bio/DB/SeqFeature.pm BioPerl-1.6.923/Bio/DB/SeqHound.pm BioPerl-1.6.923/Bio/DB/SeqI.pm BioPerl-1.6.923/Bio/DB/SeqVersion.pm BioPerl-1.6.923/Bio/DB/SwissProt.pm BioPerl-1.6.923/Bio/DB/Taxonomy.pm BioPerl-1.6.923/Bio/DB/TFBS.pm BioPerl-1.6.923/Bio/DB/Universal.pm BioPerl-1.6.923/Bio/DB/UpdateableSeqI.pm BioPerl-1.6.923/Bio/DB/WebDBSeqI.pm BioPerl-1.6.923/Bio/DB/Expression BioPerl-1.6.923/Bio/DB/Expression/geo.pm BioPerl-1.6.923/Bio/DB/Flat BioPerl-1.6.923/Bio/DB/Flat/BDB.pm BioPerl-1.6.923/Bio/DB/Flat/BinarySearch.pm BioPerl-1.6.923/Bio/DB/Flat/BDB BioPerl-1.6.923/Bio/DB/Flat/BDB/embl.pm BioPerl-1.6.923/Bio/DB/Flat/BDB/fasta.pm BioPerl-1.6.923/Bio/DB/Flat/BDB/genbank.pm BioPerl-1.6.923/Bio/DB/Flat/BDB/swiss.pm BioPerl-1.6.923/Bio/DB/GFF BioPerl-1.6.923/Bio/DB/GFF/Aggregator.pm BioPerl-1.6.923/Bio/DB/GFF/Featname.pm BioPerl-1.6.923/Bio/DB/GFF/Feature.pm BioPerl-1.6.923/Bio/DB/GFF/Homol.pm BioPerl-1.6.923/Bio/DB/GFF/RelSegment.pm BioPerl-1.6.923/Bio/DB/GFF/Segment.pm BioPerl-1.6.923/Bio/DB/GFF/Typename.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor BioPerl-1.6.923/Bio/DB/GFF/Adaptor/ace.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/berkeleydb.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/biofetch.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/biofetch_oracle.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/memory.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/berkeleydb BioPerl-1.6.923/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/iterator.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/mysql.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/oracle.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/oracleace.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/pg.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/memory BioPerl-1.6.923/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm BioPerl-1.6.923/Bio/DB/GFF/Adaptor/memory/iterator.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator BioPerl-1.6.923/Bio/DB/GFF/Aggregator/alignment.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/clone.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/coding.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/gene.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/match.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/none.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/orf.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/processed_transcript.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/so_transcript.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/transcript.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_acembly.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_genscan.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_refgene.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_softberry.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm BioPerl-1.6.923/Bio/DB/GFF/Aggregator/ucsc_unigene.pm BioPerl-1.6.923/Bio/DB/GFF/Util BioPerl-1.6.923/Bio/DB/GFF/Util/Binning.pm BioPerl-1.6.923/Bio/DB/GFF/Util/Rearrange.pm BioPerl-1.6.923/Bio/DB/HIV BioPerl-1.6.923/Bio/DB/HIV/HIVAnnotProcessor.pm BioPerl-1.6.923/Bio/DB/HIV/HIVQueryHelper.pm BioPerl-1.6.923/Bio/DB/HIV/lanl-schema.xml BioPerl-1.6.923/Bio/DB/Query BioPerl-1.6.923/Bio/DB/Query/GenBank.pm BioPerl-1.6.923/Bio/DB/Query/HIVQuery.pm BioPerl-1.6.923/Bio/DB/Query/WebQuery.pm BioPerl-1.6.923/Bio/DB/SeqFeature BioPerl-1.6.923/Bio/DB/SeqFeature/NormalizedFeature.pm BioPerl-1.6.923/Bio/DB/SeqFeature/NormalizedFeatureI.pm BioPerl-1.6.923/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Segment.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store BioPerl-1.6.923/Bio/DB/SeqFeature/Store/bdb.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/berkeleydb.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/berkeleydb3.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/GFF2Loader.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/GFF3Loader.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/Loader.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/LoadHelper.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/memory.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/DBI BioPerl-1.6.923/Bio/DB/SeqFeature/Store/DBI/Iterator.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/DBI/mysql.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/DBI/Pg.pm BioPerl-1.6.923/Bio/DB/SeqFeature/Store/DBI/SQLite.pm BioPerl-1.6.923/Bio/DB/SeqVersion BioPerl-1.6.923/Bio/DB/SeqVersion/gi.pm BioPerl-1.6.923/Bio/DB/Taxonomy BioPerl-1.6.923/Bio/DB/Taxonomy/entrez.pm BioPerl-1.6.923/Bio/DB/Taxonomy/flatfile.pm BioPerl-1.6.923/Bio/DB/Taxonomy/greengenes.pm BioPerl-1.6.923/Bio/DB/Taxonomy/list.pm BioPerl-1.6.923/Bio/DB/Taxonomy/silva.pm BioPerl-1.6.923/Bio/DB/TFBS BioPerl-1.6.923/Bio/DB/TFBS/transfac_pro.pm BioPerl-1.6.923/Bio/Draw BioPerl-1.6.923/Bio/Draw/Pictogram.pm BioPerl-1.6.923/Bio/Event BioPerl-1.6.923/Bio/Event/EventGeneratorI.pm BioPerl-1.6.923/Bio/Event/EventHandlerI.pm BioPerl-1.6.923/Bio/Factory BioPerl-1.6.923/Bio/Factory/AnalysisI.pm BioPerl-1.6.923/Bio/Factory/ApplicationFactoryI.pm BioPerl-1.6.923/Bio/Factory/DriverFactory.pm BioPerl-1.6.923/Bio/Factory/FTLocationFactory.pm BioPerl-1.6.923/Bio/Factory/LocationFactoryI.pm BioPerl-1.6.923/Bio/Factory/MapFactoryI.pm BioPerl-1.6.923/Bio/Factory/ObjectBuilderI.pm BioPerl-1.6.923/Bio/Factory/ObjectFactory.pm BioPerl-1.6.923/Bio/Factory/ObjectFactoryI.pm BioPerl-1.6.923/Bio/Factory/SeqAnalysisParserFactory.pm BioPerl-1.6.923/Bio/Factory/SeqAnalysisParserFactoryI.pm BioPerl-1.6.923/Bio/Factory/SequenceFactoryI.pm BioPerl-1.6.923/Bio/Factory/SequenceProcessorI.pm BioPerl-1.6.923/Bio/Factory/SequenceStreamI.pm BioPerl-1.6.923/Bio/Factory/TreeFactoryI.pm BioPerl-1.6.923/Bio/Index BioPerl-1.6.923/Bio/Index/Abstract.pm BioPerl-1.6.923/Bio/Index/AbstractSeq.pm BioPerl-1.6.923/Bio/Index/Blast.pm BioPerl-1.6.923/Bio/Index/BlastTable.pm BioPerl-1.6.923/Bio/Index/EMBL.pm BioPerl-1.6.923/Bio/Index/Fasta.pm BioPerl-1.6.923/Bio/Index/Fastq.pm BioPerl-1.6.923/Bio/Index/GenBank.pm BioPerl-1.6.923/Bio/Index/Hmmer.pm BioPerl-1.6.923/Bio/Index/Qual.pm BioPerl-1.6.923/Bio/Index/Stockholm.pm BioPerl-1.6.923/Bio/Index/SwissPfam.pm BioPerl-1.6.923/Bio/Index/Swissprot.pm BioPerl-1.6.923/Bio/LiveSeq BioPerl-1.6.923/Bio/LiveSeq/AARange.pm BioPerl-1.6.923/Bio/LiveSeq/Chain.pm BioPerl-1.6.923/Bio/LiveSeq/ChainI.pm BioPerl-1.6.923/Bio/LiveSeq/DNA.pm BioPerl-1.6.923/Bio/LiveSeq/Exon.pm BioPerl-1.6.923/Bio/LiveSeq/Gene.pm BioPerl-1.6.923/Bio/LiveSeq/Intron.pm BioPerl-1.6.923/Bio/LiveSeq/Mutation.pm BioPerl-1.6.923/Bio/LiveSeq/Mutator.pm BioPerl-1.6.923/Bio/LiveSeq/Prim_Transcript.pm BioPerl-1.6.923/Bio/LiveSeq/Range.pm BioPerl-1.6.923/Bio/LiveSeq/Repeat_Region.pm BioPerl-1.6.923/Bio/LiveSeq/Repeat_Unit.pm BioPerl-1.6.923/Bio/LiveSeq/SeqI.pm BioPerl-1.6.923/Bio/LiveSeq/Transcript.pm BioPerl-1.6.923/Bio/LiveSeq/Translation.pm BioPerl-1.6.923/Bio/LiveSeq/IO BioPerl-1.6.923/Bio/LiveSeq/IO/BioPerl.pm BioPerl-1.6.923/Bio/LiveSeq/IO/Loader.pm BioPerl-1.6.923/Bio/LiveSeq/IO/README BioPerl-1.6.923/Bio/Location BioPerl-1.6.923/Bio/Location/Atomic.pm BioPerl-1.6.923/Bio/Location/AvWithinCoordPolicy.pm BioPerl-1.6.923/Bio/Location/CoordinatePolicyI.pm BioPerl-1.6.923/Bio/Location/Fuzzy.pm BioPerl-1.6.923/Bio/Location/FuzzyLocationI.pm BioPerl-1.6.923/Bio/Location/NarrowestCoordPolicy.pm BioPerl-1.6.923/Bio/Location/Simple.pm BioPerl-1.6.923/Bio/Location/Split.pm BioPerl-1.6.923/Bio/Location/SplitLocationI.pm BioPerl-1.6.923/Bio/Location/WidestCoordPolicy.pm BioPerl-1.6.923/Bio/Map BioPerl-1.6.923/Bio/Map/Clone.pm BioPerl-1.6.923/Bio/Map/Contig.pm BioPerl-1.6.923/Bio/Map/CytoMap.pm BioPerl-1.6.923/Bio/Map/CytoMarker.pm BioPerl-1.6.923/Bio/Map/CytoPosition.pm BioPerl-1.6.923/Bio/Map/EntityI.pm BioPerl-1.6.923/Bio/Map/FPCMarker.pm BioPerl-1.6.923/Bio/Map/Gene.pm BioPerl-1.6.923/Bio/Map/GeneMap.pm BioPerl-1.6.923/Bio/Map/GenePosition.pm BioPerl-1.6.923/Bio/Map/GeneRelative.pm BioPerl-1.6.923/Bio/Map/LinkageMap.pm BioPerl-1.6.923/Bio/Map/LinkagePosition.pm BioPerl-1.6.923/Bio/Map/MapI.pm BioPerl-1.6.923/Bio/Map/Mappable.pm BioPerl-1.6.923/Bio/Map/MappableI.pm BioPerl-1.6.923/Bio/Map/Marker.pm BioPerl-1.6.923/Bio/Map/MarkerI.pm BioPerl-1.6.923/Bio/Map/Microsatellite.pm BioPerl-1.6.923/Bio/Map/OrderedPosition.pm BioPerl-1.6.923/Bio/Map/OrderedPositionWithDistance.pm BioPerl-1.6.923/Bio/Map/Physical.pm BioPerl-1.6.923/Bio/Map/Position.pm BioPerl-1.6.923/Bio/Map/PositionHandler.pm BioPerl-1.6.923/Bio/Map/PositionHandlerI.pm BioPerl-1.6.923/Bio/Map/PositionI.pm BioPerl-1.6.923/Bio/Map/PositionWithSequence.pm BioPerl-1.6.923/Bio/Map/Prediction.pm BioPerl-1.6.923/Bio/Map/Relative.pm BioPerl-1.6.923/Bio/Map/RelativeI.pm BioPerl-1.6.923/Bio/Map/SimpleMap.pm BioPerl-1.6.923/Bio/Map/TranscriptionFactor.pm BioPerl-1.6.923/Bio/MapIO BioPerl-1.6.923/Bio/MapIO/fpc.pm BioPerl-1.6.923/Bio/MapIO/mapmaker.pm BioPerl-1.6.923/Bio/Matrix BioPerl-1.6.923/Bio/Matrix/Generic.pm BioPerl-1.6.923/Bio/Matrix/IO.pm BioPerl-1.6.923/Bio/Matrix/MatrixI.pm BioPerl-1.6.923/Bio/Matrix/Mlagan.pm BioPerl-1.6.923/Bio/Matrix/PhylipDist.pm BioPerl-1.6.923/Bio/Matrix/Scoring.pm BioPerl-1.6.923/Bio/Matrix/IO BioPerl-1.6.923/Bio/Matrix/IO/mlagan.pm BioPerl-1.6.923/Bio/Matrix/IO/phylip.pm BioPerl-1.6.923/Bio/Matrix/IO/scoring.pm BioPerl-1.6.923/Bio/Matrix/PSM BioPerl-1.6.923/Bio/Matrix/PSM/InstanceSite.pm BioPerl-1.6.923/Bio/Matrix/PSM/InstanceSiteI.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO.pm BioPerl-1.6.923/Bio/Matrix/PSM/ProtMatrix.pm BioPerl-1.6.923/Bio/Matrix/PSM/ProtPsm.pm BioPerl-1.6.923/Bio/Matrix/PSM/Psm.pm BioPerl-1.6.923/Bio/Matrix/PSM/PsmHeader.pm BioPerl-1.6.923/Bio/Matrix/PSM/PsmHeaderI.pm BioPerl-1.6.923/Bio/Matrix/PSM/PsmI.pm BioPerl-1.6.923/Bio/Matrix/PSM/SiteMatrix.pm BioPerl-1.6.923/Bio/Matrix/PSM/SiteMatrixI.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO BioPerl-1.6.923/Bio/Matrix/PSM/IO/mast.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO/masta.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO/meme.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO/psiblast.pm BioPerl-1.6.923/Bio/Matrix/PSM/IO/transfac.pm BioPerl-1.6.923/Bio/MolEvol BioPerl-1.6.923/Bio/MolEvol/CodonModel.pm BioPerl-1.6.923/Bio/Nexml BioPerl-1.6.923/Bio/Nexml/Factory.pm BioPerl-1.6.923/Bio/Ontology BioPerl-1.6.923/Bio/Ontology/DocumentRegistry.pm BioPerl-1.6.923/Bio/Ontology/GOterm.pm BioPerl-1.6.923/Bio/Ontology/InterProTerm.pm BioPerl-1.6.923/Bio/Ontology/OBOEngine.pm BioPerl-1.6.923/Bio/Ontology/OBOterm.pm BioPerl-1.6.923/Bio/Ontology/Ontology.pm BioPerl-1.6.923/Bio/Ontology/OntologyEngineI.pm BioPerl-1.6.923/Bio/Ontology/OntologyI.pm BioPerl-1.6.923/Bio/Ontology/OntologyStore.pm BioPerl-1.6.923/Bio/Ontology/Path.pm BioPerl-1.6.923/Bio/Ontology/PathI.pm BioPerl-1.6.923/Bio/Ontology/Relationship.pm BioPerl-1.6.923/Bio/Ontology/RelationshipFactory.pm BioPerl-1.6.923/Bio/Ontology/RelationshipI.pm BioPerl-1.6.923/Bio/Ontology/RelationshipType.pm BioPerl-1.6.923/Bio/Ontology/SimpleOntologyEngine.pm BioPerl-1.6.923/Bio/Ontology/Term.pm BioPerl-1.6.923/Bio/Ontology/TermFactory.pm BioPerl-1.6.923/Bio/Ontology/TermI.pm BioPerl-1.6.923/Bio/Ontology/SimpleGOEngine BioPerl-1.6.923/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm BioPerl-1.6.923/Bio/OntologyIO BioPerl-1.6.923/Bio/OntologyIO/dagflat.pm BioPerl-1.6.923/Bio/OntologyIO/goflat.pm BioPerl-1.6.923/Bio/OntologyIO/InterProParser.pm BioPerl-1.6.923/Bio/OntologyIO/obo.pm BioPerl-1.6.923/Bio/OntologyIO/simplehierarchy.pm BioPerl-1.6.923/Bio/OntologyIO/soflat.pm BioPerl-1.6.923/Bio/OntologyIO/Handlers BioPerl-1.6.923/Bio/OntologyIO/Handlers/BaseSAXHandler.pm BioPerl-1.6.923/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm BioPerl-1.6.923/Bio/OntologyIO/Handlers/InterProHandler.pm BioPerl-1.6.923/Bio/Phenotype BioPerl-1.6.923/Bio/Phenotype/Correlate.pm BioPerl-1.6.923/Bio/Phenotype/Measure.pm BioPerl-1.6.923/Bio/Phenotype/Phenotype.pm BioPerl-1.6.923/Bio/Phenotype/PhenotypeI.pm BioPerl-1.6.923/Bio/Phenotype/MeSH BioPerl-1.6.923/Bio/Phenotype/MeSH/Term.pm BioPerl-1.6.923/Bio/Phenotype/MeSH/Twig.pm BioPerl-1.6.923/Bio/Phenotype/OMIM BioPerl-1.6.923/Bio/Phenotype/OMIM/MiniMIMentry.pm BioPerl-1.6.923/Bio/Phenotype/OMIM/OMIMentry.pm BioPerl-1.6.923/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm BioPerl-1.6.923/Bio/Phenotype/OMIM/OMIMparser.pm BioPerl-1.6.923/Bio/PhyloNetwork BioPerl-1.6.923/Bio/PhyloNetwork/Factory.pm BioPerl-1.6.923/Bio/PhyloNetwork/FactoryX.pm BioPerl-1.6.923/Bio/PhyloNetwork/GraphViz.pm BioPerl-1.6.923/Bio/PhyloNetwork/muVector.pm BioPerl-1.6.923/Bio/PhyloNetwork/RandomFactory.pm BioPerl-1.6.923/Bio/PhyloNetwork/TreeFactory.pm BioPerl-1.6.923/Bio/PhyloNetwork/TreeFactoryMulti.pm BioPerl-1.6.923/Bio/PhyloNetwork/TreeFactoryX.pm BioPerl-1.6.923/Bio/PopGen BioPerl-1.6.923/Bio/PopGen/Genotype.pm BioPerl-1.6.923/Bio/PopGen/GenotypeI.pm BioPerl-1.6.923/Bio/PopGen/HtSNP.pm BioPerl-1.6.923/Bio/PopGen/Individual.pm BioPerl-1.6.923/Bio/PopGen/IndividualI.pm BioPerl-1.6.923/Bio/PopGen/IO.pm BioPerl-1.6.923/Bio/PopGen/Marker.pm BioPerl-1.6.923/Bio/PopGen/MarkerI.pm BioPerl-1.6.923/Bio/PopGen/PopStats.pm BioPerl-1.6.923/Bio/PopGen/Population.pm BioPerl-1.6.923/Bio/PopGen/PopulationI.pm BioPerl-1.6.923/Bio/PopGen/Statistics.pm BioPerl-1.6.923/Bio/PopGen/TagHaplotype.pm BioPerl-1.6.923/Bio/PopGen/Utilities.pm BioPerl-1.6.923/Bio/PopGen/IO BioPerl-1.6.923/Bio/PopGen/IO/csv.pm BioPerl-1.6.923/Bio/PopGen/IO/hapmap.pm BioPerl-1.6.923/Bio/PopGen/IO/phase.pm BioPerl-1.6.923/Bio/PopGen/IO/prettybase.pm BioPerl-1.6.923/Bio/PopGen/Simulation BioPerl-1.6.923/Bio/PopGen/Simulation/Coalescent.pm BioPerl-1.6.923/Bio/PopGen/Simulation/GeneticDrift.pm BioPerl-1.6.923/Bio/Restriction BioPerl-1.6.923/Bio/Restriction/Analysis.pm BioPerl-1.6.923/Bio/Restriction/Enzyme.pm BioPerl-1.6.923/Bio/Restriction/EnzymeCollection.pm BioPerl-1.6.923/Bio/Restriction/EnzymeI.pm BioPerl-1.6.923/Bio/Restriction/IO.pm BioPerl-1.6.923/Bio/Restriction/Enzyme BioPerl-1.6.923/Bio/Restriction/Enzyme/MultiCut.pm BioPerl-1.6.923/Bio/Restriction/Enzyme/MultiSite.pm BioPerl-1.6.923/Bio/Restriction/IO BioPerl-1.6.923/Bio/Restriction/IO/bairoch.pm BioPerl-1.6.923/Bio/Restriction/IO/base.pm BioPerl-1.6.923/Bio/Restriction/IO/itype2.pm BioPerl-1.6.923/Bio/Restriction/IO/prototype.pm BioPerl-1.6.923/Bio/Restriction/IO/withrefm.pm BioPerl-1.6.923/Bio/Root BioPerl-1.6.923/Bio/Root/Build.pm BioPerl-1.6.923/Bio/Root/Exception.pm BioPerl-1.6.923/Bio/Root/HTTPget.pm BioPerl-1.6.923/Bio/Root/IO.pm BioPerl-1.6.923/Bio/Root/Root.pm BioPerl-1.6.923/Bio/Root/RootI.pm BioPerl-1.6.923/Bio/Root/Storable.pm BioPerl-1.6.923/Bio/Root/Test.pm BioPerl-1.6.923/Bio/Root/Utilities.pm BioPerl-1.6.923/Bio/Root/Version.pm BioPerl-1.6.923/Bio/Search BioPerl-1.6.923/Bio/Search/BlastStatistics.pm BioPerl-1.6.923/Bio/Search/BlastUtils.pm BioPerl-1.6.923/Bio/Search/DatabaseI.pm BioPerl-1.6.923/Bio/Search/GenericDatabase.pm BioPerl-1.6.923/Bio/Search/GenericStatistics.pm BioPerl-1.6.923/Bio/Search/Processor.pm BioPerl-1.6.923/Bio/Search/SearchUtils.pm BioPerl-1.6.923/Bio/Search/StatisticsI.pm BioPerl-1.6.923/Bio/Search/Hit BioPerl-1.6.923/Bio/Search/Hit/BlastHit.pm BioPerl-1.6.923/Bio/Search/Hit/BlastPullHit.pm BioPerl-1.6.923/Bio/Search/Hit/Fasta.pm BioPerl-1.6.923/Bio/Search/Hit/GenericHit.pm BioPerl-1.6.923/Bio/Search/Hit/HitFactory.pm BioPerl-1.6.923/Bio/Search/Hit/HitI.pm BioPerl-1.6.923/Bio/Search/Hit/hmmer3Hit.pm BioPerl-1.6.923/Bio/Search/Hit/HMMERHit.pm BioPerl-1.6.923/Bio/Search/Hit/HmmpfamHit.pm BioPerl-1.6.923/Bio/Search/Hit/ModelHit.pm BioPerl-1.6.923/Bio/Search/Hit/PsiBlastHit.pm BioPerl-1.6.923/Bio/Search/Hit/PullHitI.pm BioPerl-1.6.923/Bio/Search/HSP BioPerl-1.6.923/Bio/Search/HSP/BlastHSP.pm BioPerl-1.6.923/Bio/Search/HSP/BlastPullHSP.pm BioPerl-1.6.923/Bio/Search/HSP/FastaHSP.pm BioPerl-1.6.923/Bio/Search/HSP/GenericHSP.pm BioPerl-1.6.923/Bio/Search/HSP/HMMERHSP.pm BioPerl-1.6.923/Bio/Search/HSP/HmmpfamHSP.pm BioPerl-1.6.923/Bio/Search/HSP/HSPFactory.pm BioPerl-1.6.923/Bio/Search/HSP/HSPI.pm BioPerl-1.6.923/Bio/Search/HSP/ModelHSP.pm BioPerl-1.6.923/Bio/Search/HSP/PsiBlastHSP.pm BioPerl-1.6.923/Bio/Search/HSP/PSLHSP.pm BioPerl-1.6.923/Bio/Search/HSP/PullHSPI.pm BioPerl-1.6.923/Bio/Search/HSP/WABAHSP.pm BioPerl-1.6.923/Bio/Search/Iteration BioPerl-1.6.923/Bio/Search/Iteration/GenericIteration.pm BioPerl-1.6.923/Bio/Search/Iteration/IterationI.pm BioPerl-1.6.923/Bio/Search/Result BioPerl-1.6.923/Bio/Search/Result/BlastPullResult.pm BioPerl-1.6.923/Bio/Search/Result/BlastResult.pm BioPerl-1.6.923/Bio/Search/Result/CrossMatchResult.pm BioPerl-1.6.923/Bio/Search/Result/GenericResult.pm BioPerl-1.6.923/Bio/Search/Result/hmmer3Result.pm BioPerl-1.6.923/Bio/Search/Result/HMMERResult.pm BioPerl-1.6.923/Bio/Search/Result/HmmpfamResult.pm BioPerl-1.6.923/Bio/Search/Result/PullResultI.pm BioPerl-1.6.923/Bio/Search/Result/ResultFactory.pm BioPerl-1.6.923/Bio/Search/Result/ResultI.pm BioPerl-1.6.923/Bio/Search/Result/WABAResult.pm BioPerl-1.6.923/Bio/Search/Tiling BioPerl-1.6.923/Bio/Search/Tiling/MapTileUtils.pm BioPerl-1.6.923/Bio/Search/Tiling/MapTiling.pm BioPerl-1.6.923/Bio/Search/Tiling/TilingI.pm BioPerl-1.6.923/Bio/SearchIO BioPerl-1.6.923/Bio/SearchIO/axt.pm BioPerl-1.6.923/Bio/SearchIO/blast.pm BioPerl-1.6.923/Bio/SearchIO/blast_pull.pm BioPerl-1.6.923/Bio/SearchIO/blasttable.pm BioPerl-1.6.923/Bio/SearchIO/blastxml.pm BioPerl-1.6.923/Bio/SearchIO/cross_match.pm BioPerl-1.6.923/Bio/SearchIO/erpin.pm BioPerl-1.6.923/Bio/SearchIO/EventHandlerI.pm BioPerl-1.6.923/Bio/SearchIO/exonerate.pm BioPerl-1.6.923/Bio/SearchIO/fasta.pm BioPerl-1.6.923/Bio/SearchIO/FastHitEventBuilder.pm BioPerl-1.6.923/Bio/SearchIO/gmap_f9.pm BioPerl-1.6.923/Bio/SearchIO/hmmer.pm BioPerl-1.6.923/Bio/SearchIO/hmmer2.pm BioPerl-1.6.923/Bio/SearchIO/hmmer3.pm BioPerl-1.6.923/Bio/SearchIO/hmmer_pull.pm BioPerl-1.6.923/Bio/SearchIO/infernal.pm BioPerl-1.6.923/Bio/SearchIO/IteratedSearchResultEventBuilder.pm BioPerl-1.6.923/Bio/SearchIO/megablast.pm BioPerl-1.6.923/Bio/SearchIO/psl.pm BioPerl-1.6.923/Bio/SearchIO/rnamotif.pm BioPerl-1.6.923/Bio/SearchIO/SearchResultEventBuilder.pm BioPerl-1.6.923/Bio/SearchIO/SearchWriterI.pm BioPerl-1.6.923/Bio/SearchIO/sim4.pm BioPerl-1.6.923/Bio/SearchIO/waba.pm BioPerl-1.6.923/Bio/SearchIO/wise.pm BioPerl-1.6.923/Bio/SearchIO/Writer BioPerl-1.6.923/Bio/SearchIO/Writer/BSMLResultWriter.pm BioPerl-1.6.923/Bio/SearchIO/Writer/GbrowseGFF.pm BioPerl-1.6.923/Bio/SearchIO/Writer/HitTableWriter.pm BioPerl-1.6.923/Bio/SearchIO/Writer/HSPTableWriter.pm BioPerl-1.6.923/Bio/SearchIO/Writer/HTMLResultWriter.pm BioPerl-1.6.923/Bio/SearchIO/Writer/ResultTableWriter.pm BioPerl-1.6.923/Bio/SearchIO/Writer/TextResultWriter.pm BioPerl-1.6.923/Bio/SearchIO/XML BioPerl-1.6.923/Bio/SearchIO/XML/BlastHandler.pm BioPerl-1.6.923/Bio/SearchIO/XML/PsiBlastHandler.pm BioPerl-1.6.923/Bio/Seq BioPerl-1.6.923/Bio/Seq/BaseSeqProcessor.pm BioPerl-1.6.923/Bio/Seq/EncodedSeq.pm BioPerl-1.6.923/Bio/Seq/LargeLocatableSeq.pm BioPerl-1.6.923/Bio/Seq/LargePrimarySeq.pm BioPerl-1.6.923/Bio/Seq/LargeSeq.pm BioPerl-1.6.923/Bio/Seq/LargeSeqI.pm BioPerl-1.6.923/Bio/Seq/Meta.pm BioPerl-1.6.923/Bio/Seq/MetaI.pm BioPerl-1.6.923/Bio/Seq/PrimaryQual.pm BioPerl-1.6.923/Bio/Seq/PrimedSeq.pm BioPerl-1.6.923/Bio/Seq/QualI.pm BioPerl-1.6.923/Bio/Seq/Quality.pm BioPerl-1.6.923/Bio/Seq/RichSeq.pm BioPerl-1.6.923/Bio/Seq/RichSeqI.pm BioPerl-1.6.923/Bio/Seq/SeqBuilder.pm BioPerl-1.6.923/Bio/Seq/SeqFactory.pm BioPerl-1.6.923/Bio/Seq/SeqFastaSpeedFactory.pm BioPerl-1.6.923/Bio/Seq/SequenceTrace.pm BioPerl-1.6.923/Bio/Seq/SeqWithQuality.pm BioPerl-1.6.923/Bio/Seq/SimulatedRead.pm BioPerl-1.6.923/Bio/Seq/TraceI.pm BioPerl-1.6.923/Bio/Seq/Meta BioPerl-1.6.923/Bio/Seq/Meta/Array.pm BioPerl-1.6.923/Bio/SeqEvolution BioPerl-1.6.923/Bio/SeqEvolution/DNAPoint.pm BioPerl-1.6.923/Bio/SeqEvolution/EvolutionI.pm BioPerl-1.6.923/Bio/SeqEvolution/Factory.pm BioPerl-1.6.923/Bio/SeqFeature BioPerl-1.6.923/Bio/SeqFeature/Amplicon.pm BioPerl-1.6.923/Bio/SeqFeature/AnnotationAdaptor.pm BioPerl-1.6.923/Bio/SeqFeature/Collection.pm BioPerl-1.6.923/Bio/SeqFeature/CollectionI.pm BioPerl-1.6.923/Bio/SeqFeature/Computation.pm BioPerl-1.6.923/Bio/SeqFeature/FeaturePair.pm BioPerl-1.6.923/Bio/SeqFeature/Generic.pm BioPerl-1.6.923/Bio/SeqFeature/Lite.pm BioPerl-1.6.923/Bio/SeqFeature/PositionProxy.pm BioPerl-1.6.923/Bio/SeqFeature/Primer.pm BioPerl-1.6.923/Bio/SeqFeature/Similarity.pm BioPerl-1.6.923/Bio/SeqFeature/SimilarityPair.pm BioPerl-1.6.923/Bio/SeqFeature/SubSeq.pm BioPerl-1.6.923/Bio/SeqFeature/TypedSeqFeatureI.pm BioPerl-1.6.923/Bio/SeqFeature/Gene BioPerl-1.6.923/Bio/SeqFeature/Gene/Exon.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/ExonI.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/GeneStructure.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/GeneStructureI.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/Intron.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/NC_Feature.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/Poly_A_site.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/Promoter.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/Transcript.