PATH=C:\cpanfly-5.24-64\var\megalib\bin;C:\Perl-5.24-64\site\bin;C:\Perl-5.24-64\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\instantclient_11_2-64;C:\cpanfly-5.24-64\var\megalib\bin;C:\Perl-5.24-64\site\bin;C:\Perl-5.24-64\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\instantclient_11_2-64;C:\cpanfly-5.24-64\var\megalib\bin;C:\Perl-5.24-64\site\bin;C:\Perl-5.24-64\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\instantclient_11_2-64;C:\p4;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Git\cmd;C:\Program Files (x86)\CMake\bin
Start 2016-11-07T04:24:43
ActivePerl-2400 CPAN-2.10
PATH=C:/CPANFL~1.24-/var/libs/bin;C:\CPANFL~1.24-\var\megalib\bin;C:\PERL-5~1.24-\site\bin;C:\PERL-5~1.24-\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\INSTAN~1;C:\CPANFL~1.24-\var\megalib\bin;C:\PERL-5~1.24-\site\bin;C:\PERL-5~1.24-\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\INSTAN~1;C:\CPANFL~1.24-\var\megalib\bin;C:\PERL-5~1.24-\site\bin;C:\PERL-5~1.24-\bin;C:\MinGW-64\bin;C:\cygwin\bin;C:\INSTAN~1;C:\p4;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WINDOW~1\v1.0\;C:\PROGRA~1\Git\cmd;C:\PROGRA~2\CMake\bin
Reading 'C:\cpanfly-5.24-64\var\cpan\Metadata'
  Database was generated on Mon, 07 Nov 2016 02:29:02 GMT
Fetching with LWP:
http://ppm.activestate.com/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
Fetching with LWP:
http://ppm.activestate.com/CPAN/authors/id/C/CJ/CJFIELDS/CHECKSUMS
Checksum for C:\cpanfly-5.24-64\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.007001.tar.gz ok
BioPerl-1.007001
BioPerl-1.007001/.travis.yml
BioPerl-1.007001/AUTHORS
BioPerl-1.007001/BioPerl.pm
BioPerl-1.007001/BUGS
BioPerl-1.007001/Build.PL
BioPerl-1.007001/Changes
BioPerl-1.007001/DEPENDENCIES
BioPerl-1.007001/DEPRECATED
BioPerl-1.007001/INSTALL-WIN.md
BioPerl-1.007001/INSTALL.md
BioPerl-1.007001/INSTALL.SKIP
BioPerl-1.007001/LICENSE
BioPerl-1.007001/MANIFEST
BioPerl-1.007001/META.json
BioPerl-1.007001/META.yml
BioPerl-1.007001/README.md
BioPerl-1.007001/Bio
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BioPerl-1.007001/Bio/Taxonomy/Taxon.pm
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BioPerl-1.007001/Bio/Tools
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BioPerl-1.007001/Bio/Tools/EPCR.pm
BioPerl-1.007001/Bio/Tools/Eponine.pm
BioPerl-1.007001/Bio/Tools/Est2Genome.pm
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BioPerl-1.007001/Bio/Tools/Fgenesh.pm
BioPerl-1.007001/Bio/Tools/FootPrinter.pm
BioPerl-1.007001/Bio/Tools/Gel.pm
BioPerl-1.007001/Bio/Tools/Geneid.pm
BioPerl-1.007001/Bio/Tools/Genemark.pm
BioPerl-1.007001/Bio/Tools/Genewise.pm
BioPerl-1.007001/Bio/Tools/Genomewise.pm
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BioPerl-1.007001/Bio/Tools/GFF.pm
BioPerl-1.007001/Bio/Tools/Glimmer.pm
BioPerl-1.007001/Bio/Tools/Grail.pm
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BioPerl-1.007001/Bio/Tools/Tmhmm.pm
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BioPerl-1.007001/Bio/Tools/EMBOSS
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BioPerl-1.007001/Bio/Tools/HMMER
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BioPerl-1.007001/Bio/Tools/Phylo
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BioPerl-1.007001/Bio/Tools/Phylo/Gumby.pm
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BioPerl-1.007001/Bio/Tools/Phylo/Phylip
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BioPerl-1.007001/Bio/Tools/Prediction
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BioPerl-1.007001/Bio/Tools/Prediction/Gene.pm
BioPerl-1.007001/Bio/Tools/Primer
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BioPerl-1.007001/Bio/Tools/Primer/Feature.pm
BioPerl-1.007001/Bio/Tools/Primer/Pair.pm
BioPerl-1.007001/Bio/Tools/Primer/Assessor
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BioPerl-1.007001/Bio/Tools/Run
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BioPerl-1.007001/Bio/Tools/SeqPattern
BioPerl-1.007001/Bio/Tools/SeqPattern/Backtranslate.pm
BioPerl-1.007001/Bio/Tools/Signalp
BioPerl-1.007001/Bio/Tools/Signalp/ExtendedSignalp.pm
BioPerl-1.007001/Bio/Tools/Sim4
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BioPerl-1.007001/Bio/Tools/SiRNA/Ruleset
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BioPerl-1.007001/Bio/Tools/SiRNA/Ruleset/tuschl.pm
BioPerl-1.007001/Bio/Tools/Spidey
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BioPerl-1.007001/Bio/Tree
BioPerl-1.007001/Bio/Tree/AlleleNode.pm
BioPerl-1.007001/Bio/Tree/AnnotatableNode.pm
BioPerl-1.007001/Bio/Tree/Compatible.pm
BioPerl-1.007001/Bio/Tree/DistanceFactory.pm
BioPerl-1.007001/Bio/Tree/Node.pm
BioPerl-1.007001/Bio/Tree/NodeI.pm
BioPerl-1.007001/Bio/Tree/NodeNHX.pm
BioPerl-1.007001/Bio/Tree/RandomFactory.pm
BioPerl-1.007001/Bio/Tree/Statistics.pm
BioPerl-1.007001/Bio/Tree/Tree.pm
BioPerl-1.007001/Bio/Tree/TreeFunctionsI.pm
BioPerl-1.007001/Bio/Tree/TreeI.pm
BioPerl-1.007001/Bio/Tree/Draw
BioPerl-1.007001/Bio/Tree/Draw/Cladogram.pm
BioPerl-1.007001/Bio/TreeIO
BioPerl-1.007001/Bio/TreeIO/cluster.pm
BioPerl-1.007001/Bio/TreeIO/lintree.pm
BioPerl-1.007001/Bio/TreeIO/newick.pm
BioPerl-1.007001/Bio/TreeIO/NewickParser.pm
BioPerl-1.007001/Bio/TreeIO/nexml.pm
BioPerl-1.007001/Bio/TreeIO/nexus.pm
BioPerl-1.007001/Bio/TreeIO/nhx.pm
BioPerl-1.007001/Bio/TreeIO/pag.pm
BioPerl-1.007001/Bio/TreeIO/phyloxml.pm
BioPerl-1.007001/Bio/TreeIO/svggraph.pm
BioPerl-1.007001/Bio/TreeIO/tabtree.pm
BioPerl-1.007001/Bio/TreeIO/TreeEventBuilder.pm
BioPerl-1.007001/Bio/Variation
BioPerl-1.007001/Bio/Variation/AAChange.pm
BioPerl-1.007001/Bio/Variation/AAReverseMutate.pm
BioPerl-1.007001/Bio/Variation/Allele.pm
BioPerl-1.007001/Bio/Variation/DNAMutation.pm
BioPerl-1.007001/Bio/Variation/IO.pm
BioPerl-1.007001/Bio/Variation/README
BioPerl-1.007001/Bio/Variation/RNAChange.pm
BioPerl-1.007001/Bio/Variation/SeqDiff.pm
BioPerl-1.007001/Bio/Variation/SNP.pm
BioPerl-1.007001/Bio/Variation/VariantI.pm
BioPerl-1.007001/Bio/Variation/IO
BioPerl-1.007001/Bio/Variation/IO/flat.pm
BioPerl-1.007001/Bio/Variation/IO/xml.pm
BioPerl-1.007001/deobfuscator
BioPerl-1.007001/deobfuscator/makedoc.PL
BioPerl-1.007001/deobfuscator/Deobfuscator
BioPerl-1.007001/deobfuscator/Deobfuscator/Build.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/Changes
BioPerl-1.007001/deobfuscator/Deobfuscator/excluded_modules.txt
BioPerl-1.007001/deobfuscator/Deobfuscator/LICENSE
BioPerl-1.007001/deobfuscator/Deobfuscator/Makefile.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/MANIFEST
BioPerl-1.007001/deobfuscator/Deobfuscator/META.yml
BioPerl-1.007001/deobfuscator/Deobfuscator/README
BioPerl-1.007001/deobfuscator/Deobfuscator/bin
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/deob_index.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/lib
BioPerl-1.007001/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.007001/deobfuscator/Deobfuscator/t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/00.load.t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/pod.t
BioPerl-1.007001/examples
BioPerl-1.007001/examples/bioperl.pl
BioPerl-1.007001/examples/generate_random_seq.pl
BioPerl-1.007001/examples/longorf.pl
BioPerl-1.007001/examples/make_primers.pl
BioPerl-1.007001/examples/rev_and_trans.pl
BioPerl-1.007001/examples/revcom_dir.pl
BioPerl-1.007001/examples/subsequence.cgi
BioPerl-1.007001/examples/align
BioPerl-1.007001/examples/align/align_on_codons.pl
BioPerl-1.007001/examples/align/aligntutorial.pl
BioPerl-1.007001/examples/align/clustalw.pl
BioPerl-1.007001/examples/align/FastAlign.pl
BioPerl-1.007001/examples/align/simplealign.pl
BioPerl-1.007001/examples/Bio-DB-GFF
BioPerl-1.007001/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.007001/examples/cluster
BioPerl-1.007001/examples/cluster/dbsnp.pl
BioPerl-1.007001/examples/contributed
BioPerl-1.007001/examples/contributed/nmrpdb_parse.pl
BioPerl-1.007001/examples/contributed/prosite2perl.pl
BioPerl-1.007001/examples/contributed/rebase2list.pl
BioPerl-1.007001/examples/db
BioPerl-1.007001/examples/db/dbfetch
BioPerl-1.007001/examples/db/est_tissue_query.pl
BioPerl-1.007001/examples/db/gb2features.pl
BioPerl-1.007001/examples/db/get_seqs.pl
BioPerl-1.007001/examples/db/getGenBank.pl
BioPerl-1.007001/examples/db/rfetch.pl
BioPerl-1.007001/examples/db/use_registry.pl
BioPerl-1.007001/examples/liveseq
BioPerl-1.007001/examples/liveseq/change_gene.pl
BioPerl-1.007001/examples/popgen
BioPerl-1.007001/examples/popgen/parse_calc_stats.pl
BioPerl-1.007001/examples/quality
BioPerl-1.007001/examples/quality/svgtrace.pl
BioPerl-1.007001/examples/root
BioPerl-1.007001/examples/root/exceptions1.pl
BioPerl-1.007001/examples/root/exceptions2.pl
BioPerl-1.007001/examples/root/exceptions3.pl
BioPerl-1.007001/examples/root/exceptions4.pl
BioPerl-1.007001/examples/root/README
BioPerl-1.007001/examples/searchio
BioPerl-1.007001/examples/searchio/blast_example.pl
BioPerl-1.007001/examples/searchio/custom_writer.pl
BioPerl-1.007001/examples/searchio/hitwriter.pl
BioPerl-1.007001/examples/searchio/hspwriter.pl
BioPerl-1.007001/examples/searchio/htmlwriter.pl
BioPerl-1.007001/examples/searchio/psiblast_features.pl