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/TranscriptI.pm BioPerl-1.6.923/Bio/SeqFeature/Gene/UTR.pm BioPerl-1.6.923/Bio/SeqFeature/SiRNA BioPerl-1.6.923/Bio/SeqFeature/SiRNA/Oligo.pm BioPerl-1.6.923/Bio/SeqFeature/SiRNA/Pair.pm BioPerl-1.6.923/Bio/SeqFeature/Tools BioPerl-1.6.923/Bio/SeqFeature/Tools/FeatureNamer.pm BioPerl-1.6.923/Bio/SeqFeature/Tools/IDHandler.pm BioPerl-1.6.923/Bio/SeqFeature/Tools/TypeMapper.pm BioPerl-1.6.923/Bio/SeqFeature/Tools/Unflattener.pm BioPerl-1.6.923/Bio/SeqIO BioPerl-1.6.923/Bio/SeqIO/abi.pm BioPerl-1.6.923/Bio/SeqIO/ace.pm BioPerl-1.6.923/Bio/SeqIO/agave.pm BioPerl-1.6.923/Bio/SeqIO/alf.pm BioPerl-1.6.923/Bio/SeqIO/asciitree.pm BioPerl-1.6.923/Bio/SeqIO/bsml.pm BioPerl-1.6.923/Bio/SeqIO/bsml_sax.pm BioPerl-1.6.923/Bio/SeqIO/chadoxml.pm BioPerl-1.6.923/Bio/SeqIO/chaos.pm BioPerl-1.6.923/Bio/SeqIO/chaosxml.pm BioPerl-1.6.923/Bio/SeqIO/ctf.pm BioPerl-1.6.923/Bio/SeqIO/embl.pm BioPerl-1.6.923/Bio/SeqIO/embldriver.pm BioPerl-1.6.923/Bio/SeqIO/entrezgene.pm BioPerl-1.6.923/Bio/SeqIO/excel.pm BioPerl-1.6.923/Bio/SeqIO/exp.pm BioPerl-1.6.923/Bio/SeqIO/fasta.pm BioPerl-1.6.923/Bio/SeqIO/fastq.pm BioPerl-1.6.923/Bio/SeqIO/flybase_chadoxml.pm BioPerl-1.6.923/Bio/SeqIO/FTHelper.pm BioPerl-1.6.923/Bio/SeqIO/game.pm BioPerl-1.6.923/Bio/SeqIO/gbdriver.pm BioPerl-1.6.923/Bio/SeqIO/gbxml.pm BioPerl-1.6.923/Bio/SeqIO/gcg.pm BioPerl-1.6.923/Bio/SeqIO/genbank.pm BioPerl-1.6.923/Bio/SeqIO/interpro.pm BioPerl-1.6.923/Bio/SeqIO/kegg.pm BioPerl-1.6.923/Bio/SeqIO/largefasta.pm BioPerl-1.6.923/Bio/SeqIO/lasergene.pm BioPerl-1.6.923/Bio/SeqIO/locuslink.pm BioPerl-1.6.923/Bio/SeqIO/mbsout.pm BioPerl-1.6.923/Bio/SeqIO/metafasta.pm BioPerl-1.6.923/Bio/SeqIO/msout.pm BioPerl-1.6.923/Bio/SeqIO/MultiFile.pm BioPerl-1.6.923/Bio/SeqIO/nexml.pm BioPerl-1.6.923/Bio/SeqIO/phd.pm BioPerl-1.6.923/Bio/SeqIO/pir.pm BioPerl-1.6.923/Bio/SeqIO/pln.pm BioPerl-1.6.923/Bio/SeqIO/qual.pm BioPerl-1.6.923/Bio/SeqIO/raw.pm BioPerl-1.6.923/Bio/SeqIO/scf.pm BioPerl-1.6.923/Bio/SeqIO/seqxml.pm BioPerl-1.6.923/Bio/SeqIO/strider.pm BioPerl-1.6.923/Bio/SeqIO/swiss.pm BioPerl-1.6.923/Bio/SeqIO/swissdriver.pm BioPerl-1.6.923/Bio/SeqIO/tab.pm BioPerl-1.6.923/Bio/SeqIO/table.pm BioPerl-1.6.923/Bio/SeqIO/tigr.pm BioPerl-1.6.923/Bio/SeqIO/tigrxml.pm BioPerl-1.6.923/Bio/SeqIO/tinyseq.pm BioPerl-1.6.923/Bio/SeqIO/ztr.pm BioPerl-1.6.923/Bio/SeqIO/game BioPerl-1.6.923/Bio/SeqIO/game/featHandler.pm BioPerl-1.6.923/Bio/SeqIO/game/gameHandler.pm BioPerl-1.6.923/Bio/SeqIO/game/gameSubs.pm BioPerl-1.6.923/Bio/SeqIO/game/gameWriter.pm BioPerl-1.6.923/Bio/SeqIO/game/seqHandler.pm BioPerl-1.6.923/Bio/SeqIO/Handler BioPerl-1.6.923/Bio/SeqIO/Handler/GenericRichSeqHandler.pm BioPerl-1.6.923/Bio/SeqIO/tinyseq BioPerl-1.6.923/Bio/SeqIO/tinyseq/tinyseqHandler.pm BioPerl-1.6.923/Bio/Structure BioPerl-1.6.923/Bio/Structure/Atom.pm BioPerl-1.6.923/Bio/Structure/Chain.pm BioPerl-1.6.923/Bio/Structure/Entry.pm BioPerl-1.6.923/Bio/Structure/IO.pm BioPerl-1.6.923/Bio/Structure/Model.pm BioPerl-1.6.923/Bio/Structure/Residue.pm BioPerl-1.6.923/Bio/Structure/StructureI.pm BioPerl-1.6.923/Bio/Structure/IO BioPerl-1.6.923/Bio/Structure/IO/pdb.pm BioPerl-1.6.923/Bio/Structure/SecStr BioPerl-1.6.923/Bio/Structure/SecStr/DSSP BioPerl-1.6.923/Bio/Structure/SecStr/DSSP/Res.pm BioPerl-1.6.923/Bio/Structure/SecStr/STRIDE BioPerl-1.6.923/Bio/Structure/SecStr/STRIDE/Res.pm BioPerl-1.6.923/Bio/Symbol BioPerl-1.6.923/Bio/Symbol/Alphabet.pm BioPerl-1.6.923/Bio/Symbol/AlphabetI.pm BioPerl-1.6.923/Bio/Symbol/DNAAlphabet.pm BioPerl-1.6.923/Bio/Symbol/ProteinAlphabet.pm BioPerl-1.6.923/Bio/Symbol/README.Symbol BioPerl-1.6.923/Bio/Symbol/Symbol.pm BioPerl-1.6.923/Bio/Symbol/SymbolI.pm BioPerl-1.6.923/Bio/Taxonomy BioPerl-1.6.923/Bio/Taxonomy/FactoryI.pm BioPerl-1.6.923/Bio/Taxonomy/Node.pm BioPerl-1.6.923/Bio/Taxonomy/Taxon.pm BioPerl-1.6.923/Bio/Taxonomy/Tree.pm BioPerl-1.6.923/Bio/Tools BioPerl-1.6.923/Bio/Tools/AlignFactory.pm BioPerl-1.6.923/Bio/Tools/AmpliconSearch.pm BioPerl-1.6.923/Bio/Tools/AnalysisResult.pm BioPerl-1.6.923/Bio/Tools/Blat.pm BioPerl-1.6.923/Bio/Tools/CodonTable.pm BioPerl-1.6.923/Bio/Tools/Coil.pm BioPerl-1.6.923/Bio/Tools/dpAlign.pm BioPerl-1.6.923/Bio/Tools/ECnumber.pm BioPerl-1.6.923/Bio/Tools/EPCR.pm BioPerl-1.6.923/Bio/Tools/Eponine.pm BioPerl-1.6.923/Bio/Tools/ERPIN.pm BioPerl-1.6.923/Bio/Tools/Est2Genome.pm BioPerl-1.6.923/Bio/Tools/ESTScan.pm BioPerl-1.6.923/Bio/Tools/Fgenesh.pm BioPerl-1.6.923/Bio/Tools/FootPrinter.pm BioPerl-1.6.923/Bio/Tools/Gel.pm BioPerl-1.6.923/Bio/Tools/Geneid.pm BioPerl-1.6.923/Bio/Tools/Genemark.pm BioPerl-1.6.923/Bio/Tools/Genewise.pm BioPerl-1.6.923/Bio/Tools/Genomewise.pm BioPerl-1.6.923/Bio/Tools/Genscan.pm BioPerl-1.6.923/Bio/Tools/GFF.pm BioPerl-1.6.923/Bio/Tools/Glimmer.pm BioPerl-1.6.923/Bio/Tools/Grail.pm BioPerl-1.6.923/Bio/Tools/GuessSeqFormat.pm BioPerl-1.6.923/Bio/Tools/Hmmpfam.pm BioPerl-1.6.923/Bio/Tools/Infernal.pm BioPerl-1.6.923/Bio/Tools/ipcress.pm BioPerl-1.6.923/Bio/Tools/isPcr.pm BioPerl-1.6.923/Bio/Tools/IUPAC.pm BioPerl-1.6.923/Bio/Tools/Lucy.pm BioPerl-1.6.923/Bio/Tools/Match.pm BioPerl-1.6.923/Bio/Tools/MZEF.pm BioPerl-1.6.923/Bio/Tools/OddCodes.pm BioPerl-1.6.923/Bio/Tools/pICalculator.pm BioPerl-1.6.923/Bio/Tools/Primer3.pm BioPerl-1.6.923/Bio/Tools/Prints.pm BioPerl-1.6.923/Bio/Tools/Profile.pm BioPerl-1.6.923/Bio/Tools/Promoterwise.pm BioPerl-1.6.923/Bio/Tools/PrositeScan.pm BioPerl-1.6.923/Bio/Tools/Protparam.pm BioPerl-1.6.923/Bio/Tools/Pseudowise.pm BioPerl-1.6.923/Bio/Tools/pSW.pm BioPerl-1.6.923/Bio/Tools/QRNA.pm BioPerl-1.6.923/Bio/Tools/RandomDistFunctions.pm BioPerl-1.6.923/Bio/Tools/RepeatMasker.pm BioPerl-1.6.923/Bio/Tools/RNAMotif.pm BioPerl-1.6.923/Bio/Tools/Seg.pm BioPerl-1.6.923/Bio/Tools/SeqPattern.pm BioPerl-1.6.923/Bio/Tools/SeqStats.pm BioPerl-1.6.923/Bio/Tools/SeqWords.pm BioPerl-1.6.923/Bio/Tools/Sigcleave.pm BioPerl-1.6.923/Bio/Tools/Signalp.pm BioPerl-1.6.923/Bio/Tools/SiRNA.pm BioPerl-1.6.923/Bio/Tools/TandemRepeatsFinder.pm BioPerl-1.6.923/Bio/Tools/TargetP.pm BioPerl-1.6.923/Bio/Tools/Tmhmm.pm BioPerl-1.6.923/Bio/Tools/tRNAscanSE.pm BioPerl-1.6.923/Bio/Tools/Alignment BioPerl-1.6.923/Bio/Tools/Alignment/Consed.pm BioPerl-1.6.923/Bio/Tools/Alignment/Trim.pm BioPerl-1.6.923/Bio/Tools/Analysis BioPerl-1.6.923/Bio/Tools/Analysis/SimpleAnalysisBase.pm BioPerl-1.6.923/Bio/Tools/Analysis/DNA BioPerl-1.6.923/Bio/Tools/Analysis/DNA/ESEfinder.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein BioPerl-1.6.923/Bio/Tools/Analysis/Protein/Domcut.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/ELM.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/GOR4.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/HNN.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/Mitoprot.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/NetPhos.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/Scansite.pm BioPerl-1.6.923/Bio/Tools/Analysis/Protein/Sopma.pm BioPerl-1.6.923/Bio/Tools/EMBOSS BioPerl-1.6.923/Bio/Tools/EMBOSS/Palindrome.pm BioPerl-1.6.923/Bio/Tools/HMMER BioPerl-1.6.923/Bio/Tools/HMMER/Domain.pm BioPerl-1.6.923/Bio/Tools/HMMER/Results.pm BioPerl-1.6.923/Bio/Tools/HMMER/Set.pm BioPerl-1.6.923/Bio/Tools/Phylo BioPerl-1.6.923/Bio/Tools/Phylo/Gerp.pm BioPerl-1.6.923/Bio/Tools/Phylo/Gumby.pm BioPerl-1.6.923/Bio/Tools/Phylo/Molphy.pm BioPerl-1.6.923/Bio/Tools/Phylo/PAML.pm BioPerl-1.6.923/Bio/Tools/Phylo/Molphy BioPerl-1.6.923/Bio/Tools/Phylo/Molphy/Result.pm BioPerl-1.6.923/Bio/Tools/Phylo/PAML BioPerl-1.6.923/Bio/Tools/Phylo/PAML/Codeml.pm BioPerl-1.6.923/Bio/Tools/Phylo/PAML/ModelResult.pm BioPerl-1.6.923/Bio/Tools/Phylo/PAML/Result.pm BioPerl-1.6.923/Bio/Tools/Phylo/Phylip BioPerl-1.6.923/Bio/Tools/Phylo/Phylip/ProtDist.pm BioPerl-1.6.923/Bio/Tools/Prediction BioPerl-1.6.923/Bio/Tools/Prediction/Exon.pm BioPerl-1.6.923/Bio/Tools/Prediction/Gene.pm BioPerl-1.6.923/Bio/Tools/Primer BioPerl-1.6.923/Bio/Tools/Primer/AssessorI.pm BioPerl-1.6.923/Bio/Tools/Primer/Feature.pm BioPerl-1.6.923/Bio/Tools/Primer/Pair.pm BioPerl-1.6.923/Bio/Tools/Primer/Assessor BioPerl-1.6.923/Bio/Tools/Primer/Assessor/Base.pm BioPerl-1.6.923/Bio/Tools/Run BioPerl-1.6.923/Bio/Tools/Run/GenericParameters.pm BioPerl-1.6.923/Bio/Tools/Run/hmmer3.pm BioPerl-1.6.923/Bio/Tools/Run/ParametersI.pm BioPerl-1.6.923/Bio/Tools/Run/README BioPerl-1.6.923/Bio/Tools/Run/RemoteBlast.pm BioPerl-1.6.923/Bio/Tools/Run/StandAloneBlast.pm BioPerl-1.6.923/Bio/Tools/Run/StandAloneNCBIBlast.pm BioPerl-1.6.923/Bio/Tools/Run/StandAloneWUBlast.pm BioPerl-1.6.923/Bio/Tools/Run/WrapperBase.pm BioPerl-1.6.923/Bio/Tools/Run/WrapperBase BioPerl-1.6.923/Bio/Tools/Run/WrapperBase/CommandExts.pm BioPerl-1.6.923/Bio/Tools/SeqPattern BioPerl-1.6.923/Bio/Tools/SeqPattern/Backtranslate.pm BioPerl-1.6.923/Bio/Tools/Signalp BioPerl-1.6.923/Bio/Tools/Signalp/ExtendedSignalp.pm BioPerl-1.6.923/Bio/Tools/Sim4 BioPerl-1.6.923/Bio/Tools/Sim4/Exon.pm BioPerl-1.6.923/Bio/Tools/Sim4/Results.pm BioPerl-1.6.923/Bio/Tools/SiRNA BioPerl-1.6.923/Bio/Tools/SiRNA/Ruleset BioPerl-1.6.923/Bio/Tools/SiRNA/Ruleset/saigo.pm BioPerl-1.6.923/Bio/Tools/SiRNA/Ruleset/tuschl.pm BioPerl-1.6.923/Bio/Tools/Spidey BioPerl-1.6.923/Bio/Tools/Spidey/Exon.pm BioPerl-1.6.923/Bio/Tools/Spidey/Results.pm BioPerl-1.6.923/Bio/Tree BioPerl-1.6.923/Bio/Tree/AlleleNode.pm BioPerl-1.6.923/Bio/Tree/AnnotatableNode.pm BioPerl-1.6.923/Bio/Tree/Compatible.pm BioPerl-1.6.923/Bio/Tree/DistanceFactory.pm BioPerl-1.6.923/Bio/Tree/Node.pm BioPerl-1.6.923/Bio/Tree/NodeI.pm BioPerl-1.6.923/Bio/Tree/NodeNHX.pm BioPerl-1.6.923/Bio/Tree/RandomFactory.pm BioPerl-1.6.923/Bio/Tree/Statistics.pm BioPerl-1.6.923/Bio/Tree/Tree.pm BioPerl-1.6.923/Bio/Tree/TreeFunctionsI.pm BioPerl-1.6.923/Bio/Tree/TreeI.pm BioPerl-1.6.923/Bio/Tree/Draw BioPerl-1.6.923/Bio/Tree/Draw/Cladogram.pm BioPerl-1.6.923/Bio/TreeIO BioPerl-1.6.923/Bio/TreeIO/cluster.pm BioPerl-1.6.923/Bio/TreeIO/lintree.pm BioPerl-1.6.923/Bio/TreeIO/newick.pm BioPerl-1.6.923/Bio/TreeIO/NewickParser.pm BioPerl-1.6.923/Bio/TreeIO/nexml.pm BioPerl-1.6.923/Bio/TreeIO/nexus.pm BioPerl-1.6.923/Bio/TreeIO/nhx.pm BioPerl-1.6.923/Bio/TreeIO/pag.pm BioPerl-1.6.923/Bio/TreeIO/phyloxml.pm BioPerl-1.6.923/Bio/TreeIO/svggraph.pm BioPerl-1.6.923/Bio/TreeIO/tabtree.pm BioPerl-1.6.923/Bio/TreeIO/TreeEventBuilder.pm BioPerl-1.6.923/Bio/Variation BioPerl-1.6.923/Bio/Variation/AAChange.pm BioPerl-1.6.923/Bio/Variation/AAReverseMutate.pm BioPerl-1.6.923/Bio/Variation/Allele.pm BioPerl-1.6.923/Bio/Variation/DNAMutation.pm BioPerl-1.6.923/Bio/Variation/IO.pm BioPerl-1.6.923/Bio/Variation/README BioPerl-1.6.923/Bio/Variation/RNAChange.pm BioPerl-1.6.923/Bio/Variation/SeqDiff.pm BioPerl-1.6.923/Bio/Variation/SNP.pm BioPerl-1.6.923/Bio/Variation/VariantI.pm BioPerl-1.6.923/Bio/Variation/IO BioPerl-1.6.923/Bio/Variation/IO/flat.pm BioPerl-1.6.923/Bio/Variation/IO/xml.pm BioPerl-1.6.923/doc BioPerl-1.6.923/doc/makedoc.PL BioPerl-1.6.923/doc/README BioPerl-1.6.923/doc/Deobfuscator BioPerl-1.6.923/doc/Deobfuscator/Build.PL BioPerl-1.6.923/doc/Deobfuscator/Changes BioPerl-1.6.923/doc/Deobfuscator/excluded_modules.txt BioPerl-1.6.923/doc/Deobfuscator/LICENSE BioPerl-1.6.923/doc/Deobfuscator/Makefile.PL BioPerl-1.6.923/doc/Deobfuscator/MANIFEST BioPerl-1.6.923/doc/Deobfuscator/META.yml BioPerl-1.6.923/doc/Deobfuscator/README BioPerl-1.6.923/doc/Deobfuscator/bin BioPerl-1.6.923/doc/Deobfuscator/bin/deob_index.pl BioPerl-1.6.923/doc/Deobfuscator/bin/run-deobfuscator-update.pl BioPerl-1.6.923/doc/Deobfuscator/cgi-bin BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_detail.cgi BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_flowchart.png BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_help.html BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_interface.cgi BioPerl-1.6.923/doc/Deobfuscator/lib BioPerl-1.6.923/doc/Deobfuscator/lib/Deobfuscator.pm BioPerl-1.6.923/doc/Deobfuscator/t BioPerl-1.6.923/doc/Deobfuscator/t/00.load.t BioPerl-1.6.923/doc/Deobfuscator/t/pod.t BioPerl-1.6.923/examples BioPerl-1.6.923/examples/bioperl.pl BioPerl-1.6.923/examples/generate_random_seq.pl BioPerl-1.6.923/examples/longorf.pl BioPerl-1.6.923/examples/make_primers.pl BioPerl-1.6.923/examples/rev_and_trans.pl BioPerl-1.6.923/examples/revcom_dir.pl BioPerl-1.6.923/examples/subsequence.cgi BioPerl-1.6.923/examples/align BioPerl-1.6.923/examples/align/align_on_codons.pl BioPerl-1.6.923/examples/align/aligntutorial.pl BioPerl-1.6.923/examples/align/clustalw.pl BioPerl-1.6.923/examples/align/FastAlign.pl BioPerl-1.6.923/examples/align/simplealign.pl BioPerl-1.6.923/examples/Bio-DB-GFF BioPerl-1.6.923/examples/Bio-DB-GFF/load_ucsc.pl BioPerl-1.6.923/examples/cluster BioPerl-1.6.923/examples/cluster/dbsnp.pl BioPerl-1.6.923/examples/contributed BioPerl-1.6.923/examples/contributed/nmrpdb_parse.pl BioPerl-1.6.923/examples/contributed/prosite2perl.pl BioPerl-1.6.923/examples/contributed/rebase2list.pl BioPerl-1.6.923/examples/db BioPerl-1.6.923/examples/db/dbfetch BioPerl-1.6.923/examples/db/est_tissue_query.pl BioPerl-1.6.923/examples/db/gb2features.pl BioPerl-1.6.923/examples/db/get_seqs.pl BioPerl-1.6.923/examples/db/getGenBank.pl BioPerl-1.6.923/examples/db/rfetch.pl BioPerl-1.6.923/examples/db/use_registry.pl BioPerl-1.6.923/examples/liveseq BioPerl-1.6.923/examples/liveseq/change_gene.pl BioPerl-1.6.923/examples/popgen BioPerl-1.6.923/examples/popgen/parse_calc_stats.pl BioPerl-1.6.923/examples/quality BioPerl-1.6.923/examples/quality/svgtrace.pl BioPerl-1.6.923/examples/root BioPerl-1.6.923/examples/root/exceptions1.pl BioPerl-1.6.923/examples/root/exceptions2.pl BioPerl-1.6.923/examples/root/exceptions3.pl BioPerl-1.6.923/examples/root/exceptions4.pl BioPerl-1.6.923/examples/root/README BioPerl-1.6.923/examples/root/lib BioPerl-1.6.923/examples/root/lib/TestInterface.pm BioPerl-1.6.923/examples/root/lib/TestObject.pm BioPerl-1.6.923/examples/searchio BioPerl-1.6.923/examples/searchio/blast_example.pl BioPerl-1.6.923/examples/searchio/custom_writer.pl BioPerl-1.6.923/examples/searchio/hitwriter.pl BioPerl-1.6.923/examples/searchio/hspwriter.pl BioPerl-1.6.923/examples/searchio/htmlwriter.pl BioPerl-1.6.923/examples/searchio/psiblast_features.pl BioPerl-1.6.923/examples/searchio/psiblast_iterations.pl BioPerl-1.6.923/examples/searchio/rawwriter.pl BioPerl-1.6.923/examples/searchio/resultwriter.pl BioPerl-1.6.923/examples/searchio/waba2gff.pl BioPerl-1.6.923/examples/searchio/waba2gff3.pl BioPerl-1.6.923/examples/sirna BioPerl-1.6.923/examples/sirna/rnai_finder.cgi BioPerl-1.6.923/examples/sirna/TAG BioPerl-1.6.923/examples/structure BioPerl-1.6.923/examples/structure/structure-io.pl BioPerl-1.6.923/examples/tk BioPerl-1.6.923/examples/tk/gsequence.pl BioPerl-1.6.923/examples/tk/hitdisplay.pl BioPerl-1.6.923/examples/tools BioPerl-1.6.923/examples/tools/extract_genes.pl BioPerl-1.6.923/examples/tools/gb_to_gff.pl BioPerl-1.6.923/examples/tools/gff2ps.pl BioPerl-1.6.923/examples/tools/parse_codeml.pl BioPerl-1.6.923/examples/tools/psw.pl BioPerl-1.6.923/examples/tools/reverse-translate.pl BioPerl-1.6.923/examples/tools/run_genscan.pl BioPerl-1.6.923/examples/tools/run_primer3.pl BioPerl-1.6.923/examples/tools/seq_pattern.pl BioPerl-1.6.923/examples/tools/standaloneblast.pl BioPerl-1.6.923/examples/tree BioPerl-1.6.923/examples/tree/paup2phylip.pl BioPerl-1.6.923/ide BioPerl-1.6.923/ide/bioperl.komodo BioPerl-1.6.923/ide/bioperl-mode BioPerl-1.6.923/ide/bioperl-mode/README BioPerl-1.6.923/ide/bioperl-mode/dist BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5 BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode.tar BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode.tar.md5 BioPerl-1.6.923/ide/bioperl-mode/dist/Changes BioPerl-1.6.923/ide/bioperl-mode/dist/package-me BioPerl-1.6.923/ide/bioperl-mode/dist/SKIP BioPerl-1.6.923/ide/bioperl-mode/etc BioPerl-1.6.923/ide/bioperl-mode/etc/images BioPerl-1.6.923/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm BioPerl-1.6.923/ide/bioperl-mode/etc/images/bpmode-tool.xpm BioPerl-1.6.923/ide/bioperl-mode/site-lisp BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-init.el BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-mode.el BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-skel.el BioPerl-1.6.923/ide/bioperl-mode/site-lisp/pod.el BioPerl-1.6.923/maintenance BioPerl-1.6.923/maintenance/authors.pl BioPerl-1.6.923/maintenance/check_NAME.pl BioPerl-1.6.923/maintenance/check_URLs.pl BioPerl-1.6.923/maintenance/cvs2cl_by_file.pl BioPerl-1.6.923/maintenance/dependencies.pl BioPerl-1.6.923/maintenance/deprecated.pl BioPerl-1.6.923/maintenance/find_mod_deps.pl BioPerl-1.6.923/maintenance/module_usage.pl BioPerl-1.6.923/maintenance/modules.pl BioPerl-1.6.923/maintenance/ncbi_blast_switches.pl BioPerl-1.6.923/maintenance/perltidy.conf BioPerl-1.6.923/maintenance/pod.pl BioPerl-1.6.923/maintenance/README BioPerl-1.6.923/maintenance/symlink_script.pl BioPerl-1.6.923/maintenance/version.pl BioPerl-1.6.923/maintenance/big_split BioPerl-1.6.923/maintenance/big_split/file_classification.csv BioPerl-1.6.923/maintenance/big_split/rbuels_notes.txt BioPerl-1.6.923/models BioPerl-1.6.923/models/biblio.dia BioPerl-1.6.923/models/bio_liveseq_variation.dia BioPerl-1.6.923/models/bio_map.dia BioPerl-1.6.923/models/bio_restriction.dia BioPerl-1.6.923/models/bioperl.dia BioPerl-1.6.923/models/coordinatemapper.dia BioPerl-1.6.923/models/map_proposal.txt BioPerl-1.6.923/models/maps_and_markers.dia BioPerl-1.6.923/models/popgen.dia BioPerl-1.6.923/models/population_proposal.txt BioPerl-1.6.923/models/README BioPerl-1.6.923/scripts BioPerl-1.6.923/scripts/README BioPerl-1.6.923/scripts/Bio-DB-GFF BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_fast_load_gff.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_genbank2gff.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_genbank2gff3.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_generate_histogram.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_load_gff.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_meta_gff.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_gadfly.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_sgd.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_wormbase.pl BioPerl-1.6.923/scripts/Bio-DB-GFF/README BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl BioPerl-1.6.923/scripts/das BioPerl-1.6.923/scripts/das/bp_das_server.pl BioPerl-1.6.923/scripts/das/README BioPerl-1.6.923/scripts/das/TAG BioPerl-1.6.923/scripts/DB BioPerl-1.6.923/scripts/DB/bp_biofetch_genbank_proxy.pl BioPerl-1.6.923/scripts/DB/bp_bioflat_index.pl BioPerl-1.6.923/scripts/DB/bp_biogetseq.pl BioPerl-1.6.923/scripts/DB/bp_flanks.pl BioPerl-1.6.923/scripts/DB/TAG BioPerl-1.6.923/scripts/DB-HIV BioPerl-1.6.923/scripts/DB-HIV/bp_hivq.pl BioPerl-1.6.923/scripts/index BioPerl-1.6.923/scripts/index/bp_fetch.pl BioPerl-1.6.923/scripts/index/bp_index.pl BioPerl-1.6.923/scripts/index/bp_seqret.pl BioPerl-1.6.923/scripts/index/TAG BioPerl-1.6.923/scripts/popgen BioPerl-1.6.923/scripts/popgen/bp_composite_LD.pl BioPerl-1.6.923/scripts/popgen/bp_heterogeneity_test.pl BioPerl-1.6.923/scripts/searchio BioPerl-1.6.923/scripts/searchio/bp_fastam9_to_table.pl BioPerl-1.6.923/scripts/searchio/bp_filter_search.pl BioPerl-1.6.923/scripts/searchio/bp_hmmer_to_table.pl BioPerl-1.6.923/scripts/searchio/bp_parse_hmmsearch.pl BioPerl-1.6.923/scripts/searchio/bp_search2table.pl BioPerl-1.6.923/scripts/searchio/README BioPerl-1.6.923/scripts/searchio/TAG BioPerl-1.6.923/scripts/seq BioPerl-1.6.923/scripts/seq/bp_extract_feature_seq.pl BioPerl-1.6.923/scripts/seq/bp_make_mrna_protein.pl BioPerl-1.6.923/scripts/seq/bp_seqconvert.pl BioPerl-1.6.923/scripts/seq/bp_seqcut.pl BioPerl-1.6.923/scripts/seq/bp_seqpart.pl BioPerl-1.6.923/scripts/seq/bp_seqretsplit.pl BioPerl-1.6.923/scripts/seq/bp_split_seq.pl BioPerl-1.6.923/scripts/seq/bp_translate_seq.pl BioPerl-1.6.923/scripts/seq/bp_unflatten_seq.pl BioPerl-1.6.923/scripts/seq/TAG BioPerl-1.6.923/scripts/seqstats BioPerl-1.6.923/scripts/seqstats/bp_aacomp.pl BioPerl-1.6.923/scripts/seqstats/bp_chaos_plot.pl BioPerl-1.6.923/scripts/seqstats/bp_gccalc.pl BioPerl-1.6.923/scripts/seqstats/bp_oligo_count.pl BioPerl-1.6.923/scripts/seqstats/TAG BioPerl-1.6.923/scripts/taxa BioPerl-1.6.923/scripts/taxa/bp_classify_hits_kingdom.pl BioPerl-1.6.923/scripts/taxa/bp_local_taxonomydb_query.pl BioPerl-1.6.923/scripts/taxa/bp_query_entrez_taxa.pl BioPerl-1.6.923/scripts/taxa/bp_taxid4species.pl BioPerl-1.6.923/scripts/taxa/bp_taxonomy2tree.pl BioPerl-1.6.923/scripts/taxa/TAG BioPerl-1.6.923/scripts/tree BioPerl-1.6.923/scripts/tree/bp_blast2tree.pl BioPerl-1.6.923/scripts/tree/bp_nexus2nh.pl BioPerl-1.6.923/scripts/tree/bp_tree2pag.pl BioPerl-1.6.923/scripts/tree/TAG BioPerl-1.6.923/scripts/utilities BioPerl-1.6.923/scripts/utilities/bp_dbsplit.pl BioPerl-1.6.923/scripts/utilities/bp_download_query_genbank.pl BioPerl-1.6.923/scripts/utilities/bp_mask_by_search.pl BioPerl-1.6.923/scripts/utilities/bp_mrtrans.pl BioPerl-1.6.923/scripts/utilities/bp_mutate.pl BioPerl-1.6.923/scripts/utilities/bp_netinstall.pl BioPerl-1.6.923/scripts/utilities/bp_nrdb.pl BioPerl-1.6.923/scripts/utilities/bp_pairwise_kaks.pl BioPerl-1.6.923/scripts/utilities/bp_remote_blast.pl BioPerl-1.6.923/scripts/utilities/bp_revtrans-motif.pl BioPerl-1.6.923/scripts/utilities/bp_search2alnblocks.pl BioPerl-1.6.923/scripts/utilities/bp_search2BSML.pl BioPerl-1.6.923/scripts/utilities/bp_search2gff.pl BioPerl-1.6.923/scripts/utilities/bp_search2tribe.pl BioPerl-1.6.923/scripts/utilities/bp_seq_length.pl BioPerl-1.6.923/scripts/utilities/bp_sreformat.pl BioPerl-1.6.923/scripts/utilities/README BioPerl-1.6.923/scripts/utilities/TAG BioPerl-1.6.923/t BioPerl-1.6.923/t/Alphabet.t BioPerl-1.6.923/t/nexml.t BioPerl-1.6.923/t/Perl.t BioPerl-1.6.923/t/PodSyntax.t BioPerl-1.6.923/t/SearchDist.t BioPerl-1.6.923/t/SeqEvolution.t BioPerl-1.6.923/t/Species.t BioPerl-1.6.923/t/Symbol.t BioPerl-1.6.923/t/TaxonTree.t BioPerl-1.6.923/t/Align BioPerl-1.6.923/t/Align/AlignStats.t BioPerl-1.6.923/t/Align/AlignUtil.t BioPerl-1.6.923/t/Align/Graphics.t BioPerl-1.6.923/t/Align/SimpleAlign.t BioPerl-1.6.923/t/Align/TreeBuild.t BioPerl-1.6.923/t/Align/Utilities.t BioPerl-1.6.923/t/AlignIO BioPerl-1.6.923/t/AlignIO/AlignIO.t BioPerl-1.6.923/t/AlignIO/arp.t BioPerl-1.6.923/t/AlignIO/bl2seq.t BioPerl-1.6.923/t/AlignIO/clustalw.t BioPerl-1.6.923/t/AlignIO/emboss.t BioPerl-1.6.923/t/AlignIO/fasta.t BioPerl-1.6.923/t/AlignIO/largemultifasta.t BioPerl-1.6.923/t/AlignIO/maf.t BioPerl-1.6.923/t/AlignIO/mase.t BioPerl-1.6.923/t/AlignIO/mega.t BioPerl-1.6.923/t/AlignIO/meme.t BioPerl-1.6.923/t/AlignIO/metafasta.t BioPerl-1.6.923/t/AlignIO/msf.t BioPerl-1.6.923/t/AlignIO/nexml.t BioPerl-1.6.923/t/AlignIO/nexus.t BioPerl-1.6.923/t/AlignIO/pfam.t BioPerl-1.6.923/t/AlignIO/phylip.t BioPerl-1.6.923/t/AlignIO/po.t BioPerl-1.6.923/t/AlignIO/prodom.t BioPerl-1.6.923/t/AlignIO/psi.t BioPerl-1.6.923/t/AlignIO/selex.t BioPerl-1.6.923/t/AlignIO/stockholm.t BioPerl-1.6.923/t/AlignIO/xmfa.t BioPerl-1.6.923/t/Annotation BioPerl-1.6.923/t/Annotation/Annotation.t BioPerl-1.6.923/t/Annotation/AnnotationAdaptor.t BioPerl-1.6.923/t/Assembly BioPerl-1.6.923/t/Assembly/ContigSpectrum.t BioPerl-1.6.923/t/Assembly/core.t BioPerl-1.6.923/t/Assembly/IO BioPerl-1.6.923/t/Assembly/IO/bowtie.t BioPerl-1.6.923/t/Assembly/IO/sam.t BioPerl-1.6.923/t/Cluster BioPerl-1.6.923/t/Cluster/UniGene.t BioPerl-1.6.923/t/ClusterIO BioPerl-1.6.923/t/ClusterIO/ClusterIO.t BioPerl-1.6.923/t/ClusterIO/SequenceFamily.t BioPerl-1.6.923/t/ClusterIO/unigene.t BioPerl-1.6.923/t/Coordinate BioPerl-1.6.923/t/Coordinate/CoordinateBoundaryTest.t BioPerl-1.6.923/t/Coordinate/CoordinateGraph.t BioPerl-1.6.923/t/Coordinate/CoordinateMapper.t BioPerl-1.6.923/t/Coordinate/GeneCoordinateMapper.t BioPerl-1.6.923/t/data BioPerl-1.6.923/t/data/01_basic.xml BioPerl-1.6.923/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml BioPerl-1.6.923/t/data/02_dogfish_no_taxrefs.xml BioPerl-1.6.923/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml BioPerl-1.6.923/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml BioPerl-1.6.923/t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml BioPerl-1.6.923/t/data/02_mackerel_no_taxrefs.xml BioPerl-1.6.923/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml BioPerl-1.6.923/t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml BioPerl-1.6.923/t/data/03_bootstraps.xml BioPerl-1.6.923/t/data/03_bootstraps_in_tag.xml BioPerl-1.6.923/t/data/04_labeled_ancestors.xml BioPerl-1.6.923/t/data/05_ancestral_states.xml BioPerl-1.6.923/t/data/13-pilE-F.scf BioPerl-1.6.923/t/data/1A11.pdb BioPerl-1.6.923/t/data/1A3I.pdb BioPerl-1.6.923/t/data/1BPT.pdb BioPerl-1.6.923/t/data/1ZZ19XR301R-Alignment.tblastn BioPerl-1.6.923/t/data/2008.blasttable BioPerl-1.6.923/t/data/27-contig_Newbler.ace BioPerl-1.6.923/t/data/503384.MEGABLAST.0 BioPerl-1.6.923/t/data/503384.MEGABLAST.2 BioPerl-1.6.923/t/data/5X_1895.FASTXY BioPerl-1.6.923/t/data/8HVP.pdb BioPerl-1.6.923/t/data/a_thaliana.blastn BioPerl-1.6.923/t/data/AAC12660.fa BioPerl-1.6.923/t/data/aaml.mlc BioPerl-1.6.923/t/data/aaml_pairwise.mlc BioPerl-1.6.923/t/data/AB077698.gb BioPerl-1.6.923/t/data/acefile.ace.1 BioPerl-1.6.923/t/data/acefile.singlets BioPerl-1.6.923/t/data/adh.mb_tree.nexus BioPerl-1.6.923/t/data/AE003528_ecoli.bls BioPerl-1.6.923/t/data/AE003644_Adh-genomic.gb BioPerl-1.6.923/t/data/AF032047.gbk BioPerl-1.6.923/t/data/AF165282.gb BioPerl-1.6.923/t/data/AF305198.gb BioPerl-1.6.923/t/data/AHCYL1.kegg BioPerl-1.6.923/t/data/alleles.fas BioPerl-1.6.923/t/data/alnfile.fasta BioPerl-1.6.923/t/data/amino.fa BioPerl-1.6.923/t/data/AnnIX-v003.gbk BioPerl-1.6.923/t/data/ar.embl BioPerl-1.6.923/t/data/assembly_with_singlets.ace BioPerl-1.6.923/t/data/ATF14F8.gbk BioPerl-1.6.923/t/data/atp1.matrix BioPerl-1.6.923/t/data/ay007676.gb BioPerl-1.6.923/t/data/AY095303S1.gbk BioPerl-1.6.923/t/data/ay116458.gb BioPerl-1.6.923/t/data/ay149291.gb BioPerl-1.6.923/t/data/AY763288.gb BioPerl-1.6.923/t/data/BAB68554.gb BioPerl-1.6.923/t/data/badfasta.fa BioPerl-1.6.923/t/data/barns-combined.nex BioPerl-1.6.923/t/data/baseml.pairwise BioPerl-1.6.923/t/data/baseml.usertree BioPerl-1.6.923/t/data/basic-bush.nex BioPerl-1.6.923/t/data/basic-ladder.nex BioPerl-1.6.923/t/data/BC000007.gbk BioPerl-1.6.923/t/data/BEL16-LTR_AG.embl BioPerl-1.6.923/t/data/biofpc.cor BioPerl-1.6.923/t/data/biofpc.fpc BioPerl-1.6.923/t/data/biorecipe.nhx BioPerl-1.6.923/t/data/Bird_Ovomucoids.nex BioPerl-1.6.923/t/data/BK000016-tpa.gbk BioPerl-1.6.923/t/data/bl2seq.blastn BioPerl-1.6.923/t/data/bl2seq.blastn.rev BioPerl-1.6.923/t/data/bl2seq.blastx.out BioPerl-1.6.923/t/data/bl2seq.bug940.out BioPerl-1.6.923/t/data/bl2seq.out BioPerl-1.6.923/t/data/bl2seq.tblastn.out BioPerl-1.6.923/t/data/bl2seq.tblastx.out BioPerl-1.6.923/t/data/blast.report BioPerl-1.6.923/t/data/blast_no_hit_desc.txt BioPerl-1.6.923/t/data/blast_plus.blastp BioPerl-1.6.923/t/data/blastp2215.blast BioPerl-1.6.923/t/data/blat.psLayout3 BioPerl-1.6.923/t/data/BLOSUM50 BioPerl-1.6.923/t/data/blosum62.bla BioPerl-1.6.923/t/data/BN000066-tpa.embl BioPerl-1.6.923/t/data/bootstrap.tre BioPerl-1.6.923/t/data/BOSS_DROME.FASTP_v35_04 BioPerl-1.6.923/t/data/branchSite.mlc BioPerl-1.6.923/t/data/brassica_ATH.WUBLASTN BioPerl-1.6.923/t/data/bug1986.blast2 BioPerl-1.6.923/t/data/bug1986.blastp BioPerl-1.6.923/t/data/bug2120.phd BioPerl-1.6.923/t/data/bug2246.blast BioPerl-1.6.923/t/data/bug2391.megablast BioPerl-1.6.923/t/data/bug2399.tblastn BioPerl-1.6.923/t/data/bug2453.maf BioPerl-1.6.923/t/data/bug2473.fasta BioPerl-1.6.923/t/data/bug2862.pmr BioPerl-1.6.923/t/data/bug2869.tree BioPerl-1.6.923/t/data/bug2901.fa BioPerl-1.6.923/t/data/bug2937.fasta BioPerl-1.6.923/t/data/bug2942.blastx BioPerl-1.6.923/t/data/bug2982.embl BioPerl-1.6.923/t/data/bug2982.gb BioPerl-1.6.923/t/data/bug3021.gmap BioPerl-1.6.923/t/data/bug3086.embl BioPerl-1.6.923/t/data/bug3331.mlc BioPerl-1.6.923/t/data/c200-vs-yeast.BLASTN BioPerl-1.6.923/t/data/c200-vs-yeast.BLASTN.m8 BioPerl-1.6.923/t/data/calm.swiss BioPerl-1.6.923/t/data/catalase-webblast.BLASTP BioPerl-1.6.923/t/data/cds-266.fas BioPerl-1.6.923/t/data/cds_sample.embl BioPerl-1.6.923/t/data/CG11099.fasaln BioPerl-1.6.923/t/data/CG2865.fasaln BioPerl-1.6.923/t/data/chad100.scf BioPerl-1.6.923/t/data/char-interleave.nex BioPerl-1.6.923/t/data/char-matrix-spaces.nex BioPerl-1.6.923/t/data/characters+trees.nexml.xml BioPerl-1.6.923/t/data/characters.nexml.old.xml BioPerl-1.6.923/t/data/codeml.mlc BioPerl-1.6.923/t/data/codeml315.mlc BioPerl-1.6.923/t/data/codeml4.mlc BioPerl-1.6.923/t/data/codeml43.mlc BioPerl-1.6.923/t/data/codeml43_nssites.mlc BioPerl-1.6.923/t/data/codeml45.mlc BioPerl-1.6.923/t/data/codeml45b.mlc BioPerl-1.6.923/t/data/codeml_nan.mlc BioPerl-1.6.923/t/data/codeml_nssites.mlc BioPerl-1.6.923/t/data/compLD_missingtest.prettybase BioPerl-1.6.923/t/data/compLD_test.prettybase BioPerl-1.6.923/t/data/component.ontology.test BioPerl-1.6.923/t/data/component.ontology.test2 BioPerl-1.6.923/t/data/contig-by-hand.wublastp BioPerl-1.6.923/t/data/contigspectrumtest.tigr BioPerl-1.6.923/t/data/crab.dat.cn BioPerl-1.6.923/t/data/crab.nj BioPerl-1.6.923/t/data/crab.njb BioPerl-1.6.923/t/data/crypto.sim4-0 BioPerl-1.6.923/t/data/crypto.sim4-3 BioPerl-1.6.923/t/data/crypto.sim4-4 BioPerl-1.6.923/t/data/ctgdemo.fpc BioPerl-1.6.923/t/data/cys1_dicdi.water BioPerl-1.6.923/t/data/cysprot.fa BioPerl-1.6.923/t/data/cysprot.msf BioPerl-1.6.923/t/data/cysprot.needle BioPerl-1.6.923/t/data/cysprot.tblastn BioPerl-1.6.923/t/data/cysprot.water BioPerl-1.6.923/t/data/cysprot1.fa BioPerl-1.6.923/t/data/cysprot1.FASTA BioPerl-1.6.923/t/data/cysprot1a.fa BioPerl-1.6.923/t/data/cysprot1a.msf BioPerl-1.6.923/t/data/cysprot1b.fa BioPerl-1.6.923/t/data/cysprot1b.hmmsearch BioPerl-1.6.923/t/data/cysprot1b.msf BioPerl-1.6.923/t/data/cysprot1b.newick BioPerl-1.6.923/t/data/cysprot_vs_gadfly.FASTA BioPerl-1.6.923/t/data/D10483.gbk BioPerl-1.6.923/t/data/D12555.gbk BioPerl-1.6.923/t/data/dcr1_sp.WUBLASTP BioPerl-1.6.923/t/data/dmel_2Lchunk.gb BioPerl-1.6.923/t/data/dna1.fa BioPerl-1.6.923/t/data/dna2.fa BioPerl-1.6.923/t/data/dnaE-bsub-prot.fa BioPerl-1.6.923/t/data/dnaE-bsub.fa BioPerl-1.6.923/t/data/dnaEbsub_ecoli.wublastx BioPerl-1.6.923/t/data/dnaEbsub_ecoli.wutblastn BioPerl-1.6.923/t/data/dnaEbsub_ecoli.wutblastx BioPerl-1.6.923/t/data/DQ018368.gb BioPerl-1.6.923/t/data/dq519393.gb BioPerl-1.6.923/t/data/ECAPAH02.embl BioPerl-1.6.923/t/data/echofilter.wublastn BioPerl-1.6.923/t/data/ecoli-trna-qrna.out BioPerl-1.6.923/t/data/ecoli_domains.rps.xml BioPerl-1.6.923/t/data/ecoli_domains.rpsblast BioPerl-1.6.923/t/data/ecolitst.bls BioPerl-1.6.923/t/data/ecolitst.fa BioPerl-1.6.923/t/data/ecolitst.noseqs.wublastp BioPerl-1.6.923/t/data/ecolitst.wublastp BioPerl-1.6.923/t/data/EG352462.gbxml BioPerl-1.6.923/t/data/empty.bl2seq BioPerl-1.6.923/t/data/ENr111.mfa.example.elems BioPerl-1.6.923/t/data/entrezgene.dat BioPerl-1.6.923/t/data/ex1.nucl.nhx BioPerl-1.6.923/t/data/example.hap BioPerl-1.6.923/t/data/example.phase BioPerl-1.6.923/t/data/example.vcf BioPerl-1.6.923/t/data/exonerate.output.dontwork BioPerl-1.6.923/t/data/exonerate.output.negativescore.works BioPerl-1.6.923/t/data/exonerate.output.works BioPerl-1.6.923/t/data/exonerate.whitespace_before_query.works BioPerl-1.6.923/t/data/expected.blast.out BioPerl-1.6.923/t/data/exsignalp.out BioPerl-1.6.923/t/data/factor7.embl BioPerl-1.6.923/t/data/Fang_2003.xml BioPerl-1.6.923/t/data/fgenesh.out BioPerl-1.6.923/t/data/footprinter.out BioPerl-1.6.923/t/data/forward_primer.fa BioPerl-1.6.923/t/data/forward_reverse_primers.fa BioPerl-1.6.923/t/data/frac_problems.blast BioPerl-1.6.923/t/data/frac_problems2.blast BioPerl-1.6.923/t/data/frac_problems3.blast BioPerl-1.6.923/t/data/geneid_1.0.out BioPerl-1.6.923/t/data/genemark-fragment.out BioPerl-1.6.923/t/data/genemark.out BioPerl-1.6.923/t/data/genewise.out BioPerl-1.6.923/t/data/genewise_output.paracel_btk BioPerl-1.6.923/t/data/genomewise.out BioPerl-1.6.923/t/data/genomic-seq.epcr BioPerl-1.6.923/t/data/genomic-seq.fasta BioPerl-1.6.923/t/data/genomic-seq.genscan BioPerl-1.6.923/t/data/genomic-seq.mzef BioPerl-1.6.923/t/data/Genscan.FastA BioPerl-1.6.923/t/data/gf-s71.needle BioPerl-1.6.923/t/data/Glimmer2.out BioPerl-1.6.923/t/data/glimmer3-fragment.detail BioPerl-1.6.923/t/data/glimmer3-fragment.predict BioPerl-1.6.923/t/data/Glimmer3.detail BioPerl-1.6.923/t/data/Glimmer3.predict BioPerl-1.6.923/t/data/GlimmerHMM.out BioPerl-1.6.923/t/data/GlimmerM.out BioPerl-1.6.923/t/data/gmap_f9-multiple_results.txt BioPerl-1.6.923/t/data/gmap_f9-reverse-strand.txt BioPerl-1.6.923/t/data/gmap_f9.txt BioPerl-1.6.923/t/data/GO.defs.test BioPerl-1.6.923/t/data/GO.defs.test2 BioPerl-1.6.923/t/data/headerless.psl BioPerl-1.6.923/t/data/hemoglobinA.meg BioPerl-1.6.923/t/data/hg16_chroms.gff BioPerl-1.6.923/t/data/hmmpfam.out BioPerl-1.6.923/t/data/hmmpfam_cs.out BioPerl-1.6.923/t/data/hmmpfam_fake.out BioPerl-1.6.923/t/data/hmmpfam_HSPdashline.txt BioPerl-1.6.923/t/data/hmmpfam_multiresult.out BioPerl-1.6.923/t/data/hmmscan.out BioPerl-1.6.923/t/data/hmmscan_multi_domain.out BioPerl-1.6.923/t/data/hmmscan_sec_struct.out BioPerl-1.6.923/t/data/hmmsearch.out BioPerl-1.6.923/t/data/hmmsearch3.out BioPerl-1.6.923/t/data/hs_est.est2genome BioPerl-1.6.923/t/data/hs_fugu.newick BioPerl-1.6.923/t/data/hs_owlmonkey.aln BioPerl-1.6.923/t/data/hs_owlmonkey.fas BioPerl-1.6.923/t/data/hs_owlmonkey.fasta BioPerl-1.6.923/t/data/hsinsulin.blastcl3.blastn BioPerl-1.6.923/t/data/HUMBETGLOA.fa BioPerl-1.6.923/t/data/HUMBETGLOA.FASTA BioPerl-1.6.923/t/data/HUMBETGLOA.gff BioPerl-1.6.923/t/data/HUMBETGLOA.grail BioPerl-1.6.923/t/data/HUMBETGLOA.grailexp BioPerl-1.6.923/t/data/HUMBETGLOA.mzef BioPerl-1.6.923/t/data/HUMBETGLOA.tblastx BioPerl-1.6.923/t/data/humor.maf BioPerl-1.6.923/t/data/humts1.pal BioPerl-1.6.923/t/data/hybrid2.gff3 BioPerl-1.6.923/t/data/in.fasta BioPerl-1.6.923/t/data/insulin.water BioPerl-1.6.923/t/data/interpro.xml BioPerl-1.6.923/t/data/interpro_ebi.xml BioPerl-1.6.923/t/data/interpro_relationship.xml BioPerl-1.6.923/t/data/interpro_sample.xml BioPerl-1.6.923/t/data/interpro_short.xml BioPerl-1.6.923/t/data/intrablock-comment.nex BioPerl-1.6.923/t/data/Kingdoms_DNA.nex BioPerl-1.6.923/t/data/L77119.hmmer BioPerl-1.6.923/t/data/little.largemultifasta BioPerl-1.6.923/t/data/LittleChrY.dbsnp.xml BioPerl-1.6.923/t/data/LOAD_Ccd1.dnd BioPerl-1.6.923/t/data/long-names.nex BioPerl-1.6.923/t/data/longnames.aln BioPerl-1.6.923/t/data/longnames.dnd BioPerl-1.6.923/t/data/lucy.info BioPerl-1.6.923/t/data/lucy.qual BioPerl-1.6.923/t/data/lucy.seq BioPerl-1.6.923/t/data/lucy.stderr BioPerl-1.6.923/t/data/lysozyme6.protml BioPerl-1.6.923/t/data/lysozyme6.simple.protml BioPerl-1.6.923/t/data/M0.mlc BioPerl-1.6.923/t/data/M12730.gb BioPerl-1.6.923/t/data/mapmaker.out BioPerl-1.6.923/t/data/mapmaker.txt BioPerl-1.6.923/t/data/mast.dat BioPerl-1.6.923/t/data/masta.dat BioPerl-1.6.923/t/data/match.output BioPerl-1.6.923/t/data/Mcjanrna_rdbII.gbk BioPerl-1.6.923/t/data/megablast_output.paracel_btk BioPerl-1.6.923/t/data/meme.dat BioPerl-1.6.923/t/data/mini-AE001405.gb BioPerl-1.6.923/t/data/mini-align.aln BioPerl-1.6.923/t/data/mixedmast.dat BioPerl-1.6.923/t/data/MmCT BioPerl-1.6.923/t/data/mpath.ontology.test BioPerl-1.6.923/t/data/MSGEFTUA.gb BioPerl-1.6.923/t/data/multi.blast.m8 BioPerl-1.6.923/t/data/multi.blast.m9 BioPerl-1.6.923/t/data/multi.phd BioPerl-1.6.923/t/data/multi_1.fa BioPerl-1.6.923/t/data/multi_2.fa BioPerl-1.6.923/t/data/multi_blast.bls BioPerl-1.6.923/t/data/multifa.seq BioPerl-1.6.923/t/data/multifa.seq.qual BioPerl-1.6.923/t/data/multiline-intrablock-comment.nex BioPerl-1.6.923/t/data/multiresult_blastn+.bls BioPerl-1.6.923/t/data/multiseq.bls BioPerl-1.6.923/t/data/multiseq_tags.phd BioPerl-1.6.923/t/data/mus.bls.xml BioPerl-1.6.923/t/data/mutations.dat BioPerl-1.6.923/t/data/mutations.old.dat BioPerl-1.6.923/t/data/mutations.old.xml BioPerl-1.6.923/t/data/mutations.xml BioPerl-1.6.923/t/data/myco_sites.gff BioPerl-1.6.923/t/data/NC_000007-ribosomal-slippage.gb BioPerl-1.6.923/t/data/NC_001284.gbk BioPerl-1.6.923/t/data/NC_002058_multDBLINK_bug3375.gb BioPerl-1.6.923/t/data/NC_006346.gb BioPerl-1.6.923/t/data/NC_006511-short.gbk BioPerl-1.6.923/t/data/NC_008536.gb BioPerl-1.6.923/t/data/nei_gojobori_test.aln BioPerl-1.6.923/t/data/neighbor.dist BioPerl-1.6.923/t/data/new_blastn.txt BioPerl-1.6.923/t/data/newblast.xml BioPerl-1.6.923/t/data/nhmmer-3.1.out BioPerl-1.6.923/t/data/nhx-bacteria.nhx BioPerl-1.6.923/t/data/NM_002254.gb BioPerl-1.6.923/t/data/no-genes.genscan BioPerl-1.6.923/t/data/no_cds_example.gb BioPerl-1.6.923/t/data/no_FH.embl BioPerl-1.6.923/t/data/no_hsps.blastp BioPerl-1.6.923/t/data/no_semicolon.newick BioPerl-1.6.923/t/data/noninterleaved.phy BioPerl-1.6.923/t/data/NT_021877.gbk BioPerl-1.6.923/t/data/nucmatrix.txt BioPerl-1.6.923/t/data/O_sat.wgs BioPerl-1.6.923/t/data/omim_genemap_test BioPerl-1.6.923/t/data/omim_genemap_test_nolinebreak BioPerl-1.6.923/t/data/omim_text_test BioPerl-1.6.923/t/data/P33897 BioPerl-1.6.923/t/data/P35527.gb BioPerl-1.6.923/t/data/P39765.gb BioPerl-1.6.923/t/data/PAM250 BioPerl-1.6.923/t/data/pep-266.aln BioPerl-1.6.923/t/data/pfam_tests.stk BioPerl-1.6.923/t/data/pfamOutput-bug3376.out BioPerl-1.6.923/t/data/phi.out BioPerl-1.6.923/t/data/phipsi.out BioPerl-1.6.923/t/data/phylipdist-36.out BioPerl-1.6.923/t/data/phylipdist.out BioPerl-1.6.923/t/data/phyloxml_examples.xml BioPerl-1.6.923/t/data/pictogram.fa BioPerl-1.6.923/t/data/plague_yeast.bls.xml BioPerl-1.6.923/t/data/polymorphism.dat BioPerl-1.6.923/t/data/polymorphism.old.xml BioPerl-1.6.923/t/data/polymorphism.xml BioPerl-1.6.923/t/data/popgen_saureus.dat BioPerl-1.6.923/t/data/popgen_saureus.multidat BioPerl-1.6.923/t/data/popstats.prettybase BioPerl-1.6.923/t/data/pre_rel9.swiss BioPerl-1.6.923/t/data/Primate_mtDNA.nex BioPerl-1.6.923/t/data/primedseq.fa BioPerl-1.6.923/t/data/primer3_infile.txt BioPerl-1.6.923/t/data/primer3_outfile.txt BioPerl-1.6.923/t/data/primer3_output.txt BioPerl-1.6.923/t/data/prints.out BioPerl-1.6.923/t/data/promoterwise.out BioPerl-1.6.923/t/data/protpars.phy BioPerl-1.6.923/t/data/protpars_longid.phy BioPerl-1.6.923/t/data/pseudowise.out BioPerl-1.6.923/t/data/psi_xml.dat BioPerl-1.6.923/t/data/psiblast.xml BioPerl-1.6.923/t/data/psiblastreport.out BioPerl-1.6.923/t/data/purine_v081.infernal BioPerl-1.6.923/t/data/puzzle.tre BioPerl-1.6.923/t/data/PX1CG.gb BioPerl-1.6.923/t/data/Q8GBD3.swiss BioPerl-1.6.923/t/data/qrna-relloc.out BioPerl-1.6.923/t/data/qualfile.qual BioPerl-1.6.923/t/data/quoted-strings1.nex BioPerl-1.6.923/t/data/quoted-strings2.nex BioPerl-1.6.923/t/data/Rab1.chaos-xml BioPerl-1.6.923/t/data/radical-whitespace.nex BioPerl-1.6.923/t/data/radical-whitespace_02.nex BioPerl-1.6.923/t/data/rebase.itype2 BioPerl-1.6.923/t/data/rebase.withrefm BioPerl-1.6.923/t/data/reference_ace.ace BioPerl-1.6.923/t/data/regulation_test.obo BioPerl-1.6.923/t/data/rel9.swiss BioPerl-1.6.923/t/data/repeatmasker.fa.out BioPerl-1.6.923/t/data/revcomp_mrna.gb BioPerl-1.6.923/t/data/rfam_tests.stk BioPerl-1.6.923/t/data/ribosome-slippage.gb BioPerl-1.6.923/t/data/roa1.dat BioPerl-1.6.923/t/data/roa1.gbxml BioPerl-1.6.923/t/data/roa1.genbank BioPerl-1.6.923/t/data/roa1.swiss BioPerl-1.6.923/t/data/roa1_v2.dat BioPerl-1.6.923/t/data/rpsblast.bls BioPerl-1.6.923/t/data/rpsblast_no_hits.bls BioPerl-1.6.923/t/data/sample_dataset.tigr BioPerl-1.6.923/t/data/sbay_c127.fas BioPerl-1.6.923/t/data/sbay_c545-yeast.BLASTZ.PSL BioPerl-1.6.923/t/data/seg.out BioPerl-1.6.923/t/data/semicolon.newick BioPerl-1.6.923/t/data/seqdatabase.ini BioPerl-1.6.923/t/data/seqfile.pir BioPerl-1.6.923/t/data/seqs.fas BioPerl-1.6.923/t/data/sequencefamily.dat BioPerl-1.6.923/t/data/seqxml.xml BioPerl-1.6.923/t/data/short.blx BioPerl-1.6.923/t/data/signalp.hmm.short BioPerl-1.6.923/t/data/signalp.hmm.summary BioPerl-1.6.923/t/data/signalp.negative.out BioPerl-1.6.923/t/data/signalp.nn.short BioPerl-1.6.923/t/data/signalp.nn.summary BioPerl-1.6.923/t/data/signalp.positive.out BioPerl-1.6.923/t/data/signalp.short BioPerl-1.6.923/t/data/signalp.summary BioPerl-1.6.923/t/data/sim4.for.for BioPerl-1.6.923/t/data/sim4.for.rev BioPerl-1.6.923/t/data/sim4.rev BioPerl-1.6.923/t/data/singleNSsite.mlc BioPerl-1.6.923/t/data/singlescore.gbk BioPerl-1.6.923/t/data/singlet_w_CT.ace BioPerl-1.6.923/t/data/so.obo BioPerl-1.6.923/t/data/sofa.ontology BioPerl-1.6.923/t/data/sp_subset.obo BioPerl-1.6.923/t/data/spaced_fasta.fa BioPerl-1.6.923/t/data/spaces.nex BioPerl-1.6.923/t/data/SPAN_Family4nl.nex BioPerl-1.6.923/t/data/SPAN_Family7n.nex BioPerl-1.6.923/t/data/SPAN_Family8a.nex BioPerl-1.6.923/t/data/sparsealn.needle BioPerl-1.6.923/t/data/spidey.noalignment BioPerl-1.6.923/t/data/spidey.test1 BioPerl-1.6.923/t/data/sprintf.rnamotif BioPerl-1.6.923/t/data/ssp160.embl.1 BioPerl-1.6.923/t/data/sv40_small.xml BioPerl-1.6.923/t/data/swiss.dat BioPerl-1.6.923/t/data/swisspfam.data BioPerl-1.6.923/t/data/SwissProt.dat BioPerl-1.6.923/t/data/T7.aln BioPerl-1.6.923/t/data/tab1part.mif BioPerl-1.6.923/t/data/tab2part.mif BioPerl-1.6.923/t/data/tab3part.mif BioPerl-1.6.923/t/data/tandem_repeats_finder.dat BioPerl-1.6.923/t/data/tandem_repeats_finder.noresults BioPerl-1.6.923/t/data/tandem_repeats_finder_no_desc.dat BioPerl-1.6.923/t/data/targetp.out BioPerl-1.6.923/t/data/tblastn.out BioPerl-1.6.923/t/data/test 2.txt BioPerl-1.6.923/t/data/test-3.0-1.meme BioPerl-1.6.923/t/data/test-3.0-2.meme BioPerl-1.6.923/t/data/test-4.9.meme BioPerl-1.6.923/t/data/test.abi BioPerl-1.6.923/t/data/test.ace BioPerl-1.6.923/t/data/test.bam BioPerl-1.6.923/t/data/test.bowtie BioPerl-1.6.923/t/data/test.cns.fastq BioPerl-1.6.923/t/data/test.ctf BioPerl-1.6.923/t/data/test.embl BioPerl-1.6.923/t/data/test.embl2sq BioPerl-1.6.923/t/data/test.exp BioPerl-1.6.923/t/data/test.fasta BioPerl-1.6.923/t/data/test.fastq BioPerl-1.6.923/t/data/test.game BioPerl-1.6.923/t/data/test.gcg BioPerl-1.6.923/t/data/test.gcgblast BioPerl-1.6.923/t/data/test.gcgfasta BioPerl-1.6.923/t/data/test.genbank BioPerl-1.6.923/t/data/test.genbank.noseq BioPerl-1.6.923/t/data/test.infernal BioPerl-1.6.923/t/data/test.interpro BioPerl-1.6.923/t/data/test.interpro-go.xml BioPerl-1.6.923/t/data/test.lasergene BioPerl-1.6.923/t/data/test.locuslink BioPerl-1.6.923/t/data/test.maq BioPerl-1.6.923/t/data/test.mase BioPerl-1.6.923/t/data/test.metafasta BioPerl-1.6.923/t/data/test.nh BioPerl-1.6.923/t/data/test.nhx BioPerl-1.6.923/t/data/test.pfam BioPerl-1.6.923/t/data/test.phd BioPerl-1.6.923/t/data/test.pir BioPerl-1.6.923/t/data/test.pln BioPerl-1.6.923/t/data/test.raw BioPerl-1.6.923/t/data/test.ref.fas BioPerl-1.6.923/t/data/test.swiss BioPerl-1.6.923/t/data/test.tab BioPerl-1.6.923/t/data/test.tigrxml BioPerl-1.6.923/t/data/test.tseq BioPerl-1.6.923/t/data/test.tsv BioPerl-1.6.923/t/data/test.txt BioPerl-1.6.923/t/data/test.waba BioPerl-1.6.923/t/data/test.xls BioPerl-1.6.923/t/data/test.ztr BioPerl-1.6.923/t/data/test1.blasttab3 BioPerl-1.6.923/t/data/test1.wublastp BioPerl-1.6.923/t/data/test2.infernal BioPerl-1.6.923/t/data/test2.raw BioPerl-1.6.923/t/data/test_badlf.gcg BioPerl-1.6.923/t/data/test_clear_range.fastq BioPerl-1.6.923/t/data/test_data.axt BioPerl-1.6.923/t/data/test_singlets.cns.fastq BioPerl-1.6.923/t/data/test_singlets.maq BioPerl-1.6.923/t/data/testaln.aln BioPerl-1.6.923/t/data/testaln.arp BioPerl-1.6.923/t/data/testaln.fasta BioPerl-1.6.923/t/data/testaln.fastq BioPerl-1.6.923/t/data/testaln.list BioPerl-1.6.923/t/data/testaln.mase BioPerl-1.6.923/t/data/testaln.metafasta BioPerl-1.6.923/t/data/testaln.msf BioPerl-1.6.923/t/data/testaln.nexus BioPerl-1.6.923/t/data/testaln.pfam BioPerl-1.6.923/t/data/testaln.phylip BioPerl-1.6.923/t/data/testaln.po BioPerl-1.6.923/t/data/testaln.prodom BioPerl-1.6.923/t/data/testaln.psi BioPerl-1.6.923/t/data/testaln.selex BioPerl-1.6.923/t/data/testaln.stockholm BioPerl-1.6.923/t/data/testaln.xmfa BioPerl-1.6.923/t/data/testaln2.arp BioPerl-1.6.923/t/data/testaln2.fasta BioPerl-1.6.923/t/data/testdat.exonerate BioPerl-1.6.923/t/data/testdata.crossmatch BioPerl-1.6.923/t/data/testdbaccnums.out BioPerl-1.6.923/t/data/testfile.erpin BioPerl-1.6.923/t/data/testfuzzy.genbank BioPerl-1.6.923/t/data/tiny.stk BioPerl-1.6.923/t/data/tmhmm.out BioPerl-1.6.923/t/data/tmp.fst BioPerl-1.6.923/t/data/tol-2010-02-18.nhx BioPerl-1.6.923/t/data/traits.tab BioPerl-1.6.923/t/data/traittree.nexus BioPerl-1.6.923/t/data/transfac.dat BioPerl-1.6.923/t/data/tree_nonewline.nexus BioPerl-1.6.923/t/data/Treebase-chlamy-dna.nex BioPerl-1.6.923/t/data/trees.nexml.old.xml BioPerl-1.6.923/t/data/tricky.wublast BioPerl-1.6.923/t/data/trna.strict.rnamotif BioPerl-1.6.923/t/data/U58726.gb BioPerl-1.6.923/t/data/U71225.gb BioPerl-1.6.923/t/data/U71225.gb.unix BioPerl-1.6.923/t/data/U71225.gb.win BioPerl-1.6.923/t/data/U83300.bsml BioPerl-1.6.923/t/data/UnaSmithHIV-both.nex BioPerl-1.6.923/t/data/unigene.data BioPerl-1.6.923/t/data/urease.tre.nexus BioPerl-1.6.923/t/data/version2.scf BioPerl-1.6.923/t/data/version3.scf BioPerl-1.6.923/t/data/wellcome_tol.nhx BioPerl-1.6.923/t/data/withrefm.906 BioPerl-1.6.923/t/data/worm_fam_2785.cdna BioPerl-1.6.923/t/data/X98338_Adh-mRNA.gb BioPerl-1.6.923/t/data/yeast.tRNAscanSE BioPerl-1.6.923/t/data/yn00.mlc BioPerl-1.6.923/t/data/yn00_45.mlc BioPerl-1.6.923/t/data/YP_007988852.gp BioPerl-1.6.923/t/data/ZABJ4EA7014.CH878695.1.blast.txt BioPerl-1.6.923/t/data/bad_dbfa BioPerl-1.6.923/t/data/bad_dbfa/bug3172.fa BioPerl-1.6.923/t/data/bad_dbfa/shotdb.fa BioPerl-1.6.923/t/data/biodbgff BioPerl-1.6.923/t/data/biodbgff/test.gff BioPerl-1.6.923/t/data/biodbgff/test.gff3 BioPerl-1.6.923/t/data/codeml_lysozyme BioPerl-1.6.923/t/data/codeml_lysozyme/2NG.dN BioPerl-1.6.923/t/data/codeml_lysozyme/2NG.dS BioPerl-1.6.923/t/data/codeml_lysozyme/2NG.tt BioPerl-1.6.923/t/data/codeml_lysozyme/4fold.nuc BioPerl-1.6.923/t/data/codeml_lysozyme/lnf BioPerl-1.6.923/t/data/codeml_lysozyme/lysozymeSmall.ctl BioPerl-1.6.923/t/data/codeml_lysozyme/lysozymeSmall.trees BioPerl-1.6.923/t/data/codeml_lysozyme/lysozymeSmall.txt BioPerl-1.6.923/t/data/codeml_lysozyme/mlc BioPerl-1.6.923/t/data/codeml_lysozyme/rst BioPerl-1.6.923/t/data/codeml_lysozyme/rst1 BioPerl-1.6.923/t/data/codeml_lysozyme/rub BioPerl-1.6.923/t/data/consed_project BioPerl-1.6.923/t/data/consed_project/edit_dir BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.contigs BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.log BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1 BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2 BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.log BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.problems BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.qual BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.fasta.screen.view BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.newtags BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.phrap.out BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project.screen.out BioPerl-1.6.923/t/data/consed_project/edit_dir/test_project_to_alu.cross BioPerl-1.6.923/t/data/consed_project/edit_dir/test_projectNewChromats.fof BioPerl-1.6.923/t/data/consed_project/phd_dir BioPerl-1.6.923/t/data/consed_project/phd_dir/ML4922R.phd.1 BioPerl-1.6.923/t/data/consed_project/phd_dir/ML4924F.phd.1 BioPerl-1.6.923/t/data/consed_project/phd_dir/ML4924R.phd.1 BioPerl-1.6.923/t/data/consed_project/phd_dir/ML4947F.phd.1 BioPerl-1.6.923/t/data/dbfa BioPerl-1.6.923/t/data/dbfa/1.fa BioPerl-1.6.923/t/data/dbfa/2.fa BioPerl-1.6.923/t/data/dbfa/3.fa BioPerl-1.6.923/t/data/dbfa/4.fa BioPerl-1.6.923/t/data/dbfa/5.fa BioPerl-1.6.923/t/data/dbfa/6.fa BioPerl-1.6.923/t/data/dbfa/7.fa BioPerl-1.6.923/t/data/dbfa/mixed_alphabet.fasta BioPerl-1.6.923/t/data/dbqual BioPerl-1.6.923/t/data/dbqual/1.qual BioPerl-1.6.923/t/data/dbqual/2.qual BioPerl-1.6.923/t/data/dbqual/3.qual BioPerl-1.6.923/t/data/fastq BioPerl-1.6.923/t/data/fastq/bug2335.fastq BioPerl-1.6.923/t/data/fastq/error_diff_ids.fastq BioPerl-1.6.923/t/data/fastq/error_double_qual.fastq BioPerl-1.6.923/t/data/fastq/error_double_seq.fastq BioPerl-1.6.923/t/data/fastq/error_long_qual.fastq BioPerl-1.6.923/t/data/fastq/error_no_qual.fastq BioPerl-1.6.923/t/data/fastq/error_qual_del.fastq BioPerl-1.6.923/t/data/fastq/error_qual_escape.fastq BioPerl-1.6.923/t/data/fastq/error_qual_null.fastq BioPerl-1.6.923/t/data/fastq/error_qual_space.fastq BioPerl-1.6.923/t/data/fastq/error_qual_tab.fastq BioPerl-1.6.923/t/data/fastq/error_qual_unit_sep.fastq BioPerl-1.6.923/t/data/fastq/error_qual_vtab.fastq BioPerl-1.6.923/t/data/fastq/error_short_qual.fastq BioPerl-1.6.923/t/data/fastq/error_spaces.fastq BioPerl-1.6.923/t/data/fastq/error_tabs.