BioPerl-1.007001/examples/searchio/psiblast_iterations.pl
BioPerl-1.007001/examples/searchio/rawwriter.pl
BioPerl-1.007001/examples/searchio/resultwriter.pl
BioPerl-1.007001/examples/searchio/waba2gff.pl
BioPerl-1.007001/examples/searchio/waba2gff3.pl
BioPerl-1.007001/examples/sirna
BioPerl-1.007001/examples/sirna/rnai_finder.cgi
BioPerl-1.007001/examples/sirna/TAG
BioPerl-1.007001/examples/structure
BioPerl-1.007001/examples/structure/structure-io.pl
BioPerl-1.007001/examples/tk
BioPerl-1.007001/examples/tk/gsequence.pl
BioPerl-1.007001/examples/tk/hitdisplay.pl
BioPerl-1.007001/examples/tools
BioPerl-1.007001/examples/tools/extract_genes.pl
BioPerl-1.007001/examples/tools/gb_to_gff.pl
BioPerl-1.007001/examples/tools/gff2ps.pl
BioPerl-1.007001/examples/tools/parse_codeml.pl
BioPerl-1.007001/examples/tools/psw.pl
BioPerl-1.007001/examples/tools/reverse-translate.pl
BioPerl-1.007001/examples/tools/run_genscan.pl
BioPerl-1.007001/examples/tools/run_primer3.pl
BioPerl-1.007001/examples/tools/seq_pattern.pl
BioPerl-1.007001/examples/tools/standaloneblast.pl
BioPerl-1.007001/examples/tree
BioPerl-1.007001/examples/tree/paup2phylip.pl
BioPerl-1.007001/ide
BioPerl-1.007001/ide/bioperl.komodo
BioPerl-1.007001/ide/bioperl-mode
BioPerl-1.007001/ide/bioperl-mode/README
BioPerl-1.007001/ide/bioperl-mode/dist
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/Changes
BioPerl-1.007001/ide/bioperl-mode/dist/package-me
BioPerl-1.007001/ide/bioperl-mode/dist/SKIP
BioPerl-1.007001/ide/bioperl-mode/etc
BioPerl-1.007001/ide/bioperl-mode/etc/images
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.007001/ide/bioperl-mode/site-lisp
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.007001/maintenance
BioPerl-1.007001/maintenance/authors.pl
BioPerl-1.007001/maintenance/check_NAME.pl
BioPerl-1.007001/maintenance/check_URLs.pl
BioPerl-1.007001/maintenance/cvs2cl_by_file.pl
BioPerl-1.007001/maintenance/dependencies.pl
BioPerl-1.007001/maintenance/deprecated.pl
BioPerl-1.007001/maintenance/find_mod_deps.pl
BioPerl-1.007001/maintenance/module_usage.pl
BioPerl-1.007001/maintenance/modules.pl
BioPerl-1.007001/maintenance/ncbi_blast_switches.pl
BioPerl-1.007001/maintenance/perltidy.conf
BioPerl-1.007001/maintenance/pod.pl
BioPerl-1.007001/maintenance/README
BioPerl-1.007001/maintenance/symlink_script.pl
BioPerl-1.007001/maintenance/version.pl
BioPerl-1.007001/maintenance/big_split
BioPerl-1.007001/maintenance/big_split/file_classification.csv
BioPerl-1.007001/maintenance/big_split/rbuels_notes.txt
BioPerl-1.007001/models
BioPerl-1.007001/models/biblio.dia
BioPerl-1.007001/models/bio_liveseq_variation.dia
BioPerl-1.007001/models/bio_map.dia
BioPerl-1.007001/models/bio_restriction.dia
BioPerl-1.007001/models/bioperl.dia
BioPerl-1.007001/models/coordinatemapper.dia
BioPerl-1.007001/models/map_proposal.txt
BioPerl-1.007001/models/maps_and_markers.dia
BioPerl-1.007001/models/popgen.dia
BioPerl-1.007001/models/population_proposal.txt
BioPerl-1.007001/models/README
BioPerl-1.007001/scripts
BioPerl-1.007001/scripts/README
BioPerl-1.007001/scripts/Bio-DB-GFF
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/README
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.007001/scripts/das
BioPerl-1.007001/scripts/das/bp_das_server.pl
BioPerl-1.007001/scripts/das/README
BioPerl-1.007001/scripts/das/TAG
BioPerl-1.007001/scripts/DB
BioPerl-1.007001/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.007001/scripts/DB/bp_bioflat_index.pl
BioPerl-1.007001/scripts/DB/bp_biogetseq.pl
BioPerl-1.007001/scripts/DB/bp_flanks.pl
BioPerl-1.007001/scripts/DB/TAG
BioPerl-1.007001/scripts/DB-HIV
BioPerl-1.007001/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.007001/scripts/index
BioPerl-1.007001/scripts/index/bp_fetch.pl
BioPerl-1.007001/scripts/index/bp_index.pl
BioPerl-1.007001/scripts/index/bp_seqret.pl
BioPerl-1.007001/scripts/index/TAG
BioPerl-1.007001/scripts/popgen
BioPerl-1.007001/scripts/popgen/bp_composite_LD.pl
BioPerl-1.007001/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.007001/scripts/searchio
BioPerl-1.007001/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.007001/scripts/searchio/bp_filter_search.pl
BioPerl-1.007001/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.007001/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.007001/scripts/searchio/bp_search2table.pl
BioPerl-1.007001/scripts/searchio/README
BioPerl-1.007001/scripts/searchio/TAG
BioPerl-1.007001/scripts/seq
BioPerl-1.007001/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.007001/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.007001/scripts/seq/bp_seqconvert.pl
BioPerl-1.007001/scripts/seq/bp_seqcut.pl
BioPerl-1.007001/scripts/seq/bp_seqpart.pl
BioPerl-1.007001/scripts/seq/bp_seqretsplit.pl
BioPerl-1.007001/scripts/seq/bp_split_seq.pl
BioPerl-1.007001/scripts/seq/bp_translate_seq.pl
BioPerl-1.007001/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.007001/scripts/seq/TAG
BioPerl-1.007001/scripts/seqstats
BioPerl-1.007001/scripts/seqstats/bp_aacomp.pl
BioPerl-1.007001/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.007001/scripts/seqstats/bp_gccalc.pl
BioPerl-1.007001/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.007001/scripts/seqstats/TAG
BioPerl-1.007001/scripts/taxa
BioPerl-1.007001/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.007001/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.007001/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.007001/scripts/taxa/bp_taxid4species.pl
BioPerl-1.007001/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.007001/scripts/taxa/TAG
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BioPerl-1.007001/t/Tools/Primer3.t
BioPerl-1.007001/t/Tools/Promoterwise.t
BioPerl-1.007001/t/Tools/Pseudowise.t
BioPerl-1.007001/t/Tools/QRNA.t
BioPerl-1.007001/t/Tools/RandDistFunctions.t
BioPerl-1.007001/t/Tools/RepeatMasker.t
BioPerl-1.007001/t/Tools/Seg.t
BioPerl-1.007001/t/Tools/Sigcleave.t
BioPerl-1.007001/t/Tools/Signalp.t
BioPerl-1.007001/t/Tools/Sim4.t
BioPerl-1.007001/t/Tools/SiRNA.t
BioPerl-1.007001/t/Tools/TandemRepeatsFinder.t
BioPerl-1.007001/t/Tools/TargetP.t
BioPerl-1.007001/t/Tools/Tmhmm.t
BioPerl-1.007001/t/Tools/tRNAscanSE.t
BioPerl-1.007001/t/Tools/Alignment
BioPerl-1.007001/t/Tools/Alignment/Consed.t
BioPerl-1.007001/t/Tools/Analysis
BioPerl-1.007001/t/Tools/Analysis/DNA
BioPerl-1.007001/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.007001/t/Tools/Analysis/Protein
BioPerl-1.007001/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.007001/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.007001/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.007001/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.007001/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.007001/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.007001/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.007001/t/Tools/EMBOSS
BioPerl-1.007001/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.007001/t/Tools/Phylo
BioPerl-1.007001/t/Tools/Phylo/Gerp.t
BioPerl-1.007001/t/Tools/Phylo/Molphy.t
BioPerl-1.007001/t/Tools/Phylo/PAML.t
BioPerl-1.007001/t/Tools/Phylo/Phylip
BioPerl-1.007001/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.007001/t/Tools/Run
BioPerl-1.007001/t/Tools/Run/RemoteBlast.t
BioPerl-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.007001/t/Tools/Signalp
BioPerl-1.007001/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.007001/t/Tools/Spidey
BioPerl-1.007001/t/Tools/Spidey/Spidey.t
BioPerl-1.007001/t/Tree
BioPerl-1.007001/t/Tree/Compatible.t
BioPerl-1.007001/t/Tree/Node.t
BioPerl-1.007001/t/Tree/RandomTreeFactory.t
BioPerl-1.007001/t/Tree/Tree.t
BioPerl-1.007001/t/Tree/TreeIO.t
BioPerl-1.007001/t/Tree/TreeStatistics.t
BioPerl-1.007001/t/Tree/PhyloNetwork
BioPerl-1.007001/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.007001/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.007001/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.007001/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.007001/t/Tree/TreeIO
BioPerl-1.007001/t/Tree/TreeIO/lintree.t
BioPerl-1.007001/t/Tree/TreeIO/newick.t
BioPerl-1.007001/t/Tree/TreeIO/nexml.t
BioPerl-1.007001/t/Tree/TreeIO/nexus.t
BioPerl-1.007001/t/Tree/TreeIO/nhx.t
BioPerl-1.007001/t/Tree/TreeIO/phyloxml.t
BioPerl-1.007001/t/Tree/TreeIO/svggraph.t
BioPerl-1.007001/t/Tree/TreeIO/tabtree.t
BioPerl-1.007001/t/Variation
BioPerl-1.007001/t/Variation/AAChange.t
BioPerl-1.007001/t/Variation/AAReverseMutate.t
BioPerl-1.007001/t/Variation/Allele.t
BioPerl-1.007001/t/Variation/DNAMutation.t
BioPerl-1.007001/t/Variation/RNAChange.t
BioPerl-1.007001/t/Variation/SeqDiff.t
BioPerl-1.007001/t/Variation/SNP.t
BioPerl-1.007001/t/Variation/Variation_IO.t
BioPerl-1.007001/travis_scripts
BioPerl-1.007001/travis_scripts/dependency_installs
BioPerl-1.007001/travis_scripts/trigger-dockerhub.sh
Configuring C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz with Build.PL
>>> C:\Perl-5.24-64\bin\perl.exe Build.PL
could not find ParserDetails.ini in C:/cpanfly-5.24-64/var/megalib/XML/SAX
Checking prerequisites...