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_at_plus.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_at_qual.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_at_seq.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_in_plus.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_in_qual.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_in_seq.fastq BioPerl-1.6.923/t/data/fastq/error_trunc_in_title.fastq BioPerl-1.6.923/t/data/fastq/evil_wrapping.fastq BioPerl-1.6.923/t/data/fastq/example.fasta BioPerl-1.6.923/t/data/fastq/example.fastq BioPerl-1.6.923/t/data/fastq/example.qual BioPerl-1.6.923/t/data/fastq/illumina_faked.fastq BioPerl-1.6.923/t/data/fastq/sanger_93.fastq BioPerl-1.6.923/t/data/fastq/sanger_faked.fastq BioPerl-1.6.923/t/data/fastq/solexa_example.fastq BioPerl-1.6.923/t/data/fastq/solexa_faked.fastq BioPerl-1.6.923/t/data/fastq/test1_sanger.fastq BioPerl-1.6.923/t/data/fastq/test2_solexa.fastq BioPerl-1.6.923/t/data/fastq/test3_illumina.fastq BioPerl-1.6.923/t/data/fastq/tricky.fastq BioPerl-1.6.923/t/data/fastq/wrapping_issues.fastq BioPerl-1.6.923/t/data/fastq/zero_qual.fastq BioPerl-1.6.923/t/data/map_hem BioPerl-1.6.923/t/data/map_hem/HEM1-HEM12.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM12.fa.revcom BioPerl-1.6.923/t/data/map_hem/HEM1-HEM12.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM13.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM13.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM2.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM2.fa.revcom BioPerl-1.6.923/t/data/map_hem/HEM1-HEM2.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM3.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM3.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1-HEM4.fa BioPerl-1.6.923/t/data/map_hem/HEM1-HEM4.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM1.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM1.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM12-HEM13.fa BioPerl-1.6.923/t/data/map_hem/HEM12-HEM13.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM12-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM12-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM12-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM12-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM12.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM12.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM13-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM13-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM13-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM13-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM13.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM13.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM14-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM14-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM14.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM14.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM15.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM15.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM2-HEM12.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM12.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2-HEM13.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM13.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2-HEM3.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM3.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2-HEM4.fa BioPerl-1.6.923/t/data/map_hem/HEM2-HEM4.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM2.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM2.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM3-HEM12.fa BioPerl-1.6.923/t/data/map_hem/HEM3-HEM12.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM3-HEM13.fa BioPerl-1.6.923/t/data/map_hem/HEM3-HEM13.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM3-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM3-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM3-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM3-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM3-HEM4.fa BioPerl-1.6.923/t/data/map_hem/HEM3-HEM4.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM3.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM3.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/HEM4-HEM12.fa BioPerl-1.6.923/t/data/map_hem/HEM4-HEM12.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM4-HEM13.fa BioPerl-1.6.923/t/data/map_hem/HEM4-HEM13.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM4-HEM14.fa BioPerl-1.6.923/t/data/map_hem/HEM4-HEM14.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM4-HEM15.fa BioPerl-1.6.923/t/data/map_hem/HEM4-HEM15.meme.txt BioPerl-1.6.923/t/data/map_hem/HEM4.ups.fa_ BioPerl-1.6.923/t/data/map_hem/HEM4.ups.fa_.revcom BioPerl-1.6.923/t/data/map_hem/yeast.nc.1.freq BioPerl-1.6.923/t/data/mbsout BioPerl-1.6.923/t/data/mbsout/mbsout_infile1 BioPerl-1.6.923/t/data/mbsout/mbsout_infile2 BioPerl-1.6.923/t/data/mbsout/mbsout_infile3 BioPerl-1.6.923/t/data/msout BioPerl-1.6.923/t/data/msout/bad_msout_infile1 BioPerl-1.6.923/t/data/msout/bad_msout_infile2 BioPerl-1.6.923/t/data/msout/msout_infile1 BioPerl-1.6.923/t/data/msout/msout_infile2 BioPerl-1.6.923/t/data/msout/msout_infile3 BioPerl-1.6.923/t/data/msout/msout_infile4 BioPerl-1.6.923/t/data/nexml BioPerl-1.6.923/t/data/nexml/characters.nexml.8.xml BioPerl-1.6.923/t/data/nexml/characters.nexml.xml BioPerl-1.6.923/t/data/nexml/trees.nexml.8.xml BioPerl-1.6.923/t/data/nexml/trees.nexml.xml BioPerl-1.6.923/t/data/registry BioPerl-1.6.923/t/data/registry/bdb BioPerl-1.6.923/t/data/registry/bdb/seqdatabase.ini BioPerl-1.6.923/t/data/registry/flat BioPerl-1.6.923/t/data/registry/flat/seqdatabase.ini BioPerl-1.6.923/t/data/seqfeaturedb BioPerl-1.6.923/t/data/seqfeaturedb/test.gff3 BioPerl-1.6.923/t/data/taxdump BioPerl-1.6.923/t/data/taxdump/names.dmp BioPerl-1.6.923/t/data/taxdump/nodes.dmp BioPerl-1.6.923/t/data/taxonomy BioPerl-1.6.923/t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt BioPerl-1.6.923/t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta BioPerl-1.6.923/t/data/transfac_pro BioPerl-1.6.923/t/data/transfac_pro/factor.dat BioPerl-1.6.923/t/data/transfac_pro/fragment.dat BioPerl-1.6.923/t/data/transfac_pro/gene.dat BioPerl-1.6.923/t/data/transfac_pro/matrix.dat BioPerl-1.6.923/t/data/transfac_pro/readme.txt BioPerl-1.6.923/t/data/transfac_pro/reference.dat BioPerl-1.6.923/t/data/transfac_pro/site.dat BioPerl-1.6.923/t/Draw BioPerl-1.6.923/t/Draw/Pictogram.t BioPerl-1.6.923/t/lib BioPerl-1.6.923/t/lib/Error.pm BioPerl-1.6.923/t/LiveSeq BioPerl-1.6.923/t/LiveSeq/Chain.t BioPerl-1.6.923/t/LiveSeq/LiveSeq.t BioPerl-1.6.923/t/LiveSeq/Mutation.t BioPerl-1.6.923/t/LiveSeq/Mutator.t BioPerl-1.6.923/t/LocalDB BioPerl-1.6.923/t/LocalDB/BioDBGFF.t BioPerl-1.6.923/t/LocalDB/Fasta.t BioPerl-1.6.923/t/LocalDB/Flat.t BioPerl-1.6.923/t/LocalDB/Qual.t BioPerl-1.6.923/t/LocalDB/Registry.t BioPerl-1.6.923/t/LocalDB/SeqFeature.t BioPerl-1.6.923/t/LocalDB/transfac_pro.t BioPerl-1.6.923/t/LocalDB/Index BioPerl-1.6.923/t/LocalDB/Index/Blast.t BioPerl-1.6.923/t/LocalDB/Index/BlastTable.t BioPerl-1.6.923/t/LocalDB/Index/Index.t BioPerl-1.6.923/t/LocalDB/Taxonomy BioPerl-1.6.923/t/LocalDB/Taxonomy/greengenes.t BioPerl-1.6.923/t/LocalDB/Taxonomy/silva.t BioPerl-1.6.923/t/Map BioPerl-1.6.923/t/Map/Cyto.t BioPerl-1.6.923/t/Map/Linkage.t BioPerl-1.6.923/t/Map/Map.t BioPerl-1.6.923/t/Map/MapIO.t BioPerl-1.6.923/t/Map/MicrosatelliteMarker.t BioPerl-1.6.923/t/Map/Physical.t BioPerl-1.6.923/t/Matrix BioPerl-1.6.923/t/Matrix/InstanceSite.t BioPerl-1.6.923/t/Matrix/Matrix.t BioPerl-1.6.923/t/Matrix/ProtMatrix.t BioPerl-1.6.923/t/Matrix/ProtPsm.t BioPerl-1.6.923/t/Matrix/SiteMatrix.t BioPerl-1.6.923/t/Matrix/IO BioPerl-1.6.923/t/Matrix/IO/masta.t BioPerl-1.6.923/t/Matrix/IO/psm.t BioPerl-1.6.923/t/Ontology BioPerl-1.6.923/t/Ontology/GOterm.t BioPerl-1.6.923/t/Ontology/GraphAdaptor.t BioPerl-1.6.923/t/Ontology/Ontology.t BioPerl-1.6.923/t/Ontology/OntologyEngine.t BioPerl-1.6.923/t/Ontology/OntologyStore.t BioPerl-1.6.923/t/Ontology/Relationship.t BioPerl-1.6.923/t/Ontology/RelationshipType.t BioPerl-1.6.923/t/Ontology/Term.t BioPerl-1.6.923/t/Ontology/IO BioPerl-1.6.923/t/Ontology/IO/go.t BioPerl-1.6.923/t/Ontology/IO/interpro.t BioPerl-1.6.923/t/Ontology/IO/obo.t BioPerl-1.6.923/t/Phenotype BioPerl-1.6.923/t/Phenotype/Correlate.t BioPerl-1.6.923/t/Phenotype/Measure.t BioPerl-1.6.923/t/Phenotype/MeSH.t BioPerl-1.6.923/t/Phenotype/MiniMIMentry.t BioPerl-1.6.923/t/Phenotype/OMIMentry.t BioPerl-1.6.923/t/Phenotype/OMIMentryAllelicVariant.t BioPerl-1.6.923/t/Phenotype/OMIMparser.t BioPerl-1.6.923/t/Phenotype/Phenotype.t BioPerl-1.6.923/t/PopGen BioPerl-1.6.923/t/PopGen/Coalescent.t BioPerl-1.6.923/t/PopGen/HtSNP.t BioPerl-1.6.923/t/PopGen/MK.t BioPerl-1.6.923/t/PopGen/PopGen.t BioPerl-1.6.923/t/PopGen/PopGenSims.t BioPerl-1.6.923/t/PopGen/TagHaplotype.t BioPerl-1.6.923/t/RemoteDB BioPerl-1.6.923/t/RemoteDB/BioFetch.t BioPerl-1.6.923/t/RemoteDB/CUTG.t BioPerl-1.6.923/t/RemoteDB/EMBL.t BioPerl-1.6.923/t/RemoteDB/EntrezGene.t BioPerl-1.6.923/t/RemoteDB/GenBank.t BioPerl-1.6.923/t/RemoteDB/GenPept.t BioPerl-1.6.923/t/RemoteDB/MeSH.t BioPerl-1.6.923/t/RemoteDB/RefSeq.t BioPerl-1.6.923/t/RemoteDB/SeqHound.t BioPerl-1.6.923/t/RemoteDB/SeqRead_fail.t BioPerl-1.6.923/t/RemoteDB/SeqVersion.t BioPerl-1.6.923/t/RemoteDB/SwissProt.t BioPerl-1.6.923/t/RemoteDB/Taxonomy.t BioPerl-1.6.923/t/RemoteDB/HIV BioPerl-1.6.923/t/RemoteDB/HIV/HIV.t BioPerl-1.6.923/t/RemoteDB/HIV/HIVAnnotProcessor.t BioPerl-1.6.923/t/RemoteDB/HIV/HIVQuery.t BioPerl-1.6.923/t/RemoteDB/HIV/HIVQueryHelper.t BioPerl-1.6.923/t/RemoteDB/Query BioPerl-1.6.923/t/RemoteDB/Query/GenBank.t BioPerl-1.6.923/t/Restriction BioPerl-1.6.923/t/Restriction/Analysis-refac.t BioPerl-1.6.923/t/Restriction/Analysis.t BioPerl-1.6.923/t/Restriction/Gel.t BioPerl-1.6.923/t/Restriction/IO.t BioPerl-1.6.923/t/Root BioPerl-1.6.923/t/Root/Exception.t BioPerl-1.6.923/t/Root/HTTPget.t BioPerl-1.6.923/t/Root/RootI.t BioPerl-1.6.923/t/Root/RootIO.t BioPerl-1.6.923/t/Root/Storable.t BioPerl-1.6.923/t/Root/Tempfile.t BioPerl-1.6.923/t/Root/Utilities.t BioPerl-1.6.923/t/SearchIO BioPerl-1.6.923/t/SearchIO/axt.t BioPerl-1.6.923/t/SearchIO/blast.t BioPerl-1.6.923/t/SearchIO/blast_pull.t BioPerl-1.6.923/t/SearchIO/blasttable.t BioPerl-1.6.923/t/SearchIO/blastxml.t BioPerl-1.6.923/t/SearchIO/CigarString.t BioPerl-1.6.923/t/SearchIO/cross_match.t BioPerl-1.6.923/t/SearchIO/erpin.t BioPerl-1.6.923/t/SearchIO/exonerate.t BioPerl-1.6.923/t/SearchIO/fasta.t BioPerl-1.6.923/t/SearchIO/gmap_f9.t BioPerl-1.6.923/t/SearchIO/hmmer.t BioPerl-1.6.923/t/SearchIO/hmmer_pull.t BioPerl-1.6.923/t/SearchIO/infernal.t BioPerl-1.6.923/t/SearchIO/megablast.t BioPerl-1.6.923/t/SearchIO/psl.t BioPerl-1.6.923/t/SearchIO/rnamotif.t BioPerl-1.6.923/t/SearchIO/SearchIO.t BioPerl-1.6.923/t/SearchIO/sim4.t BioPerl-1.6.923/t/SearchIO/SimilarityPair.t BioPerl-1.6.923/t/SearchIO/Tiling.t BioPerl-1.6.923/t/SearchIO/waba.t BioPerl-1.6.923/t/SearchIO/wise.t BioPerl-1.6.923/t/SearchIO/Writer BioPerl-1.6.923/t/SearchIO/Writer/GbrowseGFF.t BioPerl-1.6.923/t/SearchIO/Writer/HitTableWriter.t BioPerl-1.6.923/t/SearchIO/Writer/HSPTableWriter.t BioPerl-1.6.923/t/SearchIO/Writer/HTMLWriter.t BioPerl-1.6.923/t/SearchIO/Writer/TextWriter.t BioPerl-1.6.923/t/Seq BioPerl-1.6.923/t/Seq/DBLink.t BioPerl-1.6.923/t/Seq/EncodedSeq.t BioPerl-1.6.923/t/Seq/LargeLocatableSeq.t BioPerl-1.6.923/t/Seq/LargePSeq.t BioPerl-1.6.923/t/Seq/LocatableSeq.t BioPerl-1.6.923/t/Seq/MetaSeq.t BioPerl-1.6.923/t/Seq/PrimaryQual.t BioPerl-1.6.923/t/Seq/PrimarySeq.t BioPerl-1.6.923/t/Seq/PrimedSeq.t BioPerl-1.6.923/t/Seq/Quality.t BioPerl-1.6.923/t/Seq/Seq.t BioPerl-1.6.923/t/Seq/SimulatedRead.t BioPerl-1.6.923/t/Seq/WithQuality.t BioPerl-1.6.923/t/SeqFeature BioPerl-1.6.923/t/SeqFeature/Amplicon.t BioPerl-1.6.923/t/SeqFeature/Clone.t BioPerl-1.6.923/t/SeqFeature/Collection.t BioPerl-1.6.923/t/SeqFeature/Computation.t BioPerl-1.6.923/t/SeqFeature/FeaturePair.t BioPerl-1.6.923/t/SeqFeature/Gene.t BioPerl-1.6.923/t/SeqFeature/Generic.t BioPerl-1.6.923/t/SeqFeature/Location.t BioPerl-1.6.923/t/SeqFeature/LocationFactory.t BioPerl-1.6.923/t/SeqFeature/Primer.t BioPerl-1.6.923/t/SeqFeature/Range.t BioPerl-1.6.923/t/SeqFeature/RangeI.t BioPerl-1.6.923/t/SeqFeature/SeqAnalysisParser.t BioPerl-1.6.923/t/SeqFeature/SubSeq.t BioPerl-1.6.923/t/SeqFeature/Unflattener.t BioPerl-1.6.923/t/SeqFeature/Unflattener2.t BioPerl-1.6.923/t/SeqIO BioPerl-1.6.923/t/SeqIO/abi.t BioPerl-1.6.923/t/SeqIO/ace.t BioPerl-1.6.923/t/SeqIO/agave.t BioPerl-1.6.923/t/SeqIO/alf.t BioPerl-1.6.923/t/SeqIO/asciitree.t BioPerl-1.6.923/t/SeqIO/bsml.t BioPerl-1.6.923/t/SeqIO/bsml_sax.t BioPerl-1.6.923/t/SeqIO/chadoxml.t BioPerl-1.6.923/t/SeqIO/chaos.t BioPerl-1.6.923/t/SeqIO/chaosxml.t BioPerl-1.6.923/t/SeqIO/ctf.t BioPerl-1.6.923/t/SeqIO/embl.t BioPerl-1.6.923/t/SeqIO/entrezgene.t BioPerl-1.6.923/t/SeqIO/excel.t BioPerl-1.6.923/t/SeqIO/exp.t BioPerl-1.6.923/t/SeqIO/fasta.t BioPerl-1.6.923/t/SeqIO/fastq.t BioPerl-1.6.923/t/SeqIO/flybase_chadoxml.t BioPerl-1.6.923/t/SeqIO/game.t BioPerl-1.6.923/t/SeqIO/gbxml.t BioPerl-1.6.923/t/SeqIO/gcg.t BioPerl-1.6.923/t/SeqIO/genbank.t BioPerl-1.6.923/t/SeqIO/Handler.t BioPerl-1.6.923/t/SeqIO/interpro.t BioPerl-1.6.923/t/SeqIO/kegg.t BioPerl-1.6.923/t/SeqIO/largefasta.t BioPerl-1.6.923/t/SeqIO/lasergene.t BioPerl-1.6.923/t/SeqIO/locuslink.t BioPerl-1.6.923/t/SeqIO/mbsout.t BioPerl-1.6.923/t/SeqIO/metafasta.t BioPerl-1.6.923/t/SeqIO/msout.t BioPerl-1.6.923/t/SeqIO/MultiFile.t BioPerl-1.6.923/t/SeqIO/Multiple_fasta.t BioPerl-1.6.923/t/SeqIO/nexml.t BioPerl-1.6.923/t/SeqIO/phd.t BioPerl-1.6.923/t/SeqIO/pir.t BioPerl-1.6.923/t/SeqIO/pln.t BioPerl-1.6.923/t/SeqIO/qual.t BioPerl-1.6.923/t/SeqIO/raw.t BioPerl-1.6.923/t/SeqIO/scf.t BioPerl-1.6.923/t/SeqIO/SeqBuilder.t BioPerl-1.6.923/t/SeqIO/SeqIO.t BioPerl-1.6.923/t/SeqIO/seqxml.t BioPerl-1.6.923/t/SeqIO/Splicedseq.t BioPerl-1.6.923/t/SeqIO/strider.t BioPerl-1.6.923/t/SeqIO/swiss.t BioPerl-1.6.923/t/SeqIO/tab.t BioPerl-1.6.923/t/SeqIO/table.t BioPerl-1.6.923/t/SeqIO/tigr.t BioPerl-1.6.923/t/SeqIO/tigrxml.t BioPerl-1.6.923/t/SeqIO/tinyseq.t BioPerl-1.6.923/t/SeqIO/ztr.t BioPerl-1.6.923/t/SeqTools BioPerl-1.6.923/t/SeqTools/Backtranslate.t BioPerl-1.6.923/t/SeqTools/CodonTable.t BioPerl-1.6.923/t/SeqTools/ECnumber.t BioPerl-1.6.923/t/SeqTools/GuessSeqFormat.t BioPerl-1.6.923/t/SeqTools/OddCodes.t BioPerl-1.6.923/t/SeqTools/SeqPattern.t BioPerl-1.6.923/t/SeqTools/SeqStats.t BioPerl-1.6.923/t/SeqTools/SeqUtils.t BioPerl-1.6.923/t/SeqTools/SeqWords.t BioPerl-1.6.923/t/Structure BioPerl-1.6.923/t/Structure/IO.t BioPerl-1.6.923/t/Structure/Structure.t BioPerl-1.6.923/t/Tools BioPerl-1.6.923/t/Tools/AmpliconSearch.t BioPerl-1.6.923/t/Tools/ePCR.t BioPerl-1.6.923/t/Tools/Est2Genome.t BioPerl-1.6.923/t/Tools/FootPrinter.t BioPerl-1.6.923/t/Tools/Geneid.t BioPerl-1.6.923/t/Tools/Genewise.t BioPerl-1.6.923/t/Tools/Genomewise.t BioPerl-1.6.923/t/Tools/Genpred.t BioPerl-1.6.923/t/Tools/GFF.t BioPerl-1.6.923/t/Tools/GuessSeqFormat.t BioPerl-1.6.923/t/Tools/Hmmer.t BioPerl-1.6.923/t/Tools/IUPAC.t BioPerl-1.6.923/t/Tools/Lucy.t BioPerl-1.6.923/t/Tools/Match.t BioPerl-1.6.923/t/Tools/pICalculator.t BioPerl-1.6.923/t/Tools/Primer3.t BioPerl-1.6.923/t/Tools/Promoterwise.t BioPerl-1.6.923/t/Tools/Pseudowise.t BioPerl-1.6.923/t/Tools/QRNA.t BioPerl-1.6.923/t/Tools/RandDistFunctions.t BioPerl-1.6.923/t/Tools/RepeatMasker.t BioPerl-1.6.923/t/Tools/rnamotif.t BioPerl-1.6.923/t/Tools/Seg.t BioPerl-1.6.923/t/Tools/Sigcleave.t BioPerl-1.6.923/t/Tools/Signalp.t BioPerl-1.6.923/t/Tools/Sim4.t BioPerl-1.6.923/t/Tools/SiRNA.t BioPerl-1.6.923/t/Tools/TandemRepeatsFinder.t BioPerl-1.6.923/t/Tools/TargetP.t BioPerl-1.6.923/t/Tools/Tmhmm.t BioPerl-1.6.923/t/Tools/tRNAscanSE.t BioPerl-1.6.923/t/Tools/Alignment BioPerl-1.6.923/t/Tools/Alignment/Consed.t BioPerl-1.6.923/t/Tools/Analysis BioPerl-1.6.923/t/Tools/Analysis/DNA BioPerl-1.6.923/t/Tools/Analysis/DNA/ESEfinder.t BioPerl-1.6.923/t/Tools/Analysis/Protein BioPerl-1.6.923/t/Tools/Analysis/Protein/Domcut.t BioPerl-1.6.923/t/Tools/Analysis/Protein/ELM.t BioPerl-1.6.923/t/Tools/Analysis/Protein/GOR4.t BioPerl-1.6.923/t/Tools/Analysis/Protein/HNN.t BioPerl-1.6.923/t/Tools/Analysis/Protein/Mitoprot.t BioPerl-1.6.923/t/Tools/Analysis/Protein/NetPhos.t BioPerl-1.6.923/t/Tools/Analysis/Protein/Scansite.t BioPerl-1.6.923/t/Tools/Analysis/Protein/Sopma.t BioPerl-1.6.923/t/Tools/EMBOSS BioPerl-1.6.923/t/Tools/EMBOSS/Palindrome.t BioPerl-1.6.923/t/Tools/Phylo BioPerl-1.6.923/t/Tools/Phylo/Gerp.t BioPerl-1.6.923/t/Tools/Phylo/Molphy.t BioPerl-1.6.923/t/Tools/Phylo/PAML.t BioPerl-1.6.923/t/Tools/Phylo/Phylip BioPerl-1.6.923/t/Tools/Phylo/Phylip/ProtDist.t BioPerl-1.6.923/t/Tools/Run BioPerl-1.6.923/t/Tools/Run/Dummy.pm BioPerl-1.6.923/t/Tools/Run/RemoteBlast.t BioPerl-1.6.923/t/Tools/Run/RemoteBlast_rpsblast.t BioPerl-1.6.923/t/Tools/Run/StandAloneBlast.t BioPerl-1.6.923/t/Tools/Run/WBCommandExts.t BioPerl-1.6.923/t/Tools/Run/WrapperBase.t BioPerl-1.6.923/t/Tools/Run/Dummy BioPerl-1.6.923/t/Tools/Run/Dummy/Config.pm BioPerl-1.6.923/t/Tools/Signalp BioPerl-1.6.923/t/Tools/Signalp/ExtendedSignalp.t BioPerl-1.6.923/t/Tools/Spidey BioPerl-1.6.923/t/Tools/Spidey/Spidey.t BioPerl-1.6.923/t/Tree BioPerl-1.6.923/t/Tree/Compatible.t BioPerl-1.6.923/t/Tree/Node.t BioPerl-1.6.923/t/Tree/RandomTreeFactory.t BioPerl-1.6.923/t/Tree/Tree.t BioPerl-1.6.923/t/Tree/TreeIO.t BioPerl-1.6.923/t/Tree/TreeStatistics.t BioPerl-1.6.923/t/Tree/PhyloNetwork BioPerl-1.6.923/t/Tree/PhyloNetwork/Factory.t BioPerl-1.6.923/t/Tree/PhyloNetwork/GraphViz.t BioPerl-1.6.923/t/Tree/PhyloNetwork/MuVector.t BioPerl-1.6.923/t/Tree/PhyloNetwork/PhyloNetwork.t BioPerl-1.6.923/t/Tree/PhyloNetwork/RandomFactory.t BioPerl-1.6.923/t/Tree/PhyloNetwork/TreeFactory.t BioPerl-1.6.923/t/Tree/TreeIO BioPerl-1.6.923/t/Tree/TreeIO/lintree.t BioPerl-1.6.923/t/Tree/TreeIO/newick.t BioPerl-1.6.923/t/Tree/TreeIO/nexml.t BioPerl-1.6.923/t/Tree/TreeIO/nexus.t BioPerl-1.6.923/t/Tree/TreeIO/nhx.t BioPerl-1.6.923/t/Tree/TreeIO/phyloxml.t BioPerl-1.6.923/t/Tree/TreeIO/svggraph.t BioPerl-1.6.923/t/Tree/TreeIO/tabtree.t BioPerl-1.6.923/t/Variation BioPerl-1.6.923/t/Variation/AAChange.t BioPerl-1.6.923/t/Variation/AAReverseMutate.t BioPerl-1.6.923/t/Variation/Allele.t BioPerl-1.6.923/t/Variation/DNAMutation.t BioPerl-1.6.923/t/Variation/RNAChange.t BioPerl-1.6.923/t/Variation/SeqDiff.t BioPerl-1.6.923/t/Variation/SNP.t BioPerl-1.6.923/t/Variation/Variation_IO.t BioPerl-1.6.923/travis_scripts BioPerl-1.6.923/travis_scripts/dependency_installs CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz >>> C:\Perl64-5.16\bin\perl.exe Build.PL could not find ParserDetails.ini in C:/cpanfly-5.16/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 ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation 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 '1.006923' ---- Unsatisfied dependencies detected during ---- ---- CJFIELDS/BioPerl-1.6.923.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-1.831.tar.gz Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0 PMQS/DB_File-1.831.tar.gz [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0 Running Build for C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz Has already been unwrapped into directory C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.923.tar.gz' failed when processing 'PMQS/DB_File-1.831.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> C:\Perl64-5.16\bin\perl.exe ./Build Building BioPerl CJFIELDS/BioPerl-1.6.923.tar.gz C:\Perl64-5.16\bin\perl.exe ./Build -- OK Running Build test >>> C:\Perl64-5.16\bin\perl.exe ./Build test verbose=1 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 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 38 - An object of class 'Bio::Matrix::PhylipDist' isa 'Bio::Matrix::PhylipDist' ok 39 ok 40 ok 41 ok 42 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' ok 43 ok 44 - Warn if seqs don't overlap ok 45 ok t/Align/AlignUtil.t .................... 1..47 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - An object of class 'Bio::SimpleAlign' 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 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 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 - An object of class 'Bio::AlignIO::clustalw' 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 - An object of class 'Bio::Align::Graphics' 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..206 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 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' ok 7 - pfam input test ok 8 - match_line ok 9 - An object of class 'Bio::SimpleAlign' 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 - select_noncont_by_name ok 18 - select_noncont_by_name ok 19 - select_noncont_by_name ok 20 - select_noncont_by_name ok 21 - each_seq ok 22 - get_nse ok 23 - id ok 24 - num_gaps ok 25 - each_alphabetically ok 26 - column_from_residue_number ok 27 - display_name get/set ok 28 - display_name get ok 29 - consensus_string ok 30 - consensus_string ok 31 - consensus_string ok 32 ok 33 - each_seq_with_id ok 34 - is_flush ok 35 - id get/set ok 36 - length ok 37 - num_residues ok 38 - num_sequences ok 39 - overall_percentage_identity ok 40 - overall_percentage_identity (align) ok 41 - overall_percentage_identity (short) ok 42 - overall_percentage_identity (long) ok 43 - average_percentage_identity ok 44 ok 45 - set_displayname_count ok 46 ok 47 - set_displayname_flat ok 48 ok 49 - set_displayname_normal ok 50 ok 51 ok 52 - uppercase, map_chars ok 53 - match_line ok 54 - remove_seqs ok 55 - remove_seqs ok 56 - add_seq ok 57 - add_seq ok 58 - get_seq_by_pos ok 59 - get_seq_by_pos ok 60 ok 61 ok 62 ok 63 - purge ok 64 - purge ok 65 - IO::String consensus_iupac ok 66 - IO::String write_aln normal ok 67 - IO::String write_aln slice ok 68 - IO::String write_aln slice ok 69 - IO::String write_aln slice ok 70 - IO::String write_aln slice ok 71 - IO::String write_aln slice ok 72 ok 73 - remove_columns by position ok 74 - remove_columns by position (wrong order) ok 75 - cigar_line ok 76 - cigar_line ok 77 - cigar_line ok 78 - cigar_line ok 79 - sort_alphabetically - before ok 80 ok 81 - sort_alphabetically - after ok 82 - remove_gaps ok 83 - remove_gaps all_gaps_only ok 84 - set_new_reference ok 85 - set_new_reference ok 86 - uniq_seq ok 87 - bug 2099 ok 88 - bug 2099 ok 89 - bug 2793 ok 90 - bug 2793 ok 91 - bug 2793 ok 92 - bug 2793 ok 93 - Bad sequence, bad! ok 94 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' ok 95 - added 3 seqs ok 96 - first 2 features added ok 97 - 3rd feature added ok 98 ok 99 - slice 1 len ok 100 - correct masked seq ok 101 - correct masked seq ok 102 - correct masked seq ok 103 ok 104 - slice 2 len ok 105 - correct masked seq ok 106 - correct masked seq ok 107 - correct masked seq ok 108 ok 109 - slice 3 len ok 110 - correct masked seq ok 111 - correct masked seq ok 112 - correct masked seq ok 113 ok 114 - slice 4 len ok 115 - correct masked seq ok 116 - correct masked seq ok 117 - correct masked seq ok 118 - initial display id ok ok 119 - safe display id ok ok 120 - restored display id ok ok 121 - sort by list ok ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 - BIC:GGATCCATT[C/C]CTACT ok 129 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT ok 130 - BIC:G[G/C]ATCCATT[C/G]CTACT ok 131 - BIC:GGATCCATT[C/G]CTACT ok 132 - BIC:GGATCCATT[C/G]CTAC[T/A] ok 133 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] ok 134 - BIC:GGATCCATT[C/G]CTACT ok 135 - BIC:GGATCCATT{C.C}CTACT ok 136 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT ok 137 - BIC:G{G.C}ATCCATT{C.G}CTACT ok 138 - BIC:GGATCCATT{C.G}CTACT ok 139 - BIC:GGATCCATT{C.G}CTAC{T.A} ok 140 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} ok 141 - BIC:GGATCCATT{C.G}CTACT 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 200 - consensus string looks ok ok 201 - conservation length ok 202 - conservation scores ok 203 - looks like correct unmasked alignment (from clustalw) ok 204 - looks like correct masked alignment (from clustalw) ok 205 ok 206 - 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 t/AlignIO/AlignIO.t .................... 1..29 ok 1 - use Bio::AlignIO; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' ok 3 - input filehandle method test : metafasta ok 4 - input filehandle method test : po ok 5 - input filehandle method test : nexus ok 6 - input filehandle method test : clustalw ok 7 - input filehandle method test : prodom ok 8 - input filehandle method test : fasta ok 9 - input filehandle method test : arp ok 10 - input filehandle method test : xmfa ok 11 - input filehandle method test : mase ok 12 - input filehandle method test : psi ok 13 - input filehandle method test : phylip ok 14 - input filehandle method test : pfam ok 15 - input filehandle method test : selex ok 16 - input filehandle method test : stockholm ok 17 - input filehandle method test : msf ok 18 - filehandle output test : metafasta ok 19 - filehandle output test : po ok 20 - filehandle output test : nexus ok 21 - filehandle output test : clustalw ok 22 - filehandle output test : fasta ok 23 - filehandle output test : xmfa ok 24 - filehandle output test : psi ok 25 - filehandle output test : phylip ok 26 - filehandle output test : pfam ok 27 - filehandle output test : selex ok 28 - filehandle output test : stockholm ok 29 - filehandle output test : msf ok t/AlignIO/arp.t ........................ 1..48 ok 1 - use Bio::AlignIO::arp; ok 2 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 10 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 11 ok 12 ok 13 ok 14 ok 15 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 17 - ARP get_nse() ok 18 - ARP num_sequences() ok 19 - ARP id() ok 20 - ARP description() ok 21 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 22 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 23 ok 24 ok 25 ok 26 ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 28 - ARP get_nse() ok 29 - ARP num_sequences() ok 30 - ARP id() ok 31 - ARP description() ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 33 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 34 ok 35 ok 36 ok 37 ok 38 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 39 - ARP get_nse() ok 40 - ARP num_sequences() ok 41 - ARP id() ok 42 - ARP description() ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 44 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 45 ok 46 ok 47 ok 48 ok t/AlignIO/bl2seq.t ..................... 1..7 ok 1 - use Bio::AlignIO::bl2seq; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - BLAST bl2seq format test ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 5 ok 6 ok 7 ok t/AlignIO/clustalw.t ................... 1..6 ok 1 - use Bio::AlignIO::clustalw; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - clustalw consensus_string test ok 4 - clustalw (.aln) output test ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 6 - clustalw (.aln) input test ok t/AlignIO/emboss.t ..................... 1..37 ok 1 - use Bio::AlignIO::emboss; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 11 ok 12 ok 13 ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 15 ok 16 ok 17 ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 19 ok 20 ok 21 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 33 ok 34 ok 35 ok 36 ok 37 ok t/AlignIO/fasta.t ...................... 1..10 ok 1 - use Bio::AlignIO::fasta; ok 2 - An object of class 'Bio::SimpleAlign' 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 t/AlignIO/largemultifasta.t ............ 1..7 ok 1 - use Bio::AlignIO::largemultifasta; ok 2 - An object of class 'Bio::SimpleAlign' 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 t/AlignIO/maf.t ........................ 1..11 ok 1 - use Bio::AlignIO::maf; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - maf input test ok 4 ok 5 - An object of class 'Bio::SimpleAlign' 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 t/AlignIO/mase.t ....................... 1..3 ok 1 - use Bio::AlignIO::mase; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - mase input test ok t/AlignIO/mega.t ....................... 1..6 ok 1 - use Bio::AlignIO::mega; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 ok 4 ok 5 ok 6 - mega output test ok t/AlignIO/meme.t ....................... 1..20 ok 1 - use Bio::AlignIO::meme; ok 2 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok 6 ok 7 ok 8 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 17 ok 18 ok 19 ok 20 ok t/AlignIO/metafasta.t .................. 1..4 ok 1 - use Bio::AlignIO::metafasta; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - consensus_string on metafasta ok 4 - symbol_chars() using metafasta ok t/AlignIO/msf.t ........................ 1..4 ok 1 - use Bio::AlignIO::msf; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - msf input test ok 4 - msf output test ok # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support t/AlignIO/nexml.t ...................... 1..125 ok 1 - use Bio::AlignIO::nexml; ok 2 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 3 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 4 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 5 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 6 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 7 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 8 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 9 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 10 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 11 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 12 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 13 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 14 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 15 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 16 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 17 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 18 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 19 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 20 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 21 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 22 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 23 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 24 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 25 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 26 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 27 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 28 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 29 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 30 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 31 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 32 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 33 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 34 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 35 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 36 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 37 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 38 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 39 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 40 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 41 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 42 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 43 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 44 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 45 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 46 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 47 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 48 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 49 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 50 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 51 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 52 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 53 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 54 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 55 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 56 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 57 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 58 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 59 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 60 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 61 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 62 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 63 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 64 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 65 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 66 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 67 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 68 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 69 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 70 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 71 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 72 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 73 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 74 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 75 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 76 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 77 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 78 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 79 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 80 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 81 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 82 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 83 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 84 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 85 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 86 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 87 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 88 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 89 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 90 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 91 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 92 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 93 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 94 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 95 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 96 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 97 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 98 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 99 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 100 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 101 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 102 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 103 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 104 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 105 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 106 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 107 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 108 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 109 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 110 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 111 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 112 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 113 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 114 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 115 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 116 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 117 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 118 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 119 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 120 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 121 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 122 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 123 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 124 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 125 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok t/AlignIO/nexus.t ...................... 1..43 ok 1 - use Bio::AlignIO::nexus; ok 2 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - nexus output test ok 6 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 8 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 12 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 14 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 15 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 16 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 18 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 20 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 22 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 23 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 24 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 26 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 28 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 30 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 32 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 33 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 34 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 35 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 36 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 38 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 40 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 41 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 42 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 43 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok t/AlignIO/pfam.t ....................... 1..5 ok 1 - use Bio::AlignIO::pfam; ok 2 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - pfam output test ok t/AlignIO/phylip.t ..................... 1..17 ok 1 - use Bio::AlignIO::phylip; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 5 ok 6 ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 8 ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 ok 11 - phylip output test ok 12 ok 13 ok 14 not ok 15 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 81. # got: undef # expected: '0' not ok 16 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 82. # got: '50' # expected: '47' ok 17 - newline between header and sequences is parsed correctly ok t/AlignIO/po.t ......................... 1..11 ok 1 - use Bio::AlignIO::po; ok 2 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO' ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 7 - po output test ok 8 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 ok 11 ok t/AlignIO/prodom.t ..................... 1..3 ok 1 - use Bio::AlignIO::prodom; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - prodom input test ok t/AlignIO/psi.t ........................ 1..5 ok 1 - use Bio::AlignIO::psi; ok 2 - An object of class 'Bio::AlignIO::psi' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok t/AlignIO/selex.t ...................... 1..4 ok 1 - use Bio::AlignIO::selex; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - selex format test ok 4 - selex output test ok t/AlignIO/stockholm.t .................. 1..87 ok 1 - use Bio::AlignIO::stockholm; ok 2 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 36 - Rfam meta data ok 37 - Rfam meta data ok 38 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 39 ok 40 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 41 ok 42 ok 43 ok 44 ok 45 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' ok 46 - Pfam annotation ok 47 ok 48 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 49 ok 50 ok 51 ok 52 ok 53 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 - An object of class 'Bio::Seq::Meta' 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 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI' ok 72 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta' ok 73 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' ok 74 - An object of class 'Bio::Annotation::Target' 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 85 ok 86 ok 87 ok t/AlignIO/xmfa.t ....................... 1..30 ok 1 - use Bio::AlignIO::xmfa; ok 2 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::Symbol::Alphabet' isa 'Bio::Symbol::Alphabet' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - An object of class 'Bio::Symbol::DNAAlphabet' 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 - An object of class 'Bio::Symbol::ProteinAlphabet' 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 t/Annotation/Annotation.t .............. 