  recommends:
    *  DB_File is not installed
    *  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 '1.007001'
  CJFIELDS/BioPerl-1.007001.tar.gz
  C:\Perl-5.24-64\bin\perl.exe Build.PL -- OK
Running Build for C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
>>> C:\Perl-5.24-64\bin\perl.exe ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.007001.tar.gz
  C:\Perl-5.24-64\bin\perl.exe ./Build -- OK
Running Build test
>>> C:\Perl-5.24-64\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..14
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 14
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 : arp
ok 4 - input filehandle method test : po
ok 5 - input filehandle method test : xmfa
ok 6 - input filehandle method test : metafasta
ok 7 - input filehandle method test : mase
ok 8 - input filehandle method test : prodom
ok 9 - input filehandle method test : stockholm
ok 10 - input filehandle method test : selex
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : phylip
ok 13 - input filehandle method test : msf
ok 14 - input filehandle method test : clustalw
ok 15 - input filehandle method test : fasta
ok 16 - input filehandle method test : pfam
ok 17 - input filehandle method test : nexus
ok 18 - filehandle output test : po
ok 19 - filehandle output test : xmfa
ok 20 - filehandle output test : metafasta
ok 21 - filehandle output test : stockholm
ok 22 - filehandle output test : selex
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : phylip
ok 25 - filehandle output test : msf
ok 26 - filehandle output test : clustalw
ok 27 - filehandle output test : fasta
ok 28 - filehandle output test : pfam
ok 29 - filehandle output test : nexus
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 output test
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 6 - clustalw 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..12
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 
ok 5 - fasta input test for description
ok 6 - fasta input test for id
ok 7 - fasta input test, captures formatted start/end
ok 8 - fasta input test for end
ok 9 - fasta input test for description
ok 10 - fasta output test
ok 11 - filehandle input test  
ok 12 - 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..20
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
ok 15
not ok 16 # TODO problems with default strand

#   Failed (TODO) test at t/AlignIO/phylip.t line 78.
#          got: undef
#     expected: '0'
ok 17 - newline between header and sequences is parsed correctly
ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 20
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
t/Assembly/ContigSpectrum.t ............ skipped: The optional module DB_File (or dependencies thereof) was not installed
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/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
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){{ <-- HERE (.*?)}}/ at C:\cpanfly-5.24-64\var\megalib/Inline/SMITH.pm line 63.
Subroutine dl_load_flags redefined at (eval 105) line 8.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at (eval 105) line 9.
t/LocalDB/Fasta.t ...................... 
1..109
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 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta'
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 - Make single ID
ok 91
ok 92
ok 93 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 94 - Make multiple IDs, bug \#3389
ok 95
ok 96
ok 97 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 98 - Index a set of files
ok 99
ok 100
ok 101
ok 102
ok 103 - threw Regexp ((?^:FASTA header doesn't match))
ok 104 - threw Regexp ((?^:Blank lines can only precede header lines))
ok 105
ok 106 - length is correct in sequences past spaces
ok 107
ok 108 - subseq is correct
ok 109 - subseq is correct
ok
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
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
t/LocalDB/SeqFeature.t ................. skipped: The optional module DB_File (or dependencies thereof) was not installed
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
t/LocalDB/Taxonomy/sqlite.t ............ skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/transfac_pro.t ............... skipped: The optional module DB_File (or dependencies thereof) was not installed
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
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ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
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 Repeat in ontology InterPro
ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 22 - term Cdc20/Fizzy in ontology InterPro
ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 24 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 26 - term Active Site in ontology InterPro
ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 28 - term Conserved Site in ontology InterPro
ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 30 - term Integrins alpha chain 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 post-translational modification in ontology InterPro
ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 36 - term Kringle in ontology InterPro
ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 38 - term Binding 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 - Cdc20/Fizzy term has one parent
ok 62 - Cdc20/Fizzy term has one ancestor
ok 63 - Helix-turn-helix, AraC type  term has one parent
ok 64 - Helix-turn-helix, AraC type  term has one ancestor
ok 65 - Integrins alpha chain term has one parent
ok 66 - Integrins alpha chain term has one ancestor
ok 67 - Kringle term has one parent
ok 68 - Kringle 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
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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'
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ok 42 - operator overloading in AnnotationI is deprecated
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ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
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ok 103 - operator overloading in AnnotationI is deprecated
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t/PodSyntax.t .......................... 
1..927
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/Das/FeatureTypeI.pm
ok 113 - POD test for Bio/Das/SegmentI.pm
ok 114 - POD test for Bio/DB/Ace.pm
ok 115 - POD test for Bio/DB/BioFetch.pm
ok 116 - POD test for Bio/DB/CUTG.pm
ok 117 - POD test for Bio/DB/DBFetch.pm
ok 118 - POD test for Bio/DB/EMBL.pm
ok 119 - POD test for Bio/DB/EntrezGene.pm
ok 120 - POD test for Bio/DB/Expression.pm
ok 121 - POD test for Bio/DB/Failover.pm
ok 122 - POD test for Bio/DB/Fasta.pm
ok 123 - POD test for Bio/DB/FileCache.pm
ok 124 - POD test for Bio/DB/Flat.pm
ok 125 - POD test for Bio/DB/GenBank.pm
ok 126 - POD test for Bio/DB/GenericWebAgent.pm
ok 127 - POD test for Bio/DB/GenPept.pm
ok 128 - POD test for Bio/DB/GFF.pm
ok 129 - POD test for Bio/DB/HIV.pm
ok 130 - POD test for Bio/DB/IndexedBase.pm
ok 131 - POD test for Bio/DB/InMemoryCache.pm
ok 132 - POD test for Bio/DB/LocationI.pm
ok 133 - POD test for Bio/DB/MeSH.pm
ok 134 - POD test for Bio/DB/NCBIHelper.pm
ok 135 - POD test for Bio/DB/Qual.pm
ok 136 - POD test for Bio/DB/QueryI.pm
ok 137 - POD test for Bio/DB/RandomAccessI.pm
ok 138 - POD test for Bio/DB/ReferenceI.pm
ok 139 - POD test for Bio/DB/RefSeq.pm
ok 140 - POD test for Bio/DB/Registry.pm
ok 141 - POD test for Bio/DB/SeqFeature.pm
ok 142 - POD test for Bio/DB/SeqI.pm
ok 143 - POD test for Bio/DB/SeqVersion.pm
ok 144 - POD test for Bio/DB/SwissProt.pm
ok 145 - POD test for Bio/DB/Taxonomy.pm
ok 146 - POD test for Bio/DB/TFBS.pm
ok 147 - POD test for Bio/DB/Universal.pm
ok 148 - POD test for Bio/DB/UpdateableSeqI.pm
ok 149 - POD test for Bio/DB/WebDBSeqI.pm
ok 150 - POD test for Bio/DB/Expression/geo.pm
ok 151 - POD test for Bio/DB/Flat/BDB.pm
ok 152 - POD test for Bio/DB/Flat/BinarySearch.pm
ok 153 - POD test for Bio/DB/Flat/BDB/embl.pm
ok 154 - POD test for Bio/DB/Flat/BDB/fasta.pm
ok 155 - POD test for Bio/DB/Flat/BDB/genbank.pm
ok 156 - POD test for Bio/DB/Flat/BDB/swiss.pm
ok 157 - POD test for Bio/DB/GFF/Aggregator.pm
ok 158 - POD test for Bio/DB/GFF/Featname.pm
ok 159 - POD test for Bio/DB/GFF/Feature.pm
ok 160 - POD test for Bio/DB/GFF/Homol.pm
ok 161 - POD test for Bio/DB/GFF/RelSegment.pm
ok 162 - POD test for Bio/DB/GFF/Segment.pm
ok 163 - POD test for Bio/DB/GFF/Typename.pm
ok 164 - POD test for Bio/DB/GFF/Adaptor/ace.pm
ok 165 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 166 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm
ok 167 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 168 - POD test for Bio/DB/GFF/Adaptor/dbi.pm
ok 169 - POD test for Bio/DB/GFF/Adaptor/memory.pm
ok 170 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
ok 171 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
ok 172 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm
ok 173 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm
ok 174 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
ok 175 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
ok 176 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
ok 177 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm
ok 178 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm
ok 179 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm
ok 180 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
ok 181 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