1..152 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 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI' ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI' ok 19 ok 20 ok 21 ok 22 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 23 ok 24 ok 25 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' ok 26 ok 27 - An object of class 'Bio::Annotation::Reference' isa 'Bio::AnnotationI' 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 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::AnnotationI' 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 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 66 ok 67 ok 68 ok 69 ok 70 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue' ok 71 ok 72 ok 73 ok 74 ok 75 - use Bio::Annotation::OntologyTerm; ok 76 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term' ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed ok 83 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed ok 84 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed ok 85 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed ok 86 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI' ok 87 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' ok 88 ok 89 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm' ok 90 - Bio::Annotation::Comment ok 91 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 92 ok 93 - Bio::Annotation::Comment ok 94 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 95 - Bio::Annotation::Comment ok 96 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 97 ok 98 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target' ok 99 ok 100 ok 101 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI' ok 102 - tree_id() ok 103 - tagname() ok 104 ok 105 - add tree to AlignI ok 106 - get seq from node id ok 107 ok 108 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree' ok 109 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 110 - default itext ok 111 - roundtrip ok 112 - itext ok 113 - spxr ok 114 - indent ok 115 - xml ok 116 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 117 ok 118 - child changes ok 119 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 120 ok 121 - child changes ok 122 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 123 ok 124 - child changes ok 125 - child changes in parent node ok 126 - no tags ok 127 - before Stag node ok 128 - after Stag node ok 129 - both stag nodes ok 130 - different instances ok 131 - before TagTree ok 132 - after TagTree ok 133 - both stag nodes ok 134 - different instances ok 135 - before TagTree ok 136 - after TagTree ok 137 - stag nodes ok 138 - same instance ok 139 - before TagTree ok 140 - after TagTree ok 141 - stag nodes ok 142 - different instance ok 143 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 144 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 145 - child changes ok 146 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 147 - child changes ok 148 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 149 - child changes ok 150 ok 151 ok 152 - An object of class 'Bio::Annotation::TagTree' 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/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 558. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560 STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:309 STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138 STACK: t/Assembly/ContigSpectrum.t:13 ----------------------------------------------------------- # Failed test 'undef isa 'Bio::Assembly::IO'' # at t/Assembly/ContigSpectrum.t line 17. # undef isn't defined Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 18. # Looks like you planned 239 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..239 ok 1 - use Bio::Assembly::IO; ok 2 - use Bio::Assembly::Tools::ContigSpectrum; not ok 3 - undef isa 'Bio::Assembly::IO' Dubious, test returned 2 (wstat 512, 0x200) Failed 237/239 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/Cluster/UniGene.t .................... 1..2 ok 1 - use Bio::Cluster::UniGene; ok 2 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI' ok 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 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok 12 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok t/ClusterIO/SequenceFamily.t ........... 1..17 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 t/ClusterIO/unigene.t .................. 1..73 ok 1 - use Bio::ClusterIO; ok 2 - new Bio::ClusterIO object defined ok 3 ok 4 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok 5 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::ClusterI' ok 6 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::IdentifiableI' ok 7 - An object of class 'Bio::Cluster::UniGene' 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 - An object of class 'Bio::Seq::RichSeq' 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 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' ok 67 ok 68 - next cluster ok 69 ok 70 ok 71 ok 72 ok 73 ok t/Coordinate/CoordinateBoundaryTest.t .. 1..174 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 ok 4 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 5 ok 6 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 7 ok 8 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 9 ok 10 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 11 ok 12 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' 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 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 33 ok 34 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 35 ok 36 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' 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 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 51 ok 52 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 53 ok 54 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' 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 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 69 ok 70 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 71 ok 72 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' 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 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 89 ok 90 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 91 ok 92 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' 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 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 109 ok 110 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 111 ok 112 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 113 ok 114 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 115 ok 116 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' 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 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 133 ok 134 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 143 ok 144 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 153 ok 154 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 165 ok 166 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 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 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 15 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Location::SplitLocationI' ok 16 ok 17 ok 18 ok 19 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::LocationI' ok 20 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::Coordinate::Result::Gap' ok 38 - An object of class 'Bio::Coordinate::Result::Gap' 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 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Draw::Pictogram' 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 You are loading a Bio::DB::GFF database with GFF3 formatted data. While this will likely work fine, the Bio::DB::GFF schema does not always faithfully capture the complexity represented in GFF3 files. Unless you have a specific reason for using Bio::DB::GFF, we suggest that you use a Bio::DB::SeqFeature::Store database and its corresponding loader, bp_seqfeature_load.pl. t/LocalDB/BioDBGFF.t ................... 1..275 ok 1 - use Bio::DB::GFF; 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 # skip fetch_feature_by_gid() not implemented by this adaptor ok 102 # skip fetch_feature_by_gid() not implemented by this adaptor 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 # skip delete_groups() not implemented by this adaptor ok 133 # skip delete_groups() not implemented by this adaptor ok 134 # skip Not compatible with your Operating System 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 # skip fetch_feature_by_gid() not implemented by this adaptor ok 239 # skip fetch_feature_by_gid() not implemented by this adaptor ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 # skip preferred groups are not supported by gff3 ok 247 # skip preferred groups are not supported by gff3 ok 248 # skip preferred groups are not supported by gff3 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 # skip delete_groups() not implemented by this adaptor ok 270 # skip delete_groups() not implemented by this adaptor ok 271 # skip Not compatible with your Operating System ok 272 ok 273 ok 274 ok 275 ok # Failed test at t/LocalDB/Fasta.t line 188. # Failed test at t/LocalDB/Fasta.t line 200. # Structures begin differing at: # $got->[1] = '123' # $expected->[1] = '194473622' # Failed test at t/LocalDB/Fasta.t line 201. # got: 'gi|352962148|ref|NM_001251825.1|' # expected: undef # Failed test at t/LocalDB/Fasta.t line 211. # Structures begin differing at: # $got->[1] = '123' # $expected->[1] = '194473622' # Failed test at t/LocalDB/Fasta.t line 212. # got: 'gi|352962148|ref|NM_001251825.1|' # expected: undef # Looks like you failed 5 tests of 107. t/LocalDB/Fasta.t ...................... 1..107 ok 1 - Index a directory ok 2 ok 3 - An object of class 'Bio::DB::Fasta' isa 'Bio::DB::Fasta' 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 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' ok 29 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - bug 3126 ok 38 ok 39 ok 40 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' ok 41 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' ok 42 ok 43 ok 44 ok 45 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' ok 46 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' ok 47 ok 48 ok 49 - use Class::Unload; ok 50 - Re-open an existing index ok 51 ok 52 - Tied hash access ok 53 ok 54 ok 55 ok 56 ok 57 - Writing with SeqIO ok 58 ok 59 ok 60 - Index a single file ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream' 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 not ok 86 ok 87 ok 88 - Make single ID not ok 89 not ok 90 ok 91 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' ok 92 - Make multiple IDs, bug \#3389 not ok 93 not ok 94 ok 95 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' ok 96 - Index a set of files ok 97 ok 98 ok 99 ok 100 ok 101 - threw Regexp ((?^:FASTA header doesn't match)) ok 102 - threw Regexp ((?^:Blank lines can only precede header lines)) ok 103 ok 104 - length is correct in sequences past spaces ok 105 ok 106 - subseq is correct ok 107 - subseq is correct Dubious, test returned 5 (wstat 1280, 0x500) Failed 5/107 subtests t/LocalDB/Flat.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed 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/Qual.t ....................... 1..56 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 - An object of class 'Bio::DB::Qual' isa 'Bio::DB::Qual' 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 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' ok 23 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI' 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 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' ok 38 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI' ok 39 ok 40 ok 41 ok 42 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' ok 43 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 44 ok 45 ok 46 ok 47 ok 48 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream' ok 49 ok 50 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 51 ok 52 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 53 ok 54 ok 55 ok 56 ok 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;' # at t/LocalDB/SeqFeature.t 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 37. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 37. # 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 t/LocalDB/SeqFeature.t line 16. # BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 16. # Looks like you failed 1 test of 116. 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) 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 135) line 2. # at t/LocalDB/SeqFeature.t line 32. # Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 110 skipped subtests: 5 okay) t/LocalDB/Taxonomy/greengenes.t ........ 1..38 ok 1 - use Bio::DB::Taxonomy; ok 2 - use Bio::Tree::Tree; ok 3 ok 4 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::greengenes' ok 5 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::list' ok 6 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy' 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 t/LocalDB/Taxonomy/silva.t ............. 1..42 ok 1 - use Bio::DB::Taxonomy; ok 2 - use Bio::Tree::Tree; ok 3 ok 4 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::silva' ok 5 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::list' ok 6 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy' 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 ------------- 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88. Compilation failed in require at Bio/Root/Root.pm line 558. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88. Compilation failed in require at Bio/Root/Root.pm line 558. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/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 558. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560 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-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.923-W1_uPD C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl64-5.16/site/lib C:/Perl64-5.16/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 558. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560 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 - An object of class 'Bio::Map::CytoPosition' isa 'Bio::Map::CytoPosition' ok 15 ok 16 ok 17 ok 18 - An object of class 'Bio::Range' 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 - An object of class 'Bio::Map::SimpleMap' 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..40 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 40 # TODO Possible hash randomization-related bug, sum of contig pos values sometimes fails with off-by-one 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 - An object of class 'Bio::Matrix::Scoring' 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 - An object of class 'Bio::Matrix::Scoring' 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 - An object of class 'Bio::Ontology::GOterm' 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 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::OntologyI' ok 4 ok 5 - An object of class 'Bio::Ontology::OBOEngine' 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 - An object of class 'Bio::OntologyIO::InterProParser' 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 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 20 - term Integrins alpha chain in ontology InterPro ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 22 - term post-translational modification in ontology InterPro ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 24 - term Repeat in ontology InterPro ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 26 - term Binding Site in ontology InterPro ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 28 - term Cdc20/Fizzy in ontology InterPro ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 30 - term Conserved Site in ontology InterPro ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 32 - term Region in ontology InterPro ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 34 - term Kringle in ontology InterPro ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 36 - term Helix-turn-helix, AraC type in ontology InterPro ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 38 - term Active Site in ontology InterPro ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 40 - term Active Site in ontology InterPro ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 42 - term Binding Site in ontology InterPro ok 43 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 44 - term Conserved Site in ontology InterPro ok 45 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 46 - term Domain in ontology InterPro ok 47 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 48 - term Family in ontology InterPro ok 49 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 50 - term Region in ontology InterPro ok 51 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 52 - term Repeat in ontology InterPro ok 53 - An object of class 'Bio::Ontology::Ontology' 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 - An object of class 'Bio::Ontology::Ontology' 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 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 - An object of class 'Bio::Ontology::SimpleOntologyEngine' 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 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType' ok 5 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' ok 6 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' ok 7 - An object of class 'Bio::Ontology::Relationship' 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 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType' ok 4 - An object of class 'Bio::Ontology::RelationshipType' 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 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 - An object of class 'Bio::Ontology::Term' 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 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI' ok 45 ok 46 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::TermI' ok 47 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' ok 48 ok 49 ok 50 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Ontology::TermI' ok 51 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::AnnotationI' ok 52 ok 53 ok 54 ok t/Perl.t ............................... 1..31 ok 1 - use Bio::Perl; ok 2 ok 3 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 4 ok 5 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI' ok 6 ok 7 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 8 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 9 ok 10 ok 11 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 12 ok 13 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 14 ok 15 - An object of class 'Bio::PrimarySeq' 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 30 # skip Network tests have not been requested ok 31 # 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 - An object of class 'Bio::Phenotype::Correlate' 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 - An object of class 'Bio::Phenotype::Measure' 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 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::OMIMentryAllelicVariant' 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 - An object of class 'Bio::Phenotype::OMIM::OMIMparser' isa 'Bio::Phenotype::OMIM::OMIMparser' ok 3 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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 - An object of class 'Bio::Phenotype::Phenotype' isa 'Bio::Phenotype::PhenotypeI' ok 9 - An object of class 'Bio::Phenotype::Phenotype' 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..953 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/ClusterI.pm ok 9 - POD test for Bio/ClusterIO.pm ok 10 - POD test for Bio/DasI.pm ok 11 - POD test for Bio/DBLinkContainerI.pm ok 12 - POD test for Bio/DescribableI.pm ok 13 - POD test for Bio/FeatureHolderI.pm ok 14 - POD test for Bio/HandlerBaseI.pm ok 15 - POD test for Bio/IdCollectionI.pm ok 16 - POD test for Bio/IdentifiableI.pm ok 17 - POD test for Bio/LocatableSeq.pm ok 18 - POD test for Bio/LocationI.pm ok 19 - POD test for Bio/MapIO.pm ok 20 - POD test for Bio/NexmlIO.pm ok 21 - POD test for Bio/OntologyIO.pm ok 22 - POD test for Bio/ParameterBaseI.pm ok 23 - POD test for Bio/Perl.pm ok 24 - POD test for Bio/PhyloNetwork.pm ok 25 - POD test for Bio/PrimarySeq.pm ok 26 - POD test for Bio/PrimarySeqI.pm ok 27 - POD test for Bio/PullParserI.pm ok 28 - POD test for Bio/Range.pm ok 29 - POD test for Bio/RangeI.pm ok 30 - POD test for Bio/SearchDist.pm ok 31 - POD test for Bio/SearchIO.pm ok 32 - POD test for Bio/Seq.pm ok 33 - POD test for Bio/SeqAnalysisParserI.pm ok 34 - POD test for Bio/SeqFeatureI.pm ok 35 - POD test for Bio/SeqI.pm ok 36 - POD test for Bio/SeqIO.pm ok 37 - POD test for Bio/SeqUtils.pm ok 38 - POD test for Bio/SimpleAlign.pm ok 39 - POD test for Bio/SimpleAnalysisI.pm ok 40 - POD test for Bio/Species.pm ok 41 - POD test for Bio/Taxon.pm ok 42 - POD test for Bio/Taxonomy.pm ok 43 - POD test for Bio/TreeIO.pm ok 44 - POD test for Bio/UpdateableSeqI.pm ok 45 - POD test for Bio/WebAgent.pm ok 46 - POD test for Bio/Align/AlignI.pm ok 47 - POD test for Bio/Align/DNAStatistics.pm ok 48 - POD test for Bio/Align/Graphics.pm ok 49 - POD test for Bio/Align/PairwiseStatistics.pm ok 50 - POD test for Bio/Align/ProteinStatistics.pm ok 51 - POD test for Bio/Align/StatisticsI.pm ok 52 - POD test for Bio/Align/Utilities.pm ok 53 - POD test for Bio/AlignIO/arp.pm ok 54 - POD test for Bio/AlignIO/bl2seq.pm ok 55 - POD test for Bio/AlignIO/clustalw.pm ok 56 - POD test for Bio/AlignIO/emboss.pm ok 57 - POD test for Bio/AlignIO/fasta.pm ok 58 - POD test for Bio/AlignIO/largemultifasta.pm ok 59 - POD test for Bio/AlignIO/maf.pm ok 60 - POD test for Bio/AlignIO/mase.pm ok 61 - POD test for Bio/AlignIO/mega.pm ok 62 - POD test for Bio/AlignIO/meme.pm ok 63 - POD test for Bio/AlignIO/metafasta.pm ok 64 - POD test for Bio/AlignIO/msf.pm ok 65 - POD test for Bio/AlignIO/nexml.pm ok 66 - POD test for Bio/AlignIO/nexus.pm ok 67 - POD test for Bio/AlignIO/pfam.pm ok 68 - POD test for Bio/AlignIO/phylip.pm ok 69 - POD test for Bio/AlignIO/po.pm ok 70 - POD test for Bio/AlignIO/proda.pm ok 71 - POD test for Bio/AlignIO/prodom.pm ok 72 - POD test for Bio/AlignIO/psi.pm ok 73 - POD test for Bio/AlignIO/selex.pm ok 74 - POD test for Bio/AlignIO/stockholm.pm ok 75 - POD test