ok 182 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm
ok 183 - POD test for Bio/DB/GFF/Aggregator/alignment.pm
ok 184 - POD test for Bio/DB/GFF/Aggregator/clone.pm
ok 185 - POD test for Bio/DB/GFF/Aggregator/coding.pm
ok 186 - POD test for Bio/DB/GFF/Aggregator/gene.pm
ok 187 - POD test for Bio/DB/GFF/Aggregator/match.pm
ok 188 - POD test for Bio/DB/GFF/Aggregator/none.pm
ok 189 - POD test for Bio/DB/GFF/Aggregator/orf.pm
ok 190 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 191 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm
ok 192 - POD test for Bio/DB/GFF/Aggregator/transcript.pm
ok 193 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm
ok 194 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
ok 195 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm
ok 196 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm
ok 197 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
ok 198 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
ok 199 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm
ok 200 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
ok 201 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm
ok 202 - POD test for Bio/DB/GFF/Util/Binning.pm
ok 203 - POD test for Bio/DB/GFF/Util/Rearrange.pm
ok 204 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm
ok 205 - POD test for Bio/DB/HIV/HIVQueryHelper.pm
ok 206 - POD test for Bio/DB/Query/GenBank.pm
ok 207 - POD test for Bio/DB/Query/HIVQuery.pm
ok 208 - POD test for Bio/DB/Query/WebQuery.pm
ok 209 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm
ok 210 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm
ok 211 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
ok 212 - POD test for Bio/DB/SeqFeature/Segment.pm
ok 213 - POD test for Bio/DB/SeqFeature/Store.pm
ok 214 - POD test for Bio/DB/SeqFeature/Store/bdb.pm
ok 215 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm
ok 216 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm
ok 217 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
ok 218 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm
ok 219 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm
ok 220 - POD test for Bio/DB/SeqFeature/Store/Loader.pm
ok 221 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm
ok 222 - POD test for Bio/DB/SeqFeature/Store/memory.pm
ok 223 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm
ok 224 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm
ok 225 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm
ok 226 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm
ok 227 - POD test for Bio/DB/SeqVersion/gi.pm
ok 228 - POD test for Bio/DB/Taxonomy/entrez.pm
ok 229 - POD test for Bio/DB/Taxonomy/flatfile.pm
ok 230 - POD test for Bio/DB/Taxonomy/greengenes.pm
ok 231 - POD test for Bio/DB/Taxonomy/list.pm
ok 232 - POD test for Bio/DB/Taxonomy/silva.pm
ok 233 - POD test for Bio/DB/Taxonomy/sqlite.pm
ok 234 - POD test for Bio/DB/TFBS/transfac_pro.pm
ok 235 - POD test for Bio/Draw/Pictogram.pm
ok 236 - POD test for Bio/Event/EventGeneratorI.pm
ok 237 - POD test for Bio/Event/EventHandlerI.pm
ok 238 - POD test for Bio/Factory/AnalysisI.pm
ok 239 - POD test for Bio/Factory/ApplicationFactoryI.pm
ok 240 - POD test for Bio/Factory/DriverFactory.pm
ok 241 - POD test for Bio/Factory/FTLocationFactory.pm
ok 242 - POD test for Bio/Factory/LocationFactoryI.pm
ok 243 - POD test for Bio/Factory/MapFactoryI.pm
ok 244 - POD test for Bio/Factory/ObjectBuilderI.pm
ok 245 - POD test for Bio/Factory/ObjectFactory.pm
ok 246 - POD test for Bio/Factory/ObjectFactoryI.pm
ok 247 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm
ok 248 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm
ok 249 - POD test for Bio/Factory/SequenceFactoryI.pm
ok 250 - POD test for Bio/Factory/SequenceProcessorI.pm
ok 251 - POD test for Bio/Factory/SequenceStreamI.pm
ok 252 - POD test for Bio/Factory/TreeFactoryI.pm
ok 253 - POD test for Bio/Index/Abstract.pm
ok 254 - POD test for Bio/Index/AbstractSeq.pm
ok 255 - POD test for Bio/Index/Blast.pm
ok 256 - POD test for Bio/Index/BlastTable.pm
ok 257 - POD test for Bio/Index/EMBL.pm
ok 258 - POD test for Bio/Index/Fasta.pm
ok 259 - POD test for Bio/Index/Fastq.pm
ok 260 - POD test for Bio/Index/GenBank.pm
ok 261 - POD test for Bio/Index/Hmmer.pm
ok 262 - POD test for Bio/Index/Qual.pm
ok 263 - POD test for Bio/Index/Stockholm.pm
ok 264 - POD test for Bio/Index/SwissPfam.pm
ok 265 - POD test for Bio/Index/Swissprot.pm
ok 266 - POD test for Bio/LiveSeq/AARange.pm
ok 267 - POD test for Bio/LiveSeq/Chain.pm
ok 268 - POD test for Bio/LiveSeq/ChainI.pm
ok 269 - POD test for Bio/LiveSeq/DNA.pm
ok 270 - POD test for Bio/LiveSeq/Exon.pm
ok 271 - POD test for Bio/LiveSeq/Gene.pm
ok 272 - POD test for Bio/LiveSeq/Intron.pm
ok 273 - POD test for Bio/LiveSeq/Mutation.pm
ok 274 - POD test for Bio/LiveSeq/Mutator.pm
ok 275 - POD test for Bio/LiveSeq/Prim_Transcript.pm
ok 276 - POD test for Bio/LiveSeq/Range.pm
ok 277 - POD test for Bio/LiveSeq/Repeat_Region.pm
ok 278 - POD test for Bio/LiveSeq/Repeat_Unit.pm
ok 279 - POD test for Bio/LiveSeq/SeqI.pm
ok 280 - POD test for Bio/LiveSeq/Transcript.pm
ok 281 - POD test for Bio/LiveSeq/Translation.pm
ok 282 - POD test for Bio/LiveSeq/IO/BioPerl.pm
ok 283 - POD test for Bio/LiveSeq/IO/Loader.pm
ok 284 - POD test for Bio/Location/Atomic.pm
ok 285 - POD test for Bio/Location/AvWithinCoordPolicy.pm
ok 286 - POD test for Bio/Location/CoordinatePolicyI.pm
ok 287 - POD test for Bio/Location/Fuzzy.pm
ok 288 - POD test for Bio/Location/FuzzyLocationI.pm
ok 289 - POD test for Bio/Location/NarrowestCoordPolicy.pm
ok 290 - POD test for Bio/Location/Simple.pm
ok 291 - POD test for Bio/Location/Split.pm
ok 292 - POD test for Bio/Location/SplitLocationI.pm
ok 293 - POD test for Bio/Location/WidestCoordPolicy.pm
ok 294 - POD test for Bio/Map/Clone.pm
ok 295 - POD test for Bio/Map/Contig.pm
ok 296 - POD test for Bio/Map/CytoMap.pm
ok 297 - POD test for Bio/Map/CytoMarker.pm
ok 298 - POD test for Bio/Map/CytoPosition.pm
ok 299 - POD test for Bio/Map/EntityI.pm
ok 300 - POD test for Bio/Map/FPCMarker.pm
ok 301 - POD test for Bio/Map/Gene.pm
ok 302 - POD test for Bio/Map/GeneMap.pm
ok 303 - POD test for Bio/Map/GenePosition.pm
ok 304 - POD test for Bio/Map/GeneRelative.pm
ok 305 - POD test for Bio/Map/LinkageMap.pm
ok 306 - POD test for Bio/Map/LinkagePosition.pm
ok 307 - POD test for Bio/Map/MapI.pm
ok 308 - POD test for Bio/Map/Mappable.pm
ok 309 - POD test for Bio/Map/MappableI.pm
ok 310 - POD test for Bio/Map/Marker.pm
ok 311 - POD test for Bio/Map/MarkerI.pm
ok 312 - POD test for Bio/Map/Microsatellite.pm
ok 313 - POD test for Bio/Map/OrderedPosition.pm
ok 314 - POD test for Bio/Map/OrderedPositionWithDistance.pm
ok 315 - POD test for Bio/Map/Physical.pm
ok 316 - POD test for Bio/Map/Position.pm
ok 317 - POD test for Bio/Map/PositionHandler.pm
ok 318 - POD test for Bio/Map/PositionHandlerI.pm
ok 319 - POD test for Bio/Map/PositionI.pm
ok 320 - POD test for Bio/Map/PositionWithSequence.pm
ok 321 - POD test for Bio/Map/Prediction.pm
ok 322 - POD test for Bio/Map/Relative.pm
ok 323 - POD test for Bio/Map/RelativeI.pm
ok 324 - POD test for Bio/Map/SimpleMap.pm
ok 325 - POD test for Bio/Map/TranscriptionFactor.pm
ok 326 - POD test for Bio/MapIO/fpc.pm
ok 327 - POD test for Bio/MapIO/mapmaker.pm
ok 328 - POD test for Bio/Matrix/Generic.pm
ok 329 - POD test for Bio/Matrix/IO.pm
ok 330 - POD test for Bio/Matrix/MatrixI.pm
ok 331 - POD test for Bio/Matrix/Mlagan.pm
ok 332 - POD test for Bio/Matrix/PhylipDist.pm
ok 333 - POD test for Bio/Matrix/Scoring.pm
ok 334 - POD test for Bio/Matrix/IO/mlagan.pm
ok 335 - POD test for Bio/Matrix/IO/phylip.pm
ok 336 - POD test for Bio/Matrix/IO/scoring.pm
ok 337 - POD test for Bio/Matrix/PSM/InstanceSite.pm
ok 338 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm
ok 339 - POD test for Bio/Matrix/PSM/IO.pm
ok 340 - POD test for Bio/Matrix/PSM/ProtMatrix.pm
ok 341 - POD test for Bio/Matrix/PSM/ProtPsm.pm
ok 342 - POD test for Bio/Matrix/PSM/Psm.pm
ok 343 - POD test for Bio/Matrix/PSM/PsmHeader.pm
ok 344 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm
ok 345 - POD test for Bio/Matrix/PSM/PsmI.pm
ok 346 - POD test for Bio/Matrix/PSM/SiteMatrix.pm
ok 347 - POD test for Bio/Matrix/PSM/SiteMatrixI.pm
ok 348 - POD test for Bio/Matrix/PSM/IO/mast.pm
ok 349 - POD test for Bio/Matrix/PSM/IO/masta.pm
ok 350 - POD test for Bio/Matrix/PSM/IO/meme.pm
ok 351 - POD test for Bio/Matrix/PSM/IO/psiblast.pm
ok 352 - POD test for Bio/Matrix/PSM/IO/transfac.pm
ok 353 - POD test for Bio/MolEvol/CodonModel.pm
ok 354 - POD test for Bio/Nexml/Factory.pm
ok 355 - POD test for Bio/Ontology/DocumentRegistry.pm
ok 356 - POD test for Bio/Ontology/GOterm.pm
ok 357 - POD test for Bio/Ontology/InterProTerm.pm
ok 358 - POD test for Bio/Ontology/OBOEngine.pm
ok 359 - POD test for Bio/Ontology/OBOterm.pm
ok 360 - POD test for Bio/Ontology/Ontology.pm
ok 361 - POD test for Bio/Ontology/OntologyEngineI.pm
ok 362 - POD test for Bio/Ontology/OntologyI.pm
ok 363 - POD test for Bio/Ontology/OntologyStore.pm
ok 364 - POD test for Bio/Ontology/Path.pm
ok 365 - POD test for Bio/Ontology/PathI.pm
ok 366 - POD test for Bio/Ontology/Relationship.pm
ok 367 - POD test for Bio/Ontology/RelationshipFactory.pm
ok 368 - POD test for Bio/Ontology/RelationshipI.pm
ok 369 - POD test for Bio/Ontology/RelationshipType.pm
ok 370 - POD test for Bio/Ontology/SimpleOntologyEngine.pm
ok 371 - POD test for Bio/Ontology/Term.pm
ok 372 - POD test for Bio/Ontology/TermFactory.pm
ok 373 - POD test for Bio/Ontology/TermI.pm
ok 374 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
ok 375 - POD test for Bio/OntologyIO/dagflat.pm
ok 376 - POD test for Bio/OntologyIO/goflat.pm
ok 377 - POD test for Bio/OntologyIO/InterProParser.pm
ok 378 - POD test for Bio/OntologyIO/obo.pm
ok 379 - POD test for Bio/OntologyIO/simplehierarchy.pm
ok 380 - POD test for Bio/OntologyIO/soflat.pm
ok 381 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 382 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm
ok 383 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 384 - POD test for Bio/Phenotype/Correlate.pm
ok 385 - POD test for Bio/Phenotype/Measure.pm
ok 386 - POD test for Bio/Phenotype/Phenotype.pm
ok 387 - POD test for Bio/Phenotype/PhenotypeI.pm
ok 388 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 389 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 390 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 391 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 392 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 393 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 394 - POD test for Bio/PhyloNetwork/Factory.pm
ok 395 - POD test for Bio/PhyloNetwork/FactoryX.pm
ok 396 - POD test for Bio/PhyloNetwork/GraphViz.pm
ok 397 - POD test for Bio/PhyloNetwork/muVector.pm
ok 398 - POD test for Bio/PhyloNetwork/RandomFactory.pm
ok 399 - POD test for Bio/PhyloNetwork/TreeFactory.pm
ok 400 - POD test for Bio/PhyloNetwork/TreeFactoryMulti.pm
ok 401 - POD test for Bio/PhyloNetwork/TreeFactoryX.pm
ok 402 - POD test for Bio/PopGen/Genotype.pm
ok 403 - POD test for Bio/PopGen/GenotypeI.pm
ok 404 - POD test for Bio/PopGen/HtSNP.pm
ok 405 - POD test for Bio/PopGen/Individual.pm
ok 406 - POD test for Bio/PopGen/IndividualI.pm
ok 407 - POD test for Bio/PopGen/IO.pm
ok 408 - POD test for Bio/PopGen/Marker.pm
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ok 410 - POD test for Bio/PopGen/PopStats.pm
ok 411 - POD test for Bio/PopGen/Population.pm
ok 412 - POD test for Bio/PopGen/PopulationI.pm
ok 413 - POD test for Bio/PopGen/Statistics.pm
ok 414 - POD test for Bio/PopGen/TagHaplotype.pm
ok 415 - POD test for Bio/PopGen/Utilities.pm
ok 416 - POD test for Bio/PopGen/IO/csv.pm
ok 417 - POD test for Bio/PopGen/IO/hapmap.pm
ok 418 - POD test for Bio/PopGen/IO/phase.pm
ok 419 - POD test for Bio/PopGen/IO/prettybase.pm
ok 420 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 421 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 422 - POD test for Bio/Restriction/Analysis.pm
ok 423 - POD test for Bio/Restriction/Enzyme.pm
ok 424 - POD test for Bio/Restriction/EnzymeCollection.pm
ok 425 - POD test for Bio/Restriction/EnzymeI.pm
ok 426 - POD test for Bio/Restriction/IO.pm
ok 427 - POD test for Bio/Restriction/Enzyme/MultiCut.pm
ok 428 - POD test for Bio/Restriction/Enzyme/MultiSite.pm
ok 429 - POD test for Bio/Restriction/IO/bairoch.pm
ok 430 - POD test for Bio/Restriction/IO/base.pm
ok 431 - POD test for Bio/Restriction/IO/itype2.pm
ok 432 - POD test for Bio/Restriction/IO/prototype.pm
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ok 434 - POD test for Bio/Root/Build.pm
ok 435 - POD test for Bio/Root/Exception.pm
ok 436 - POD test for Bio/Root/HTTPget.pm
ok 437 - POD test for Bio/Root/IO.pm
ok 438 - POD test for Bio/Root/Root.pm
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ok 440 - POD test for Bio/Root/Storable.pm
ok 441 - POD test for Bio/Root/Test.pm
ok 442 - POD test for Bio/Root/TestObject.pm
ok 443 - POD test for Bio/Root/Utilities.pm
ok 444 - POD test for Bio/Root/Version.pm
ok 445 - POD test for Bio/Search/BlastStatistics.pm
ok 446 - POD test for Bio/Search/BlastUtils.pm
ok 447 - POD test for Bio/Search/DatabaseI.pm
ok 448 - POD test for Bio/Search/GenericDatabase.pm
ok 449 - POD test for Bio/Search/GenericStatistics.pm
ok 450 - POD test for Bio/Search/Processor.pm
ok 451 - POD test for Bio/Search/SearchUtils.pm
ok 452 - POD test for Bio/Search/StatisticsI.pm
ok 453 - POD test for Bio/Search/Hit/BlastHit.pm
ok 454 - POD test for Bio/Search/Hit/BlastPullHit.pm
ok 455 - POD test for Bio/Search/Hit/Fasta.pm
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ok 459 - POD test for Bio/Search/Hit/hmmer3Hit.pm
ok 460 - POD test for Bio/Search/Hit/HMMERHit.pm
ok 461 - POD test for Bio/Search/Hit/HmmpfamHit.pm
ok 462 - POD test for Bio/Search/Hit/ModelHit.pm
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ok 466 - POD test for Bio/Search/HSP/BlastPullHSP.pm
ok 467 - POD test for Bio/Search/HSP/FastaHSP.pm
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ok 469 - POD test for Bio/Search/HSP/HMMERHSP.pm
ok 470 - POD test for Bio/Search/HSP/HmmpfamHSP.pm
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ok 472 - POD test for Bio/Search/HSP/HSPI.pm
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ok 474 - POD test for Bio/Search/HSP/PsiBlastHSP.pm
ok 475 - POD test for Bio/Search/HSP/PSLHSP.pm
ok 476 - POD test for Bio/Search/HSP/PullHSPI.pm
ok 477 - POD test for Bio/Search/HSP/WABAHSP.pm
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ok 480 - POD test for Bio/Search/Result/BlastPullResult.pm
ok 481 - POD test for Bio/Search/Result/BlastResult.pm
ok 482 - POD test for Bio/Search/Result/CrossMatchResult.pm
ok 483 - POD test for Bio/Search/Result/GenericResult.pm
ok 484 - POD test for Bio/Search/Result/hmmer3Result.pm
ok 485 - POD test for Bio/Search/Result/HMMERResult.pm
ok 486 - POD test for Bio/Search/Result/HmmpfamResult.pm
ok 487 - POD test for Bio/Search/Result/INFERNALResult.pm
ok 488 - POD test for Bio/Search/Result/PullResultI.pm
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ok 491 - POD test for Bio/Search/Result/WABAResult.pm
ok 492 - POD test for Bio/Search/Tiling/MapTileUtils.pm
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ok 494 - POD test for Bio/Search/Tiling/TilingI.pm
ok 495 - POD test for Bio/SearchIO/axt.pm
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ok 497 - POD test for Bio/SearchIO/blasttable.pm
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ok 503 - POD test for Bio/SearchIO/fasta.pm
ok 504 - POD test for Bio/SearchIO/FastHitEventBuilder.pm
ok 505 - POD test for Bio/SearchIO/gmap_f9.pm
ok 506 - POD test for Bio/SearchIO/hmmer.pm
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ok 508 - POD test for Bio/SearchIO/hmmer3.pm
ok 509 - POD test for Bio/SearchIO/hmmer_pull.pm
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ok 511 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm
ok 512 - POD test for Bio/SearchIO/megablast.pm
ok 513 - POD test for Bio/SearchIO/psl.pm
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ok 515 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm
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ok 518 - POD test for Bio/SearchIO/waba.pm
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ok 520 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 521 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 522 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 523 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 524 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 525 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 526 - POD test for Bio/Seq/BaseSeqProcessor.pm
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ok 531 - POD test for Bio/Seq/LargeSeqI.pm
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ok 537 - POD test for Bio/Seq/Quality.pm
ok 538 - POD test for Bio/Seq/RichSeq.pm
ok 539 - POD test for Bio/Seq/RichSeqI.pm
ok 540 - POD test for Bio/Seq/SeqBuilder.pm
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ok 544 - POD test for Bio/Seq/SeqWithQuality.pm
ok 545 - POD test for Bio/Seq/SimulatedRead.pm
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ok 550 - POD test for Bio/SeqEvolution/Factory.pm
ok 551 - POD test for Bio/SeqFeature/Amplicon.pm
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ok 553 - POD test for Bio/SeqFeature/Collection.pm
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ok 555 - POD test for Bio/SeqFeature/Computation.pm
ok 556 - POD test for Bio/SeqFeature/FeaturePair.pm
ok 557 - POD test for Bio/SeqFeature/Generic.pm
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ok 560 - POD test for Bio/SeqFeature/Primer.pm
ok 561 - POD test for Bio/SeqFeature/Similarity.pm
ok 562 - POD test for Bio/SeqFeature/SimilarityPair.pm
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ok 564 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm
ok 565 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 566 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 567 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 568 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
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ok 570 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
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ok 572 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 573 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 574 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 575 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 576 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 577 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 578 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 579 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 580 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 581 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 582 - POD test for Bio/SeqIO/abi.pm
ok 583 - POD test for Bio/SeqIO/ace.pm
ok 584 - POD test for Bio/SeqIO/agave.pm
ok 585 - POD test for Bio/SeqIO/alf.pm