for Bio/AlignIO/xmfa.pm ok 76 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm ok 77 - POD test for Bio/Annotation/AnnotationFactory.pm ok 78 - POD test for Bio/Annotation/Collection.pm ok 79 - POD test for Bio/Annotation/Comment.pm ok 80 - POD test for Bio/Annotation/DBLink.pm ok 81 - POD test for Bio/Annotation/OntologyTerm.pm ok 82 - POD test for Bio/Annotation/Reference.pm ok 83 - POD test for Bio/Annotation/Relation.pm ok 84 - POD test for Bio/Annotation/SimpleValue.pm ok 85 - POD test for Bio/Annotation/StructuredValue.pm ok 86 - POD test for Bio/Annotation/TagTree.pm ok 87 - POD test for Bio/Annotation/Target.pm ok 88 - POD test for Bio/Annotation/Tree.pm ok 89 - POD test for Bio/Annotation/TypeManager.pm ok 90 - POD test for Bio/Assembly/Contig.pm ok 91 - POD test for Bio/Assembly/ContigAnalysis.pm ok 92 - POD test for Bio/Assembly/IO.pm ok 93 - POD test for Bio/Assembly/Scaffold.pm ok 94 - POD test for Bio/Assembly/ScaffoldI.pm ok 95 - POD test for Bio/Assembly/Singlet.pm ok 96 - POD test for Bio/Assembly/IO/ace.pm ok 97 - POD test for Bio/Assembly/IO/bowtie.pm ok 98 - POD test for Bio/Assembly/IO/maq.pm ok 99 - POD test for Bio/Assembly/IO/phrap.pm ok 100 - POD test for Bio/Assembly/IO/sam.pm ok 101 - POD test for Bio/Assembly/IO/tigr.pm ok 102 - POD test for Bio/Assembly/Tools/ContigSpectrum.pm ok 103 - POD test for Bio/Cluster/ClusterFactory.pm ok 104 - POD test for Bio/Cluster/FamilyI.pm ok 105 - POD test for Bio/Cluster/SequenceFamily.pm ok 106 - POD test for Bio/Cluster/UniGene.pm ok 107 - POD test for Bio/Cluster/UniGeneI.pm ok 108 - POD test for Bio/ClusterIO/dbsnp.pm ok 109 - POD test for Bio/ClusterIO/unigene.pm ok 110 - POD test for Bio/CodonUsage/IO.pm ok 111 - POD test for Bio/CodonUsage/Table.pm ok 112 - POD test for Bio/Coordinate/Chain.pm ok 113 - POD test for Bio/Coordinate/Collection.pm ok 114 - POD test for Bio/Coordinate/ExtrapolatingPair.pm ok 115 - POD test for Bio/Coordinate/GeneMapper.pm ok 116 - POD test for Bio/Coordinate/Graph.pm ok 117 - POD test for Bio/Coordinate/MapperI.pm ok 118 - POD test for Bio/Coordinate/Pair.pm ok 119 - POD test for Bio/Coordinate/Result.pm ok 120 - POD test for Bio/Coordinate/ResultI.pm ok 121 - POD test for Bio/Coordinate/Utils.pm ok 122 - POD test for Bio/Coordinate/Result/Gap.pm ok 123 - POD test for Bio/Coordinate/Result/Match.pm ok 124 - POD test for Bio/Das/FeatureTypeI.pm ok 125 - POD test for Bio/Das/SegmentI.pm ok 126 - POD test for Bio/DB/Ace.pm ok 127 - POD test for Bio/DB/BioFetch.pm ok 128 - POD test for Bio/DB/CUTG.pm ok 129 - POD test for Bio/DB/DBFetch.pm ok 130 - POD test for Bio/DB/EMBL.pm ok 131 - POD test for Bio/DB/EntrezGene.pm ok 132 - POD test for Bio/DB/Expression.pm ok 133 - POD test for Bio/DB/Failover.pm ok 134 - POD test for Bio/DB/Fasta.pm ok 135 - POD test for Bio/DB/FileCache.pm ok 136 - POD test for Bio/DB/Flat.pm ok 137 - POD test for Bio/DB/GenBank.pm ok 138 - POD test for Bio/DB/GenericWebAgent.pm ok 139 - POD test for Bio/DB/GenPept.pm ok 140 - POD test for Bio/DB/GFF.pm ok 141 - POD test for Bio/DB/HIV.pm ok 142 - POD test for Bio/DB/IndexedBase.pm ok 143 - POD test for Bio/DB/InMemoryCache.pm ok 144 - POD test for Bio/DB/LocationI.pm ok 145 - POD test for Bio/DB/MeSH.pm ok 146 - POD test for Bio/DB/NCBIHelper.pm ok 147 - POD test for Bio/DB/Qual.pm ok 148 - POD test for Bio/DB/QueryI.pm ok 149 - POD test for Bio/DB/RandomAccessI.pm ok 150 - POD test for Bio/DB/ReferenceI.pm ok 151 - POD test for Bio/DB/RefSeq.pm ok 152 - POD test for Bio/DB/Registry.pm ok 153 - POD test for Bio/DB/SeqFeature.pm ok 154 - POD test for Bio/DB/SeqHound.pm ok 155 - POD test for Bio/DB/SeqI.pm ok 156 - POD test for Bio/DB/SeqVersion.pm ok 157 - POD test for Bio/DB/SwissProt.pm ok 158 - POD test for Bio/DB/Taxonomy.pm ok 159 - POD test for Bio/DB/TFBS.pm ok 160 - POD test for Bio/DB/Universal.pm ok 161 - POD test for Bio/DB/UpdateableSeqI.pm ok 162 - POD test for Bio/DB/WebDBSeqI.pm ok 163 - POD test for Bio/DB/Expression/geo.pm ok 164 - POD test for Bio/DB/Flat/BDB.pm ok 165 - POD test for Bio/DB/Flat/BinarySearch.pm ok 166 - POD test for Bio/DB/Flat/BDB/embl.pm ok 167 - POD test for Bio/DB/Flat/BDB/fasta.pm ok 168 - POD test for Bio/DB/Flat/BDB/genbank.pm ok 169 - POD test for Bio/DB/Flat/BDB/swiss.pm ok 170 - POD test for Bio/DB/GFF/Aggregator.pm ok 171 - POD test for Bio/DB/GFF/Featname.pm ok 172 - POD test for Bio/DB/GFF/Feature.pm ok 173 - POD test for Bio/DB/GFF/Homol.pm ok 174 - POD test for Bio/DB/GFF/RelSegment.pm ok 175 - POD test for Bio/DB/GFF/Segment.pm ok 176 - POD test for Bio/DB/GFF/Typename.pm ok 177 - POD test for Bio/DB/GFF/Adaptor/ace.pm ok 178 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm ok 179 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm ok 180 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm ok 181 - POD test for Bio/DB/GFF/Adaptor/dbi.pm ok 182 - POD test for Bio/DB/GFF/Adaptor/memory.pm ok 183 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm ok 184 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm ok 185 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm ok 186 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm ok 187 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm ok 188 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm ok 189 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm ok 190 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm ok 191 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm ok 192 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm ok 193 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm ok 194 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm ok 195 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm ok 196 - POD test for Bio/DB/GFF/Aggregator/alignment.pm ok 197 - POD test for Bio/DB/GFF/Aggregator/clone.pm ok 198 - POD test for Bio/DB/GFF/Aggregator/coding.pm ok 199 - POD test for Bio/DB/GFF/Aggregator/gene.pm ok 200 - POD test for Bio/DB/GFF/Aggregator/match.pm ok 201 - POD test for Bio/DB/GFF/Aggregator/none.pm ok 202 - POD test for Bio/DB/GFF/Aggregator/orf.pm ok 203 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm ok 204 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm ok 205 - POD test for Bio/DB/GFF/Aggregator/transcript.pm ok 206 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm ok 207 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm ok 208 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm ok 209 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm ok 210 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm ok 211 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm ok 212 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm ok 213 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm ok 214 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm ok 215 - POD test for Bio/DB/GFF/Util/Binning.pm ok 216 - POD test for Bio/DB/GFF/Util/Rearrange.pm ok 217 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm ok 218 - POD test for Bio/DB/HIV/HIVQueryHelper.pm ok 219 - POD test for Bio/DB/Query/GenBank.pm ok 220 - POD test for Bio/DB/Query/HIVQuery.pm ok 221 - POD test for Bio/DB/Query/WebQuery.pm ok 222 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm ok 223 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm ok 224 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm ok 225 - POD test for Bio/DB/SeqFeature/Segment.pm ok 226 - POD test for Bio/DB/SeqFeature/Store.pm ok 227 - POD test for Bio/DB/SeqFeature/Store/bdb.pm ok 228 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm ok 229 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm ok 230 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm ok 231 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm ok 232 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm ok 233 - POD test for Bio/DB/SeqFeature/Store/Loader.pm ok 234 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm ok 235 - POD test for Bio/DB/SeqFeature/Store/memory.pm ok 236 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm ok 237 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm ok 238 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm ok 239 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm ok 240 - POD test for Bio/DB/SeqVersion/gi.pm ok 241 - POD test for Bio/DB/Taxonomy/entrez.pm ok 242 - POD test for Bio/DB/Taxonomy/flatfile.pm ok 243 - POD test for Bio/DB/Taxonomy/greengenes.pm ok 244 - POD test for Bio/DB/Taxonomy/list.pm ok 245 - POD test for Bio/DB/Taxonomy/silva.pm ok 246 - POD test for Bio/DB/TFBS/transfac_pro.pm ok 247 - POD test for Bio/Draw/Pictogram.pm ok 248 - POD test for Bio/Event/EventGeneratorI.pm ok 249 - POD test for Bio/Event/EventHandlerI.pm ok 250 - POD test for Bio/Factory/AnalysisI.pm ok 251 - POD test for Bio/Factory/ApplicationFactoryI.pm ok 252 - POD test for Bio/Factory/DriverFactory.pm ok 253 - POD test for Bio/Factory/FTLocationFactory.pm ok 254 - POD test for Bio/Factory/LocationFactoryI.pm ok 255 - POD test for Bio/Factory/MapFactoryI.pm ok 256 - POD test for Bio/Factory/ObjectBuilderI.pm ok 257 - POD test for Bio/Factory/ObjectFactory.pm ok 258 - POD test for Bio/Factory/ObjectFactoryI.pm ok 259 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm ok 260 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm ok 261 - POD test for Bio/Factory/SequenceFactoryI.pm ok 262 - POD test for Bio/Factory/SequenceProcessorI.pm ok 263 - POD test for Bio/Factory/SequenceStreamI.pm ok 264 - POD test for Bio/Factory/TreeFactoryI.pm ok 265 - POD test for Bio/Index/Abstract.pm ok 266 - POD test for Bio/Index/AbstractSeq.pm ok 267 - POD test for Bio/Index/Blast.pm ok 268 - POD test for Bio/Index/BlastTable.pm ok 269 - POD test for Bio/Index/EMBL.pm ok 270 - POD test for Bio/Index/Fasta.pm ok 271 - POD test for Bio/Index/Fastq.pm ok 272 - POD test for Bio/Index/GenBank.pm ok 273 - POD test for Bio/Index/Hmmer.pm ok 274 - POD test for Bio/Index/Qual.pm ok 275 - POD test for Bio/Index/Stockholm.pm ok 276 - POD test for Bio/Index/SwissPfam.pm ok 277 - POD test for Bio/Index/Swissprot.pm ok 278 - POD test for Bio/LiveSeq/AARange.pm ok 279 - POD test for Bio/LiveSeq/Chain.pm ok 280 - POD test for Bio/LiveSeq/ChainI.pm ok 281 - POD test for Bio/LiveSeq/DNA.pm ok 282 - POD test for Bio/LiveSeq/Exon.pm ok 283 - POD test for Bio/LiveSeq/Gene.pm ok 284 - POD test for Bio/LiveSeq/Intron.pm ok 285 - POD test for Bio/LiveSeq/Mutation.pm ok 286 - POD test for Bio/LiveSeq/Mutator.pm ok 287 - POD test for Bio/LiveSeq/Prim_Transcript.pm ok 288 - POD test for Bio/LiveSeq/Range.pm ok 289 - POD test for Bio/LiveSeq/Repeat_Region.pm ok 290 - POD test for Bio/LiveSeq/Repeat_Unit.pm ok 291 - POD test for Bio/LiveSeq/SeqI.pm ok 292 - POD test for Bio/LiveSeq/Transcript.pm ok 293 - POD test for Bio/LiveSeq/Translation.pm ok 294 - POD test for Bio/LiveSeq/IO/BioPerl.pm ok 295 - POD test for Bio/LiveSeq/IO/Loader.pm ok 296 - POD test for Bio/Location/Atomic.pm ok 297 - POD test for Bio/Location/AvWithinCoordPolicy.pm ok 298 - POD test for Bio/Location/CoordinatePolicyI.pm ok 299 - POD test for Bio/Location/Fuzzy.pm ok 300 - POD test for Bio/Location/FuzzyLocationI.pm ok 301 - POD test for Bio/Location/NarrowestCoordPolicy.pm ok 302 - POD test for Bio/Location/Simple.pm ok 303 - POD test for Bio/Location/Split.pm ok 304 - POD test for Bio/Location/SplitLocationI.pm ok 305 - POD test for Bio/Location/WidestCoordPolicy.pm ok 306 - POD test for Bio/Map/Clone.pm ok 307 - POD test for Bio/Map/Contig.pm ok 308 - POD test for Bio/Map/CytoMap.pm ok 309 - POD test for Bio/Map/CytoMarker.pm ok 310 - POD test for Bio/Map/CytoPosition.pm ok 311 - POD test for Bio/Map/EntityI.pm ok 312 - POD test for Bio/Map/FPCMarker.pm ok 313 - POD test for Bio/Map/Gene.pm ok 314 - POD test for Bio/Map/GeneMap.pm ok 315 - POD test for Bio/Map/GenePosition.pm ok 316 - POD test for Bio/Map/GeneRelative.pm ok 317 - POD test for Bio/Map/LinkageMap.pm ok 318 - POD test for Bio/Map/LinkagePosition.pm ok 319 - POD test for Bio/Map/MapI.pm ok 320 - POD test for Bio/Map/Mappable.pm ok 321 - POD test for Bio/Map/MappableI.pm ok 322 - POD test for Bio/Map/Marker.pm ok 323 - POD test for Bio/Map/MarkerI.pm ok 324 - POD test for Bio/Map/Microsatellite.pm ok 325 - POD test for Bio/Map/OrderedPosition.pm ok 326 - POD test for Bio/Map/OrderedPositionWithDistance.pm ok 327 - POD test for Bio/Map/Physical.pm ok 328 - POD test for Bio/Map/Position.pm ok 329 - POD test for Bio/Map/PositionHandler.pm ok 330 - POD test for Bio/Map/PositionHandlerI.pm ok 331 - POD test for Bio/Map/PositionI.pm ok 332 - POD test for Bio/Map/PositionWithSequence.pm ok 333 - POD test for Bio/Map/Prediction.pm ok 334 - POD test for Bio/Map/Relative.pm ok 335 - POD test for Bio/Map/RelativeI.pm ok 336 - POD test for Bio/Map/SimpleMap.pm ok 337 - POD test for Bio/Map/TranscriptionFactor.pm ok 338 - POD test for Bio/MapIO/fpc.pm ok 339 - POD test for Bio/MapIO/mapmaker.pm ok 340 - POD test for Bio/Matrix/Generic.pm ok 341 - POD test for Bio/Matrix/IO.pm ok 342 - POD test for Bio/Matrix/MatrixI.pm ok 343 - POD test for Bio/Matrix/Mlagan.pm ok 344 - POD test for Bio/Matrix/PhylipDist.pm ok 345 - POD test for Bio/Matrix/Scoring.pm ok 346 - POD test for Bio/Matrix/IO/mlagan.pm ok 347 - POD test for Bio/Matrix/IO/phylip.pm ok 348 - POD test for Bio/Matrix/IO/scoring.pm ok 349 - POD test for Bio/Matrix/PSM/InstanceSite.pm ok 350 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm ok 351 - POD test for Bio/Matrix/PSM/IO.pm ok 352 - POD test for Bio/Matrix/PSM/ProtMatrix.pm ok 353 - POD test for Bio/Matrix/PSM/ProtPsm.pm ok 354 - POD test for Bio/Matrix/PSM/Psm.pm ok 355 - POD test for Bio/Matrix/PSM/PsmHeader.pm ok 356 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm ok 357 - POD test for Bio/Matrix/PSM/PsmI.pm ok 358 - POD test for Bio/Matrix/PSM/SiteMatrix.pm ok 359 - POD test for Bio/Matrix/PSM/SiteMatrixI.pm ok 360 - POD test for Bio/Matrix/PSM/IO/mast.pm ok 361 - POD test for Bio/Matrix/PSM/IO/masta.pm ok 362 - POD test for Bio/Matrix/PSM/IO/meme.pm ok 363 - POD test for Bio/Matrix/PSM/IO/psiblast.pm ok 364 - POD test for Bio/Matrix/PSM/IO/transfac.pm ok 365 - POD test for Bio/MolEvol/CodonModel.pm ok 366 - POD test for Bio/Nexml/Factory.pm ok 367 - POD test for Bio/Ontology/DocumentRegistry.pm ok 368 - POD test for Bio/Ontology/GOterm.pm ok 369 - POD test for Bio/Ontology/InterProTerm.pm ok 370 - POD test for Bio/Ontology/OBOEngine.pm ok 371 - POD test for Bio/Ontology/OBOterm.pm ok 372 - POD test for Bio/Ontology/Ontology.pm ok 373 - POD test for Bio/Ontology/OntologyEngineI.pm ok 374 - POD test for Bio/Ontology/OntologyI.pm ok 375 - POD test for Bio/Ontology/OntologyStore.pm ok 376 - POD test for Bio/Ontology/Path.pm ok 377 - POD test for Bio/Ontology/PathI.pm ok 378 - POD test for Bio/Ontology/Relationship.pm ok 379 - POD test for Bio/Ontology/RelationshipFactory.pm ok 380 - POD test for Bio/Ontology/RelationshipI.pm ok 381 - POD test for Bio/Ontology/RelationshipType.pm ok 382 - POD test for Bio/Ontology/SimpleOntologyEngine.pm ok 383 - POD test for Bio/Ontology/Term.pm ok 384 - POD test for Bio/Ontology/TermFactory.pm ok 385 - POD test for Bio/Ontology/TermI.pm ok 386 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm ok 387 - POD test for Bio/OntologyIO/dagflat.pm ok 388 - POD test for Bio/OntologyIO/goflat.pm ok 389 - POD test for Bio/OntologyIO/InterProParser.pm ok 390 - POD test for Bio/OntologyIO/obo.pm ok 391 - POD test for Bio/OntologyIO/simplehierarchy.pm ok 392 - POD test for Bio/OntologyIO/soflat.pm ok 393 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm ok 394 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm ok 395 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm ok 396 - POD test for Bio/Phenotype/Correlate.pm ok 397 - POD test for Bio/Phenotype/Measure.pm ok 398 - POD test for Bio/Phenotype/Phenotype.pm ok 399 - POD test for Bio/Phenotype/PhenotypeI.pm ok 400 - POD test for Bio/Phenotype/MeSH/Term.pm ok 401 - POD test for Bio/Phenotype/MeSH/Twig.pm ok 402 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm ok 403 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm ok 404 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm ok 405 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm ok 406 - POD test for Bio/PhyloNetwork/Factory.pm ok 407 - POD test for Bio/PhyloNetwork/FactoryX.pm ok 408 - POD test for Bio/PhyloNetwork/GraphViz.pm ok 409 - POD test for Bio/PhyloNetwork/muVector.pm ok 410 - POD test for Bio/PhyloNetwork/RandomFactory.pm ok 411 - POD test for Bio/PhyloNetwork/TreeFactory.pm ok 412 - POD test for Bio/PhyloNetwork/TreeFactoryMulti.pm ok 413 - POD test for Bio/PhyloNetwork/TreeFactoryX.pm ok 414 - POD test for Bio/PopGen/Genotype.pm ok 415 - POD test for Bio/PopGen/GenotypeI.pm ok 416 - POD test for Bio/PopGen/HtSNP.pm ok 417 - POD test for Bio/PopGen/Individual.pm ok 418 - POD test for Bio/PopGen/IndividualI.pm ok 419 - POD test for Bio/PopGen/IO.pm ok 420 - POD test for Bio/PopGen/Marker.pm ok 421 - POD test for Bio/PopGen/MarkerI.pm ok 422 - POD test for Bio/PopGen/PopStats.pm ok 423 - POD test for Bio/PopGen/Population.pm ok 424 - POD test for Bio/PopGen/PopulationI.pm ok 425 - POD test for Bio/PopGen/Statistics.pm ok 426 - POD test for Bio/PopGen/TagHaplotype.pm ok 427 - POD test for Bio/PopGen/Utilities.pm ok 428 - POD test for Bio/PopGen/IO/csv.pm ok 429 - POD test for Bio/PopGen/IO/hapmap.pm ok 430 - POD test for Bio/PopGen/IO/phase.pm ok 431 - POD test for Bio/PopGen/IO/prettybase.pm ok 432 - POD test for Bio/PopGen/Simulation/Coalescent.pm ok 433 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm ok 434 - POD test for Bio/Restriction/Analysis.pm ok 435 - POD test for Bio/Restriction/Enzyme.pm ok 436 - POD test for Bio/Restriction/EnzymeCollection.pm ok 437 - POD test for Bio/Restriction/EnzymeI.pm ok 438 - POD test for Bio/Restriction/IO.pm ok 439 - POD test for Bio/Restriction/Enzyme/MultiCut.pm ok 440 - POD test for Bio/Restriction/Enzyme/MultiSite.pm ok 441 - POD test for Bio/Restriction/IO/bairoch.pm ok 442 - POD test for Bio/Restriction/IO/base.pm ok 443 - POD test for Bio/Restriction/IO/itype2.pm ok 444 - POD test for Bio/Restriction/IO/prototype.pm ok 445 - POD test for Bio/Restriction/IO/withrefm.pm ok 446 - POD test for Bio/Root/Build.pm ok 447 - POD test for Bio/Root/Exception.pm ok 448 - POD test for Bio/Root/HTTPget.pm ok 449 - POD test for Bio/Root/IO.pm ok 450 - POD test for Bio/Root/Root.pm ok 451 - POD test for Bio/Root/RootI.pm ok 452 - POD test for Bio/Root/Storable.pm ok 453 - POD test for Bio/Root/Test.pm ok 454 - POD test for Bio/Root/Utilities.pm ok 455 - POD test for Bio/Root/Version.pm ok 456 - POD test for Bio/Search/BlastStatistics.pm ok 457 - POD test for Bio/Search/BlastUtils.pm ok 458 - POD test for Bio/Search/DatabaseI.pm ok 459 - POD test for Bio/Search/GenericDatabase.pm ok 460 - POD test for Bio/Search/GenericStatistics.pm ok 461 - POD test for Bio/Search/Processor.pm ok 462 - POD test for Bio/Search/SearchUtils.pm ok 463 - POD test for Bio/Search/StatisticsI.pm ok 464 - POD test for Bio/Search/Hit/BlastHit.pm ok 465 - POD test for Bio/Search/Hit/BlastPullHit.pm ok 466 - POD test for Bio/Search/Hit/Fasta.pm ok 467 - POD test for Bio/Search/Hit/GenericHit.pm ok 468 - POD test for Bio/Search/Hit/HitFactory.pm ok 469 - POD test for Bio/Search/Hit/HitI.pm ok 470 - POD test for Bio/Search/Hit/hmmer3Hit.pm ok 471 - POD test for Bio/Search/Hit/HMMERHit.pm ok 472 - POD test for Bio/Search/Hit/HmmpfamHit.pm ok 473 - POD test for Bio/Search/Hit/ModelHit.pm ok 474 - POD test for Bio/Search/Hit/PsiBlastHit.pm ok 475 - POD test for Bio/Search/Hit/PullHitI.pm ok 476 - POD test for Bio/Search/HSP/BlastHSP.pm ok 477 - POD test for Bio/Search/HSP/BlastPullHSP.pm ok 478 - POD test for Bio/Search/HSP/FastaHSP.pm ok 479 - POD test for Bio/Search/HSP/GenericHSP.pm ok 480 - POD test for Bio/Search/HSP/HMMERHSP.pm ok 481 - POD test for Bio/Search/HSP/HmmpfamHSP.pm ok 482 - POD test for Bio/Search/HSP/HSPFactory.pm ok 483 - POD test for Bio/Search/HSP/HSPI.pm ok 484 - POD test for Bio/Search/HSP/ModelHSP.pm ok 485 - POD test for Bio/Search/HSP/PsiBlastHSP.pm ok 486 - POD test for Bio/Search/HSP/PSLHSP.pm ok 487 - POD test for Bio/Search/HSP/PullHSPI.pm ok 488 - POD test for Bio/Search/HSP/WABAHSP.pm ok 489 - POD test for Bio/Search/Iteration/GenericIteration.pm ok 490 - POD test for Bio/Search/Iteration/IterationI.pm ok 491 - POD test for Bio/Search/Result/BlastPullResult.pm ok 492 - POD test for Bio/Search/Result/BlastResult.pm ok 493 - POD test for Bio/Search/Result/CrossMatchResult.pm ok 494 - POD test for Bio/Search/Result/GenericResult.pm ok 495 - POD test for Bio/Search/Result/hmmer3Result.pm ok 496 - POD test for Bio/Search/Result/HMMERResult.pm ok 497 - POD test for Bio/Search/Result/HmmpfamResult.pm ok 498 - POD test for Bio/Search/Result/PullResultI.pm ok 499 - POD test for Bio/Search/Result/ResultFactory.pm ok 500 - POD test for Bio/Search/Result/ResultI.pm ok 501 - POD test for Bio/Search/Result/WABAResult.pm ok 502 - POD test for Bio/Search/Tiling/MapTileUtils.pm ok 503 - POD test for Bio/Search/Tiling/MapTiling.pm ok 504 - POD test for Bio/Search/Tiling/TilingI.pm ok 505 - POD test for Bio/SearchIO/axt.pm ok 506 - POD test for Bio/SearchIO/blast.pm ok 507 - POD test for Bio/SearchIO/blasttable.pm ok 508 - POD test for Bio/SearchIO/blastxml.pm ok 509 - POD test for Bio/SearchIO/blast_pull.pm ok 510 - POD test for Bio/SearchIO/cross_match.pm ok 511 - POD test for Bio/SearchIO/erpin.pm ok 512 - POD test for Bio/SearchIO/EventHandlerI.pm ok 513 - POD test for Bio/SearchIO/exonerate.pm ok 514 - POD test for Bio/SearchIO/fasta.pm ok 515 - POD test for Bio/SearchIO/FastHitEventBuilder.pm ok 516 - POD test for Bio/SearchIO/gmap_f9.pm ok 517 - POD test for Bio/SearchIO/hmmer.pm ok 518 - POD test for Bio/SearchIO/hmmer2.pm ok 519 - POD test for Bio/SearchIO/hmmer3.pm ok 520 - POD test for Bio/SearchIO/hmmer_pull.pm ok 521 - POD test for Bio/SearchIO/infernal.pm ok 522 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm ok 523 - POD test for Bio/SearchIO/megablast.pm ok 524 - POD test for Bio/SearchIO/psl.pm ok 525 - POD test for Bio/SearchIO/rnamotif.pm ok 526 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm ok 527 - POD test for Bio/SearchIO/SearchWriterI.pm ok 528 - POD test for Bio/SearchIO/sim4.pm ok 529 - POD test for Bio/SearchIO/waba.pm ok 530 - POD test for Bio/SearchIO/wise.pm ok 531 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm ok 532 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm ok 533 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm ok 534 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm ok 535 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm ok 536 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm ok 537 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm ok 538 - POD test for Bio/SearchIO/XML/BlastHandler.pm ok 539 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm ok 540 - POD test for Bio/Seq/BaseSeqProcessor.pm ok 541 - POD test for Bio/Seq/EncodedSeq.pm ok 542 - POD test for Bio/Seq/LargeLocatableSeq.pm ok 543 - POD test for Bio/Seq/LargePrimarySeq.pm ok 544 - POD test for Bio/Seq/LargeSeq.pm ok 545 - POD test for Bio/Seq/LargeSeqI.pm ok 546 - POD test for Bio/Seq/Meta.pm ok 547 - POD test for Bio/Seq/MetaI.pm ok 548 - POD test for Bio/Seq/PrimaryQual.pm ok 549 - POD test for Bio/Seq/PrimedSeq.pm ok 550 - POD test for Bio/Seq/QualI.pm ok 551 - POD test for Bio/Seq/Quality.pm ok 552 - POD test for Bio/Seq/RichSeq.pm ok 553 - POD test for Bio/Seq/RichSeqI.pm ok 554 - POD test for Bio/Seq/SeqBuilder.pm ok 555 - POD test for Bio/Seq/SeqFactory.pm ok 556 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm ok 557 - POD test for Bio/Seq/SequenceTrace.pm ok 558 - POD test for Bio/Seq/SeqWithQuality.pm ok 559 - POD test for Bio/Seq/SimulatedRead.pm ok 560 - POD test for Bio/Seq/TraceI.pm ok 561 - POD test for Bio/Seq/Meta/Array.pm ok 562 - POD test for Bio/SeqEvolution/DNAPoint.pm ok 563 - POD test for Bio/SeqEvolution/EvolutionI.pm ok 564 - POD test for Bio/SeqEvolution/Factory.pm ok 565 - POD test for Bio/SeqFeature/Amplicon.pm ok 566 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm ok 567 - POD test for Bio/SeqFeature/Collection.pm ok 568 - POD test for Bio/SeqFeature/CollectionI.pm ok 569 - POD test for Bio/SeqFeature/Computation.pm ok 570 - POD test for Bio/SeqFeature/FeaturePair.pm ok 571 - POD test for Bio/SeqFeature/Generic.pm ok 572 - POD test for Bio/SeqFeature/Lite.pm ok 573 - POD test for Bio/SeqFeature/PositionProxy.pm ok 574 - POD test for Bio/SeqFeature/Primer.pm ok 575 - POD test for Bio/SeqFeature/Similarity.pm ok 576 - POD test for Bio/SeqFeature/SimilarityPair.pm ok 577 - POD test for Bio/SeqFeature/SubSeq.pm ok 578 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm ok 579 - POD test for Bio/SeqFeature/Gene/Exon.pm ok 580 - POD test for Bio/SeqFeature/Gene/ExonI.pm ok 581 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm ok 582 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm ok 583 - POD test for Bio/SeqFeature/Gene/Intron.pm ok 584 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm ok 585 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm ok 586 - POD test for Bio/SeqFeature/Gene/Promoter.pm ok 587 - POD test for Bio/SeqFeature/Gene/Transcript.pm ok 588 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm ok 589 - POD test for Bio/SeqFeature/Gene/UTR.pm ok 590 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm ok 591 - POD test for Bio/SeqFeature/SiRNA/Pair.pm ok 592 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm ok 593 - POD test for Bio/SeqFeature/Tools/IDHandler.pm ok 594 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm ok 595 - POD test for Bio/SeqFeature/Tools/Unflattener.pm ok 596 - POD test for Bio/SeqIO/abi.pm ok 597 - POD test for Bio/SeqIO/ace.pm ok 598 - POD test for Bio/SeqIO/agave.pm ok 599 - POD test for Bio/SeqIO/alf.pm ok 600 - POD test for Bio/SeqIO/asciitree.pm ok 601 - POD test for Bio/SeqIO/bsml.pm ok 602 - POD test for Bio/SeqIO/bsml_sax.pm ok 603 - POD test for Bio/SeqIO/chadoxml.pm ok 604 - POD test for Bio/SeqIO/chaos.pm ok 605 - POD test for Bio/SeqIO/chaosxml.pm ok 606 - POD test for Bio/SeqIO/ctf.pm ok 607 - POD test for Bio/SeqIO/embl.pm ok 608 - POD test for Bio/SeqIO/embldriver.pm ok 609 - POD test for Bio/SeqIO/entrezgene.pm ok 610 - POD test for Bio/SeqIO/excel.pm ok 611 - POD test for Bio/SeqIO/exp.pm ok 612 - POD test for Bio/SeqIO/fasta.pm ok 613 - POD test for Bio/SeqIO/fastq.pm ok 614 - POD test for Bio/SeqIO/flybase_chadoxml.pm ok 615 - POD test for Bio/SeqIO/FTHelper.pm ok 616 - POD test for Bio/SeqIO/game.pm ok 617 - POD test for Bio/SeqIO/gbdriver.pm ok 618 - POD test for Bio/SeqIO/gbxml.pm ok 619 - POD test for Bio/SeqIO/gcg.pm ok 620 - POD test for Bio/SeqIO/genbank.pm ok 621 - POD test for Bio/SeqIO/interpro.pm ok 622 - POD test for Bio/SeqIO/kegg.pm ok 623 - POD test for Bio/SeqIO/largefasta.pm ok 624 - POD test for Bio/SeqIO/lasergene.pm ok 625 - POD test for Bio/SeqIO/locuslink.pm ok 626 - POD test for Bio/SeqIO/mbsout.pm ok 627 - POD test for Bio/SeqIO/metafasta.pm ok 628 - POD test for Bio/SeqIO/msout.pm ok 629 - POD test for Bio/SeqIO/MultiFile.pm ok 630 - POD test for Bio/SeqIO/nexml.pm ok 631 - POD test for Bio/SeqIO/phd.pm ok 632 - POD test for Bio/SeqIO/pir.pm ok 633 - POD test for Bio/SeqIO/pln.pm ok 634 - POD test for Bio/SeqIO/qual.pm ok 635 - POD test for Bio/SeqIO/raw.pm ok 636 - POD test for Bio/SeqIO/scf.pm ok 637 - POD test for Bio/SeqIO/seqxml.pm ok 638 - POD test for Bio/SeqIO/strider.pm ok 639 - POD test for Bio/SeqIO/swiss.pm ok 640 - POD test for Bio/SeqIO/swissdriver.pm ok 641 - POD test for Bio/SeqIO/tab.pm ok 642 - POD test for Bio/SeqIO/table.pm ok 643 - POD test for Bio/SeqIO/tigr.pm ok 644 - POD test for Bio/SeqIO/tigrxml.pm ok 645 - POD test for Bio/SeqIO/tinyseq.pm ok 646 - POD test for Bio/SeqIO/ztr.pm ok 647 - POD test for Bio/SeqIO/game/featHandler.pm ok 648 - POD test for Bio/SeqIO/game/gameHandler.pm ok 649 - POD test for Bio/SeqIO/game/gameSubs.pm ok 650 - POD test for Bio/SeqIO/game/gameWriter.pm ok 651 - POD test for Bio/SeqIO/game/seqHandler.pm ok 652 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm ok 653 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm ok 654 - POD test for Bio/Structure/Atom.pm ok 655 - POD test for Bio/Structure/Chain.pm ok 656 - POD test for Bio/Structure/Entry.pm ok 657 - POD test for Bio/Structure/IO.pm ok 658 - POD test for Bio/Structure/Model.pm ok 659 - POD test for Bio/Structure/Residue.pm ok 660 - POD test for Bio/Structure/StructureI.pm ok 661 - POD test for Bio/Structure/IO/pdb.pm ok 662 - POD test for Bio/Structure/SecStr/DSSP/Res.pm ok 663 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm ok 664 - POD test for Bio/Symbol/Alphabet.pm ok 665 - POD test for Bio/Symbol/AlphabetI.pm ok 666 - POD test for Bio/Symbol/DNAAlphabet.pm ok 667 - POD test for Bio/Symbol/ProteinAlphabet.pm ok 668 - POD test for Bio/Symbol/Symbol.pm ok 669 - POD test for Bio/Symbol/SymbolI.pm ok 670 - POD test for Bio/Taxonomy/FactoryI.pm ok 671 - POD test for Bio/Taxonomy/Node.pm ok 672 - POD test for Bio/Taxonomy/Taxon.pm ok 673 - POD test for Bio/Taxonomy/Tree.pm ok 674 - POD test for Bio/Tools/AlignFactory.pm ok 675 - POD test for Bio/Tools/AmpliconSearch.pm ok 676 - POD test for Bio/Tools/AnalysisResult.pm ok 677 - POD test for Bio/Tools/Blat.pm ok 678 - POD test for Bio/Tools/CodonTable.pm ok 679 - POD test for Bio/Tools/Coil.pm ok 680 - POD test for Bio/Tools/dpAlign.pm ok 681 - POD test for Bio/Tools/ECnumber.pm ok 682 - POD test for Bio/Tools/EPCR.pm ok 683 - POD test for Bio/Tools/Eponine.pm ok 684 - POD test for Bio/Tools/ERPIN.pm ok 685 - POD test for Bio/Tools/Est2Genome.pm ok 686 - POD test for Bio/Tools/ESTScan.pm ok 687 - POD test for Bio/Tools/Fgenesh.pm ok 688 - POD test for Bio/Tools/FootPrinter.pm ok 689 - POD test for Bio/Tools/Gel.pm ok 690 - POD test for Bio/Tools/Geneid.pm ok 691 - POD test for Bio/Tools/Genemark.pm ok 692 - POD test for Bio/Tools/Genewise.pm ok 693 - POD test for Bio/Tools/Genomewise.pm ok 694 - POD test for Bio/Tools/Genscan.pm ok 695 - POD test for Bio/Tools/GFF.pm ok 696 - POD test for Bio/Tools/Glimmer.pm ok 697 - POD test for Bio/Tools/Grail.pm ok 698 - POD test for Bio/Tools/GuessSeqFormat.pm ok 699 - POD test for Bio/Tools/Hmmpfam.pm ok 700 - POD test for Bio/Tools/Infernal.pm ok 701 - POD test for Bio/Tools/ipcress.pm ok 702 - POD test for Bio/Tools/isPcr.pm ok 703 - POD test for Bio/Tools/IUPAC.pm ok 704 - POD test for Bio/Tools/Lucy.pm ok 705 - POD test for Bio/Tools/Match.pm ok 706 - POD test for Bio/Tools/MZEF.pm ok 707 - POD test for Bio/Tools/OddCodes.pm ok 708 - POD test for Bio/Tools/pICalculator.pm ok 709 - POD test for Bio/Tools/Primer3.pm ok 710 - POD test for Bio/Tools/Prints.pm ok 711 - POD test for Bio/Tools/Profile.pm ok 712 - POD test for Bio/Tools/Promoterwise.pm ok 713 - POD test for Bio/Tools/PrositeScan.pm ok 714 - POD test for Bio/Tools/Protparam.pm ok 715 - POD test for Bio/Tools/Pseudowise.pm ok 716 - POD test for Bio/Tools/pSW.pm ok 717 - POD test for Bio/Tools/QRNA.pm ok 718 - POD test for Bio/Tools/RandomDistFunctions.pm ok 719 - POD test for Bio/Tools/RepeatMasker.pm ok 720 - POD test for Bio/Tools/RNAMotif.pm ok 721 - POD test for Bio/Tools/Seg.pm ok 722 - POD test for Bio/Tools/SeqPattern.pm ok 723 - POD test for Bio/Tools/SeqStats.pm ok 724 - POD test for Bio/Tools/SeqWords.pm ok 725 - POD test for Bio/Tools/Sigcleave.pm ok 726 - POD test for Bio/Tools/Signalp.pm ok 727 - POD test for Bio/Tools/SiRNA.pm ok 728 - POD test for Bio/Tools/TandemRepeatsFinder.pm ok 729 - POD test for Bio/Tools/TargetP.pm ok 730 - POD test for Bio/Tools/Tmhmm.pm ok 731 - POD test for Bio/Tools/tRNAscanSE.pm ok 732 - POD test for Bio/Tools/Alignment/Consed.pm ok 733 - POD test for Bio/Tools/Alignment/Trim.pm ok 734 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm ok 735 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm ok 736 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm ok 737 - POD test for Bio/Tools/Analysis/Protein/ELM.pm ok 738 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm ok 739 - POD test for Bio/Tools/Analysis/Protein/HNN.pm ok 740 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm ok 741 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm ok 742 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm ok 743 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm ok 744 - POD test for Bio/Tools/EMBOSS/Palindrome.pm ok 745 - POD test for Bio/Tools/HMMER/Domain.pm ok 746 - POD test for Bio/Tools/HMMER/Results.pm ok 747 - POD test for Bio/Tools/HMMER/Set.pm ok 748 - POD test for Bio/Tools/Phylo/Gerp.pm ok 749 - POD test for Bio/Tools/Phylo/Gumby.pm ok 750 - POD test for Bio/Tools/Phylo/Molphy.pm ok 751 - POD test for Bio/Tools/Phylo/PAML.pm ok 752 - POD test for Bio/Tools/Phylo/Molphy/Result.pm ok 753 - POD test for Bio/Tools/Phylo/PAML/Codeml.pm ok 754 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm ok 755 - POD test for Bio/Tools/Phylo/PAML/Result.pm ok 756 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm ok 757 - POD test for Bio/Tools/Prediction/Exon.pm ok 758 - POD test for Bio/Tools/Prediction/Gene.pm ok 759 - POD test for Bio/Tools/Primer/AssessorI.pm ok 760 - POD test for Bio/Tools/Primer/Feature.pm ok 761 - POD test for Bio/Tools/Primer/Pair.pm ok 762 - POD test for Bio/Tools/Primer/Assessor/Base.pm ok 763 - POD test for Bio/Tools/Run/GenericParameters.pm ok 764 - POD test for Bio/Tools/Run/hmmer3.pm (no pod) ok 765 - POD test for Bio/Tools/Run/ParametersI.pm ok 766 - POD test for Bio/Tools/Run/RemoteBlast.pm ok 767 - POD test for Bio/Tools/Run/StandAloneBlast.pm ok 768 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm ok 769 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm ok 770 - POD test for Bio/Tools/Run/WrapperBase.pm ok 771 - POD test for Bio/Tools/Run/WrapperBase/CommandExts.pm ok 772 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm ok 773 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm ok 774 - POD test for Bio/Tools/Sim4/Exon.pm ok 775 - POD test for Bio/Tools/Sim4/Results.pm ok 776 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm ok 777 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm ok 778 - POD test for Bio/Tools/Spidey/Exon.pm ok 779 - POD test for Bio/Tools/Spidey/Results.pm ok 780 - POD test for Bio/Tree/AlleleNode.pm ok 781 - POD test for Bio/Tree/AnnotatableNode.pm ok 782 - POD test for Bio/Tree/Compatible.pm ok 783 - POD test for Bio/Tree/DistanceFactory.pm ok 784 - POD test for Bio/Tree/Node.pm ok 785 - POD test for Bio/Tree/NodeI.pm ok 786 - POD test for Bio/Tree/NodeNHX.pm ok 787 - POD test for Bio/Tree/RandomFactory.pm ok 788 - POD test for Bio/Tree/Statistics.pm ok 789 - POD test for Bio/Tree/Tree.pm ok 790 - POD test for Bio/Tree/TreeFunctionsI.pm ok 791 - POD test for Bio/Tree/TreeI.pm ok 792 - POD test for Bio/Tree/Draw/Cladogram.pm ok 793 - POD test for Bio/TreeIO/cluster.pm ok 794 - POD test for Bio/TreeIO/lintree.pm ok 795 - POD test for Bio/TreeIO/newick.pm ok 796 - POD test for Bio/TreeIO/NewickParser.pm ok 797 - POD test for Bio/TreeIO/nexml.pm ok 798 - POD test for Bio/TreeIO/nexus.pm ok 799 - POD test for Bio/TreeIO/nhx.pm ok 800 - POD test for Bio/TreeIO/pag.pm ok 801 - POD test for Bio/TreeIO/phyloxml.pm ok 802 - POD test for Bio/TreeIO/svggraph.pm ok 803 - POD test for Bio/TreeIO/tabtree.pm ok 804 - POD test for Bio/TreeIO/TreeEventBuilder.pm ok 805 - POD test for Bio/Variation/AAChange.pm ok 806 - POD test for Bio/Variation/AAReverseMutate.pm ok 807 - POD test for Bio/Variation/Allele.pm ok 808 - POD test for Bio/Variation/DNAMutation.pm ok 809 - POD test for Bio/Variation/IO.pm ok 810 - POD test for Bio/Variation/RNAChange.pm ok 811 - POD test for Bio/Variation/SeqDiff.pm ok 812 - POD test for Bio/Variation/SNP.pm ok 813 - POD test for Bio/Variation/VariantI.pm ok 814 - POD test for Bio/Variation/IO/flat.pm ok 815 - POD test for Bio/Variation/IO/xml.pm ok 816 - POD test for scripts/Bio-DB-GFF/bp_bulk_load_gff.pl ok 817 - POD test for scripts/Bio-DB-GFF/bp_fast_load_gff.pl ok 818 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff.pl ok 819 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff3.pl ok 820 - POD test for scripts/Bio-DB-GFF/bp_generate_histogram.pl ok 821 - POD test for scripts/Bio-DB-GFF/bp_load_gff.pl ok 822 - POD test for scripts/Bio-DB-GFF/bp_meta_gff.pl ok 823 - POD test for scripts/Bio-DB-GFF/bp_process_gadfly.pl ok 824 - POD test for scripts/Bio-DB-GFF/bp_process_sgd.pl ok 825 - POD test for scripts/Bio-DB-GFF/bp_process_wormbase.pl ok 826 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl (no pod) ok 827 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl (no pod) ok 828 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl ok 829 - POD test for scripts/das/bp_das_server.pl (no pod) ok 830 - POD test for scripts/DB/bp_biofetch_genbank_proxy.pl ok 831 - POD test for scripts/DB/bp_bioflat_index.pl ok 832 - POD test for scripts/DB/bp_biogetseq.pl ok 833 - POD test for scripts/DB/bp_flanks.pl ok 834 - POD test for scripts/DB-HIV/bp_hivq.pl ok 835 - POD test for scripts/index/bp_fetch.pl ok 836 - POD test for scripts/index/bp_index.pl ok 837 - POD test for scripts/index/bp_seqret.pl ok 838 - POD test for scripts/popgen/bp_composite_LD.pl ok 839 - POD test for scripts/popgen/bp_heterogeneity_test.pl ok 840 - POD test for scripts/searchio/bp_fastam9_to_table.pl ok 841 - POD test for scripts/searchio/bp_filter_search.pl ok 842 - POD test for scripts/searchio/bp_hmmer_to_table.pl ok 843 - POD test for scripts/searchio/bp_parse_hmmsearch.pl ok 844 - POD test for scripts/searchio/bp_search2table.pl ok 845 - POD test for scripts/seq/bp_extract_feature_seq.pl ok 846 - POD test for scripts/seq/bp_make_mrna_protein.pl ok 847 - POD test for scripts/seq/bp_seqconvert.pl ok 848 - POD test for scripts/seq/bp_seqcut.pl ok 849 - POD test for scripts/seq/bp_seqpart.pl ok 850 - POD test for scripts/seq/bp_seqretsplit.pl ok 851 - POD test for scripts/seq/bp_split_seq.pl ok 852 - POD test for scripts/seq/bp_translate_seq.pl ok 853 - POD test for scripts/seq/bp_unflatten_seq.pl ok 854 - POD test for scripts/seqstats/bp_aacomp.pl ok 855 - POD test for scripts/seqstats/bp_chaos_plot.pl ok 856 - POD test for scripts/seqstats/bp_gccalc.pl ok 857 - POD test for scripts/seqstats/bp_oligo_count.pl ok 858 - POD test for scripts/taxa/bp_classify_hits_kingdom.pl ok 859 - POD test for scripts/taxa/bp_local_taxonomydb_query.pl ok 860 - POD test for scripts/taxa/bp_query_entrez_taxa.pl ok 861 - POD test for scripts/taxa/bp_taxid4species.pl ok 862 - POD test for scripts/taxa/bp_taxonomy2tree.pl ok 863 - POD test for scripts/tree/bp_blast2tree.pl ok 864 - POD test for scripts/tree/bp_nexus2nh.pl ok 865 - POD test for scripts/tree/bp_tree2pag.pl ok 866 - POD test for scripts/utilities/bp_dbsplit.pl ok 867 - POD test for scripts/utilities/bp_download_query_genbank.pl ok 868 - POD test for scripts/utilities/bp_mask_by_search.pl ok 869 - POD test for scripts/utilities/bp_mrtrans.pl ok 870 - POD test for scripts/utilities/bp_mutate.pl ok 871 - POD test for scripts/utilities/bp_netinstall.pl ok 872 - POD test for scripts/utilities/bp_nrdb.pl ok 873 - POD test for scripts/utilities/bp_pairwise_kaks.pl ok 874 - POD test for scripts/utilities/bp_remote_blast.pl ok 875 - POD test for scripts/utilities/bp_revtrans-motif.pl ok 876 - POD test for scripts/utilities/bp_search2alnblocks.pl ok 877 - POD test for scripts/utilities/bp_search2BSML.pl ok 878 - POD test for scripts/utilities/bp_search2gff.pl ok 879 - POD test for scripts/utilities/bp_search2tribe.pl ok 880 - POD test for scripts/utilities/bp_seq_length.pl ok 881 - POD test for scripts/utilities/bp_sreformat.pl ok 882 - POD test for examples/bioperl.pl (no pod) ok 883 - POD test for examples/generate_random_seq.pl (no pod) ok 884 - POD test for examples/longorf.pl ok 885 - POD test for examples/make_primers.pl (no pod) ok 886 - POD test for examples/revcom_dir.pl (no pod) ok 887 - POD test for examples/rev_and_trans.pl (no pod) ok 888 - POD test for examples/subsequence.cgi (no pod) ok 889 - POD test for examples/align/aligntutorial.pl (no pod) ok 890 - POD test for examples/align/align_on_codons.pl (no pod) ok 891 - POD test for examples/align/clustalw.pl (no pod) ok 892 - POD test for examples/align/FastAlign.pl ok 893 - POD test for examples/align/simplealign.pl (no pod) ok 894 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod) ok 895 - POD test for examples/cluster/dbsnp.pl (no pod) ok 896 - POD test for examples/contributed/nmrpdb_parse.pl (no pod) ok 897 - POD test for examples/contributed/prosite2perl.pl (no pod) ok 898 - POD test for examples/contributed/rebase2list.pl (no pod) ok 899 - POD test for examples/db/dbfetch ok 900 - POD test for examples/db/est_tissue_query.pl (no pod) ok 901 - POD test for examples/db/gb2features.pl (no pod) ok 902 - POD test for examples/db/getGenBank.pl (no pod) ok 903 - POD test for examples/db/get_seqs.pl (no pod) ok 904 - POD test for examples/db/rfetch.pl (no pod) ok 905 - POD test for examples/db/use_registry.pl (no pod) ok 906 - POD test for examples/liveseq/change_gene.pl (no pod) ok 907 - POD test for examples/popgen/parse_calc_stats.pl (no pod) ok 908 - POD test for examples/quality/svgtrace.pl (no pod) ok 909 - POD test for examples/root/exceptions1.pl (no pod) ok 910 - POD test for examples/root/exceptions2.pl (no pod) ok 911 - POD test for examples/root/exceptions3.pl (no pod) ok 912 - POD test for examples/root/exceptions4.pl (no pod) ok 913 - POD test for examples/root/lib/TestInterface.pm ok 914 - POD test for examples/root/lib/TestObject.pm ok 915 - POD test for examples/searchio/blast_example.pl (no pod) ok 916 - POD test for examples/searchio/custom_writer.pl (no pod) ok 917 - POD test for examples/searchio/hitwriter.pl (no pod) ok 918 - POD test for examples/searchio/hspwriter.pl (no pod) ok 919 - POD test for examples/searchio/htmlwriter.pl (no pod) ok 920 - POD test for examples/searchio/psiblast_features.pl (no pod) ok 921 - POD test for examples/searchio/psiblast_iterations.pl (no pod) ok 922 - POD test for examples/searchio/rawwriter.pl (no pod) ok 923 - POD test for examples/searchio/resultwriter.pl (no pod) ok 924 - POD test for examples/searchio/waba2gff.pl (no pod) ok 925 - POD test for examples/searchio/waba2gff3.pl ok 926 - POD test for examples/sirna/rnai_finder.cgi ok 927 - POD test for examples/structure/structure-io.pl (no pod) ok 928 - POD test for examples/tk/gsequence.pl (no pod) ok 929 - POD test for examples/tk/hitdisplay.pl (no pod) ok 930 - POD test for examples/tools/extract_genes.pl ok 931 - POD test for examples/tools/gb_to_gff.pl (no pod) ok 932 - POD test for examples/tools/gff2ps.pl ok 933 - POD test for examples/tools/parse_codeml.pl (no pod) ok 934 - POD test for examples/tools/psw.pl (no pod) ok 935 - POD test for examples/tools/reverse-translate.pl ok 936 - POD test for examples/tools/run_genscan.pl (no pod) ok 937 - POD test for examples/tools/run_primer3.pl ok 938 - POD test for examples/tools/seq_pattern.pl (no pod) ok 939 - POD test for examples/tools/standaloneblast.pl (no pod) ok 940 - POD test for examples/tree/paup2phylip.pl (no pod) ok 941 - POD test for maintenance/authors.pl ok 942 - POD test for maintenance/check_NAME.pl ok 943 - POD test for maintenance/check_URLs.pl ok 944 - POD test for maintenance/cvs2cl_by_file.pl ok 945 - POD test for maintenance/dependencies.pl ok 946 - POD test for maintenance/deprecated.pl ok 947 - POD test for maintenance/find_mod_deps.pl ok 948 - POD test for maintenance/modules.pl ok 949 - POD test for maintenance/module_usage.pl (no pod) ok 950 - POD test for maintenance/ncbi_blast_switches.pl (no pod) ok 951 - POD test for maintenance/pod.pl ok 952 - POD test for maintenance/symlink_script.pl ok 953 - POD test for maintenance/version.pl ok 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 - An object of class 'Bio::PopGen::Statistics' isa 'Bio::PopGen::Statistics' ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 6 - An object of class 'Bio::PopGen::Population' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 27 - An object of class 'Bio::PopGen::Population' 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 Timeout (max run time is 420s) C:\Perl64-5.16\bin\perl.exe exits with 37.