ok 586 - POD test for Bio/SeqIO/asciitree.pm
ok 587 - POD test for Bio/SeqIO/bsml.pm
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ok 591 - POD test for Bio/SeqIO/chaosxml.pm
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ok 593 - POD test for Bio/SeqIO/embl.pm
ok 594 - POD test for Bio/SeqIO/embldriver.pm
ok 595 - POD test for Bio/SeqIO/entrezgene.pm
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ok 598 - POD test for Bio/SeqIO/fasta.pm
ok 599 - POD test for Bio/SeqIO/fastq.pm
ok 600 - POD test for Bio/SeqIO/flybase_chadoxml.pm
ok 601 - POD test for Bio/SeqIO/FTHelper.pm
ok 602 - POD test for Bio/SeqIO/game.pm
ok 603 - POD test for Bio/SeqIO/gbdriver.pm
ok 604 - POD test for Bio/SeqIO/gbxml.pm
ok 605 - POD test for Bio/SeqIO/gcg.pm
ok 606 - POD test for Bio/SeqIO/genbank.pm
ok 607 - POD test for Bio/SeqIO/interpro.pm
ok 608 - POD test for Bio/SeqIO/kegg.pm
ok 609 - POD test for Bio/SeqIO/largefasta.pm
ok 610 - POD test for Bio/SeqIO/lasergene.pm
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ok 613 - POD test for Bio/SeqIO/metafasta.pm
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ok 615 - POD test for Bio/SeqIO/MultiFile.pm
ok 616 - POD test for Bio/SeqIO/nexml.pm
ok 617 - POD test for Bio/SeqIO/phd.pm
ok 618 - POD test for Bio/SeqIO/pir.pm
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ok 620 - POD test for Bio/SeqIO/qual.pm
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ok 622 - POD test for Bio/SeqIO/scf.pm
ok 623 - POD test for Bio/SeqIO/seqxml.pm
ok 624 - POD test for Bio/SeqIO/strider.pm
ok 625 - POD test for Bio/SeqIO/swiss.pm
ok 626 - POD test for Bio/SeqIO/swissdriver.pm
ok 627 - POD test for Bio/SeqIO/tab.pm
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ok 630 - POD test for Bio/SeqIO/tigrxml.pm
ok 631 - POD test for Bio/SeqIO/tinyseq.pm
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ok 633 - POD test for Bio/SeqIO/game/featHandler.pm
ok 634 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 635 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 636 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 637 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 638 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 639 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 640 - POD test for Bio/Structure/Atom.pm
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ok 642 - POD test for Bio/Structure/Entry.pm
ok 643 - POD test for Bio/Structure/IO.pm
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ok 650 - POD test for Bio/Symbol/Alphabet.pm
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ok 653 - POD test for Bio/Symbol/ProteinAlphabet.pm
ok 654 - POD test for Bio/Symbol/Symbol.pm
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ok 656 - POD test for Bio/Taxonomy/FactoryI.pm
ok 657 - POD test for Bio/Taxonomy/Node.pm
ok 658 - POD test for Bio/Taxonomy/Taxon.pm
ok 659 - POD test for Bio/Taxonomy/Tree.pm
ok 660 - POD test for Bio/Tools/AlignFactory.pm
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ok 667 - POD test for Bio/Tools/ECnumber.pm
ok 668 - POD test for Bio/Tools/EPCR.pm
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ok 677 - POD test for Bio/Tools/Genewise.pm
ok 678 - POD test for Bio/Tools/Genomewise.pm
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ok 682 - POD test for Bio/Tools/Grail.pm
ok 683 - POD test for Bio/Tools/GuessSeqFormat.pm
ok 684 - POD test for Bio/Tools/Hmmpfam.pm
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ok 738 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
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ok 750 - POD test for Bio/Tools/Sim4/Exon.pm
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ok 754 - POD test for Bio/Tools/Spidey/Exon.pm
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ok 772 - POD test for Bio/TreeIO/NewickParser.pm
ok 773 - POD test for Bio/TreeIO/nexml.pm
ok 774 - POD test for Bio/TreeIO/nexus.pm
ok 775 - POD test for Bio/TreeIO/nhx.pm
ok 776 - POD test for Bio/TreeIO/pag.pm
ok 777 - POD test for Bio/TreeIO/phyloxml.pm
ok 778 - POD test for Bio/TreeIO/svggraph.pm
ok 779 - POD test for Bio/TreeIO/tabtree.pm
ok 780 - POD test for Bio/TreeIO/TreeEventBuilder.pm
ok 781 - POD test for Bio/Variation/AAChange.pm
ok 782 - POD test for Bio/Variation/AAReverseMutate.pm
ok 783 - POD test for Bio/Variation/Allele.pm
ok 784 - POD test for Bio/Variation/DNAMutation.pm
ok 785 - POD test for Bio/Variation/IO.pm
ok 786 - POD test for Bio/Variation/RNAChange.pm
ok 787 - POD test for Bio/Variation/SeqDiff.pm
ok 788 - POD test for Bio/Variation/SNP.pm
ok 789 - POD test for Bio/Variation/VariantI.pm
ok 790 - POD test for Bio/Variation/IO/flat.pm
ok 791 - POD test for Bio/Variation/IO/xml.pm
ok 792 - POD test for scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
ok 793 - POD test for scripts/Bio-DB-GFF/bp_fast_load_gff.pl
ok 794 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff.pl
ok 795 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff3.pl
ok 796 - POD test for scripts/Bio-DB-GFF/bp_generate_histogram.pl
ok 797 - POD test for scripts/Bio-DB-GFF/bp_load_gff.pl
ok 798 - POD test for scripts/Bio-DB-GFF/bp_meta_gff.pl
ok 799 - POD test for scripts/Bio-DB-GFF/bp_process_gadfly.pl
ok 800 - POD test for scripts/Bio-DB-GFF/bp_process_sgd.pl
ok 801 - POD test for scripts/Bio-DB-GFF/bp_process_wormbase.pl
ok 802 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl (no pod)
ok 803 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl (no pod)
ok 804 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
ok 805 - POD test for scripts/das/bp_das_server.pl (no pod)
ok 806 - POD test for scripts/DB/bp_biofetch_genbank_proxy.pl
ok 807 - POD test for scripts/DB/bp_bioflat_index.pl
ok 808 - POD test for scripts/DB/bp_biogetseq.pl
ok 809 - POD test for scripts/DB/bp_flanks.pl
ok 810 - POD test for scripts/DB-HIV/bp_hivq.pl
ok 811 - POD test for scripts/index/bp_fetch.pl
ok 812 - POD test for scripts/index/bp_index.pl
ok 813 - POD test for scripts/index/bp_seqret.pl
ok 814 - POD test for scripts/popgen/bp_composite_LD.pl
ok 815 - POD test for scripts/popgen/bp_heterogeneity_test.pl
ok 816 - POD test for scripts/searchio/bp_fastam9_to_table.pl
ok 817 - POD test for scripts/searchio/bp_filter_search.pl
ok 818 - POD test for scripts/searchio/bp_hmmer_to_table.pl
ok 819 - POD test for scripts/searchio/bp_parse_hmmsearch.pl
ok 820 - POD test for scripts/searchio/bp_search2table.pl
ok 821 - POD test for scripts/seq/bp_extract_feature_seq.pl
ok 822 - POD test for scripts/seq/bp_make_mrna_protein.pl
ok 823 - POD test for scripts/seq/bp_seqconvert.pl
ok 824 - POD test for scripts/seq/bp_seqcut.pl
ok 825 - POD test for scripts/seq/bp_seqpart.pl
ok 826 - POD test for scripts/seq/bp_seqretsplit.pl
ok 827 - POD test for scripts/seq/bp_split_seq.pl
ok 828 - POD test for scripts/seq/bp_translate_seq.pl
ok 829 - POD test for scripts/seq/bp_unflatten_seq.pl
ok 830 - POD test for scripts/seqstats/bp_aacomp.pl
ok 831 - POD test for scripts/seqstats/bp_chaos_plot.pl
ok 832 - POD test for scripts/seqstats/bp_gccalc.pl
ok 833 - POD test for scripts/seqstats/bp_oligo_count.pl
ok 834 - POD test for scripts/taxa/bp_classify_hits_kingdom.pl
ok 835 - POD test for scripts/taxa/bp_local_taxonomydb_query.pl
ok 836 - POD test for scripts/taxa/bp_query_entrez_taxa.pl
ok 837 - POD test for scripts/taxa/bp_taxid4species.pl
ok 838 - POD test for scripts/taxa/bp_taxonomy2tree.pl
ok 839 - POD test for scripts/tree/bp_blast2tree.pl
ok 840 - POD test for scripts/tree/bp_nexus2nh.pl
ok 841 - POD test for scripts/tree/bp_tree2pag.pl
ok 842 - POD test for scripts/utilities/bp_dbsplit.pl
ok 843 - POD test for scripts/utilities/bp_download_query_genbank.pl
ok 844 - POD test for scripts/utilities/bp_find-blast-matches.pl
ok 845 - POD test for scripts/utilities/bp_mask_by_search.pl
ok 846 - POD test for scripts/utilities/bp_mrtrans.pl
ok 847 - POD test for scripts/utilities/bp_mutate.pl
ok 848 - POD test for scripts/utilities/bp_netinstall.pl
ok 849 - POD test for scripts/utilities/bp_nrdb.pl
ok 850 - POD test for scripts/utilities/bp_pairwise_kaks.pl
ok 851 - POD test for scripts/utilities/bp_remote_blast.pl
ok 852 - POD test for scripts/utilities/bp_revtrans-motif.pl
ok 853 - POD test for scripts/utilities/bp_search2alnblocks.pl
ok 854 - POD test for scripts/utilities/bp_search2gff.pl
ok 855 - POD test for scripts/utilities/bp_search2tribe.pl
ok 856 - POD test for scripts/utilities/bp_seq_length.pl
ok 857 - POD test for scripts/utilities/bp_sreformat.pl
ok 858 - POD test for examples/bioperl.pl (no pod)
ok 859 - POD test for examples/generate_random_seq.pl (no pod)
ok 860 - POD test for examples/longorf.pl
ok 861 - POD test for examples/make_primers.pl (no pod)
ok 862 - POD test for examples/revcom_dir.pl (no pod)
ok 863 - POD test for examples/rev_and_trans.pl (no pod)
ok 864 - POD test for examples/subsequence.cgi (no pod)
ok 865 - POD test for examples/align/aligntutorial.pl (no pod)
ok 866 - POD test for examples/align/align_on_codons.pl (no pod)
ok 867 - POD test for examples/align/clustalw.pl (no pod)
ok 868 - POD test for examples/align/FastAlign.pl
ok 869 - POD test for examples/align/simplealign.pl (no pod)
ok 870 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 871 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 872 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 873 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 874 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 875 - POD test for examples/db/dbfetch
ok 876 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 877 - POD test for examples/db/gb2features.pl (no pod)
ok 878 - POD test for examples/db/getGenBank.pl (no pod)
ok 879 - POD test for examples/db/get_seqs.pl (no pod)
ok 880 - POD test for examples/db/rfetch.pl (no pod)
ok 881 - POD test for examples/db/use_registry.pl (no pod)
ok 882 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 883 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 884 - POD test for examples/quality/svgtrace.pl (no pod)
ok 885 - POD test for examples/root/exceptions1.pl (no pod)
ok 886 - POD test for examples/root/exceptions2.pl (no pod)
ok 887 - POD test for examples/root/exceptions3.pl (no pod)
ok 888 - POD test for examples/root/exceptions4.pl (no pod)
ok 889 - POD test for examples/searchio/blast_example.pl (no pod)
ok 890 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 891 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 892 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 893 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 894 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 895 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 896 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 897 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 898 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 899 - POD test for examples/searchio/waba2gff3.pl
ok 900 - POD test for examples/sirna/rnai_finder.cgi
ok 901 - POD test for examples/structure/structure-io.pl (no pod)
ok 902 - POD test for examples/tk/gsequence.pl (no pod)
ok 903 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 904 - POD test for examples/tools/extract_genes.pl
ok 905 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 906 - POD test for examples/tools/gff2ps.pl
ok 907 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 908 - POD test for examples/tools/psw.pl (no pod)
ok 909 - POD test for examples/tools/reverse-translate.pl
ok 910 - POD test for examples/tools/run_genscan.pl (no pod)
ok 911 - POD test for examples/tools/run_primer3.pl
ok 912 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 913 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 914 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 915 - POD test for maintenance/authors.pl
ok 916 - POD test for maintenance/check_NAME.pl
ok 917 - POD test for maintenance/check_URLs.pl
ok 918 - POD test for maintenance/cvs2cl_by_file.pl
ok 919 - POD test for maintenance/dependencies.pl
ok 920 - POD test for maintenance/deprecated.pl
ok 921 - POD test for maintenance/find_mod_deps.pl
ok 922 - POD test for maintenance/modules.pl
ok 923 - POD test for maintenance/module_usage.pl (no pod)
ok 924 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 925 - POD test for maintenance/pod.pl
ok 926 - POD test for maintenance/symlink_script.pl
ok 927 - 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
t/PopGen/PopGen.t ...................... 
1..105
ok 1 - use IO::String;
ok 2 - use Bio::PopGen::Individual;
ok 3 - use Bio::PopGen::Genotype;
ok 4 - use Bio::PopGen::Population;
ok 5 - use Bio::PopGen::IO;
ok 6 - use Bio::PopGen::PopStats;
ok 7 - use Bio::AlignIO;
ok 8 - use Bio::PopGen::Statistics;
ok 9 - use Bio::PopGen::Utilities;
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 - mrsa,mssa aflp1
ok 41 - all pops, aflp1
ok 42 - mrsa,envpop aflp1,aflp2
ok 43
ok 44
ok 45
ok 46 - mssa,mrsa all_bands
ok 47 - env,mssa mkr1
ok 48 - env,mssa,mrsa all bands
ok 49 - env,mssa,mrsa mkr2
ok 50 - mrsa,nc all_bands
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 - Pi on 3-allele data
ok 105 - Theta on 3-allele data
ok
t/PopGen/PopGenSims.t .................. 
1..23
ok 1 - use Bio::PopGen::Simulation::GeneticDrift;
ok 2 - Allele freqs should sum to 1
ok 3 - Allele freqs should sum to 1
ok 4 - Allele freqs should sum to 1
ok 5 - Allele freqs should sum to 1
ok 6 - Allele freqs should sum to 1
ok 7 - Allele freqs should sum to 1
ok 8 - Allele freqs should sum to 1
ok 9 - Allele freqs should sum to 1
ok 10 - Allele freqs should sum to 1
ok 11 - Allele freqs should sum to 1
ok 12
ok 13 - All frequencies should be <= 1
ok 14 - Allele freqs should sum to 1
ok 15 - Allele freqs should sum to 1
ok 16 - Allele freqs should sum to 1
ok 17 - Allele freqs should sum to 1
ok 18 - Allele freqs should sum to 1
ok 19 - Allele freqs should sum to 1
ok 20 - Allele freqs should sum to 1
ok 21 - Allele freqs should sum to 1
ok 22 - Allele freqs should sum to 1
ok 23 - Allele freqs should sum to 1
ok
t/PopGen/TagHaplotype.t ................ 
1..3
ok 1 - use Bio::PopGen::TagHaplotype;
ok 2
ok 3
ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... 
1..37
ok 1 - use Bio::DB::CUTG;
ok 2 - use Bio::CodonUsage::Table;
ok 3 - use Bio::CodonUsage::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Tools::SeqStats;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... 
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - An object of class 'Bio::DB::HIV' isa 'Bio::DB::HIV'
ok 5 - An object of class 'Bio::DB::HIV' isa 'Bio::Root::Root'
ok 6 - Bio::DB::HIV->can(...)
ok 7 - Bio::DB::HIV->can(...)
ok 8 - Bio::DB::HIV->can(...)
ok 9 - lanl_base set in default object
ok 10 - map_db set in default object
ok 11 - make_search_if set in default object
ok 12 - search_ set in default object
ok 13 - url_base_address set in default object
ok 14 - default sequence request format (fasta)
ok 15 - sorry till implemented
ok 16 - sorry till implemented
ok 17 - HIVQuery type exception check
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... 
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - An object of class 'Bio::DB::HIV::HIVAnnotProcessor' isa 'Bio::DB::HIV::HIVAnnotProcessor'
ok 5 - An object of class 'Bio::DB::HIV::HIVAnnotProcessor' isa 'Bio::Root::Root'
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
t/RemoteDB/HIV/HIVQuery.t .............. 
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - An object of class 'Bio::DB::Query::HIVQuery' isa 'Bio::DB::Query::HIVQuery'
ok 8 - An object of class 'Bio::DB::Query::HIVQuery' isa 'Bio::Root::Root'
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 - use HTML::Parser;
ok 24 - help html to file
ok 25 - help html parsed
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - An object of class 'HIVSchema' isa 'HIVSchema'
ok 3 - An object of class 'QRY' isa 'QRY'
ok 4 - An object of class 'R' isa 'R'
ok 5 - An object of class 'Q' isa 'Q'
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} 
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} 
ok 40 - above query is null
ok
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... 
1..16
ok 1 - use Bio::DB::RefSeq;
ok 2 - use Bio::DB::GenBank;
ok 3 - use Bio::DB::EMBL;
ok 4
ok 5
ok 6
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ 
ok 1 - use Bio::DB::SeqVersion;
ok 2
ok 3 # skip Network tests have not been requested
ok 4 # skip Network tests have not been requested
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
1..10
ok
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
t/RemoteDB/Taxonomy.t .................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Restriction/Analysis-refac.t ......... 
1..91
ok 1 - use Bio::Restriction::IO;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Restriction::EnzymeCollection;
ok 4 - use Bio::Restriction::Enzyme;
ok 5 - read withrefm file
ok 6 - parse withrefm file
ok 7 - HindIII: nonambiguous intrasite cutter
ok 8 - AarI: nonambiguous extrasite cutter
ok 9 - AasI: ambiguous intrasite cutter
ok 10 - BceSI: ambiguous extrasite cutter
ok 11 - AjuI: cutter with central recog site
ok 12 - TaqII: multi-extrasite cutter
ok 13
ok 14 - HindIII plus
ok 15 - HindIII minus
ok 16 - AasI plus
ok 17 - AasI  minus
ok 18 - AarI plus
ok 19 - AarI  minus
ok 20 - BceSI plus
ok 21 - BceSI  minus
ok 22 - AjuI plus
ok 23 - AjuI minus
ok 24 - TaqII plus
ok 25 - TaqII minus
ok 26 - build real B:R::Analysis object
ok 27 - 13 fragments
ok 28 - circularize
ok 29 - recut
ok 30 - circ: AasI
# site at origin
ok 31 - circ: still 13 fragments (cut site at origin)
ok 32 - use Bio::Restriction::IO;
ok 33 - use Bio::Restriction::Analysis;
ok 34 - read withrefm file
ok 35 - parse withrefm file
ok 36 - Collection initiated
ok 37 - AbeI: found ok into collection
ok 38 - AccBSI: found ok into collection
ok 39 - AciI: found ok into collection
ok 40 - Asp26HI: found ok into collection
ok 41 - BmgBI: found ok into collection
ok 42 - AbeI plus
ok 43 - AbeI minus
ok 44 - AbeI fragment
ok 45 - AbeI positions
ok 46 - AbeI Overhang
ok 47 - AbeI name
ok 48 - AbeI site
ok 49 - AbeI revcom_site
ok 50 - AbeI cut
ok 51 - AbeI complementary_cut
ok 52 - AccBSI plus
ok 53 - AccBSI minus
ok 54 - AccBSI fragment
ok 55 - AccBSI positions
ok 56 - AccBSI Overhang
ok 57 - AccBSI name
ok 58 - AccBSI site
ok 59 - AccBSI revcom_site
ok 60 - AccBSI cut
ok 61 - AccBSI complementary_cut
ok 62 - AciI plus
ok 63 - AciI minus
ok 64 - AciI fragment
ok 65 - AciI positions
ok 66 - AciI Overhang
ok 67 - AciI name
ok 68 - AciI site
ok 69 - AciI revcom_site
ok 70 - AciI cut
ok 71 - AciI complementary_cut
ok 72 - Asp26HI plus
ok 73 - Asp26HI minus
ok 74 - Asp26HI fragment
ok 75 - Asp26HI positions
ok 76 - Asp26HI Overhang
ok 77 - Asp26HI name
ok 78 - Asp26HI site
ok 79 - Asp26HI revcom_site
ok 80 - Asp26HI cut
ok 81 - Asp26HI complementary_cut
ok 82 - BmgBI plus
ok 83 - BmgBI minus
ok 84 - BmgBI fragment
ok 85 - BmgBI positions
ok 86 - BmgBI Overhang
ok 87 - BmgBI name
ok 88 - BmgBI site
ok 89 - BmgBI revcom_site
ok 90 - BmgBI cut
ok 91 - BmgBI complementary_cut
ok
t/Restriction/Analysis.t ............... 
1..182
ok 1 - use Bio::Restriction::Enzyme;
ok 2 - use Bio::Restriction::Enzyme::MultiCut;
ok 3 - use Bio::Restriction::Enzyme::MultiSite;
ok 4 - use Bio::Restriction::EnzymeCollection;
ok 5 - use Bio::Restriction::Analysis;
ok 6 - use Bio::SeqIO;
ok 7
ok 8 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::EnzymeI'
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - bug 2179
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76 - An object of class 'Bio::Restriction::Enzyme::MultiSite' isa 'Bio::Restriction::EnzymeI'
ok 77 - An object of class 'Bio::Restriction::Enzyme::MultiSite' isa 'Bio::Restriction::EnzymeI'
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87 - An object of class 'Bio::Restriction::Enzyme::MultiCut' isa 'Bio::Restriction::EnzymeI'
ok 88 - An object of class 'Bio::Restriction::Enzyme::MultiCut' isa 'Bio::Restriction::EnzymeI'
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::Enzyme'
ok 100
ok 101
ok 102 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::Enzyme'
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118 - number of unique cutters
ok 119 - number of RsaI fragments
ok 120 - number of maximum cutters
ok 121 - number of zero cutters
ok 122 - number of cutters
ok 123 - number of 3x cutters
ok 124 - 4 MseI fragments
ok 125 - 3 MseI cut sites
ok 126 - expected 2 PspEI fragments
ok 127
ok 128
ok 129 - expected 2 sizes for PspEI
ok 130
ok 131 - expected 2 sizes for PspEI
ok 132
ok 133 - not circular expected 1 fragments for MwoI as it doesnt cut
ok 134
ok 135
ok 136 - number of RsaI fragments
ok 137 - 3 circular MseI fragments
ok 138 - 3 circular MseI cut sites
ok 139 - number for AciI a non-palindromic enzyme
ok 140 - 1 fragment for MwoI as it cuts across the circ point
ok 141
ok 142
ok 143
ok 144
ok 145 - 7 fragments in the multiple digest
ok 146 - 7 positions in the multiple digest
ok 147 - 7 sizes in the multiple digest
ok 148
ok 149 -  expected 9 cuts for HindI
ok 150 - expect 9 fragment maps for HindI
ok 151 - sequence for GT
ok 152 - start at 40
ok 153 - end at 41
ok 154 - sequence for GGATTAAAAAAAGAGT
ok 155 - start at 42
ok 156 - end at 57
ok 157 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT
ok 158 - start at 58
ok 159 - end at 92
ok 160 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA
ok 161 - start at 93
ok 162 - end at 123
ok 163 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA
ok 164 - start at 124
ok 165 - end at 155
ok 166 - sequence for CAGACAGATAAAAATTACAGAGTACA
ok 167 - start at 156
ok 168 - end at 181
ok 169 - sequence for CAACATCCATGAAACGCATTAGCA
ok 170 - start at 182
ok 171 - end at 205
ok 172 - sequence for CCA
ok 173 - start at 206
ok 174 - end at 208
ok 175 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT
ok 176 - start at 209
ok 177 - end at 39
ok 178
ok 179 - bug 2139
ok 180 - number of HindIII fragments
ok 181 - number of EcoRI fragments
ok 182 - number of RsaI fragments
ok
t/Restriction/Gel.t .................... 
1..9
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Tools::Gel;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
t/Restriction/IO.t ..................... 
1..17
ok 1 - use Bio::Restriction::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 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok
t/Root/Exception.t ..................... 
1..7
ok 1 - use Bio::Root::TestObject;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/IO.t ............................ 
1..154
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO'
ok 4 - Throw
ok 5 - threw Regexp ((?^:Testing throw))
ok 6 - Warn
ok 7 - threw Regexp ((?^:Testing throw))
ok 8 - Stack trace
ok 9
ok 10 - Verbosity
ok 11
ok 12
ok 13
ok 14 - executable file
ok 15 - non-executable file
ok 16 - executable dir
ok 17
ok 18
ok 19
ok 20 - Read from file
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - Write to file
ok 31
ok 32
ok 33
ok 34
ok 35 - Read+write to file
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - Read from File::Temp handle
ok 47 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO'
ok 48 - is a write handle
ok 49 - no warnings in ->close()
ok 50
ok 51 - Exclusive arguments
ok 52 - threw Regexp ((?^:Input file given twice))
ok 53 - threw Regexp ((?^:File or filehandle provided with -string))
ok 54 - threw Regexp ((?^:Providing both a file and a filehandle for reading))
ok 55 - threw Regexp ((?^:File or filehandle provided with -string))
ok 56 - threw Regexp ((?^:File or filehandle provided with -string))
ok 57 - Same file
ok 58 - Pushback
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 - _print
ok 72
ok 73 - _insert at middle of file
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - _insert in empty file
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 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: #
ok 110
ok 111
ok 112 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: #
ok 113
ok 114
ok 115 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: #
ok 116
ok 117
ok 118 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: #
ok 119
ok 120
ok 121
ok 122 - Bio::Root::IO->new can handle a Path::Class object
ok 123 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO'
ok 124 - Read string
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO'
ok 137 - A reference of type 'GLOB' isa 'GLOB'
ok 138
ok 139
ok 140 - auto UNLINK => 1
ok 141
ok 142
ok 143 - tempfile deleted
ok 144 - A reference of type 'GLOB' isa 'GLOB'
ok 145
ok 146 - UNLINK => 0
ok 147
ok 148
ok 149 - A reference of type 'GLOB' isa 'GLOB'
ok 150 - tempfile suffix
ok 151
ok 152 - A reference of type 'GLOB' isa 'GLOB'
ok 153 - tempfile() in scalar context
ok 154
ok
t/Root/RootI.t ......................... 
1..61
ok 1 - use Bio::Root::Root;
ok 2
ok 3 - An object of class 'Bio::Root::Root' isa 'Bio::Root::RootI'
ok 4 - threw Regexp ((?^:Testing throw))
ok 5 - threw Regexp ((?^:EXCEPTION: Bio::Root::NotImplemented))
ok 6 - threw Regexp ((?^:EXCEPTION ))
ok 7 - threw Regexp ((?^:Testing throw))
ok 8
ok 9 - threw Regexp ((?^:Testing throw))
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - simple
ok 16
ok 17 - warns for versions below current version
ok 18 - warns for versions below current version
ok 19 - throws for versions above current version
ok 20 - throws for versions above current version
ok 21 - throws for versions equal to current version
ok 22 - simple
ok 23 - simple
ok 24 - warns for versions below current version
ok 25 - warns for versions below current version
ok 26 - throws for versions above current version
ok 27 - throws for versions above current version
ok 28 - arg callable since method was created
ok 29 - mal-formed arg callable since method was created with good name
ok 30 - Bio::Foo2->can('t3')
ok 31 - Methods don't pollute original Bio::Root::Root namespace
ok 32 - Bio::Foo2->can('test_4')
ok 33 - Methods don't pollute original Bio::Root::Root namespace
ok 34 - Bio::Foo3->can('t5')
ok 35 - arg not in method list not created
ok 36 - Bio::Foo3->can('t5')
ok 37 - Methods don't pollute original Bio::Root::Root namespace
ok 38 - verbose was set correctly
ok 39 - synonym was set correctly
ok 40 - real method of synonym was set correctly
ok 41 - mal-formed arg correctly resolved to created method
ok 42 - synonym of set method was set correctly
ok 43 - Bio::Foo4->can('t7')
ok 44 - Methods don't pollute original Bio::Root::Root namespace
ok 45 - Bio::Foo4->can('test7')
ok 46 - Methods don't pollute original Bio::Root::Root namespace
ok 47 - Bio::Foo4->can('test_8')
ok 48 - Methods don't pollute original Bio::Root::Root namespace
ok 49 - Bio::Foo4->can('t8')
ok 50 - Methods don't pollute original Bio::Root::Root namespace
ok 51 - clone
ok 52 - clone
ok 53 - clone
ok 54 - clone changed, original didn't
ok 55 - parameters passed to clone() modify object
ok 56 - original is not modified
ok 57 - warns for versions >= current version
ok 58 - warns for versions >= current version
ok 59 - throws for versions >= current version
ok 60 - throws for versions >= current version
ok 61 - No warnings/exceptions below current version
ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/Root/Storable.t ...................... 
1..35
ok 1 - use Bio::Root::Storable;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip.exe' found. Using C:\cygwin\bin/gzip.exe.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip.exe' found. Using C:\cygwin\bin/gzip.exe.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip.exe' found. Using C:\cygwin\bin/gzip.exe.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip.exe' found. Using C:\cygwin\bin/gzip.exe.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip.exe' found. Using C:\cygwin\bin/gzip.exe.
---------------------------------------------------
t/Root/Utilities.t ..................... 
1..56
ok 1 - use Bio::Root::Utilities;
ok 2 - An object of class 'Bio::Root::Utilities' isa 'Bio::Root::Utilities'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - file_date()
ok 38 - unix (\n or 012 or ^J)
ok 39 - date format
ok 40 - date format
ok 41 - date format
ok 42 - date format
ok 43 - date format
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t ............... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
t/SearchIO/SearchIO.t .................. 
1..19
ok 1 - use Bio::SearchIO;
ok 2 - blastxml for f.xml
ok 3 - exonerate for f.exon
ok 4 - fasta for f.osearch
ok 5 - blast for f.blx
ok 6 - blast for f.tblx
ok 7 - blast for filename.bls
ok 8 - fasta for f.fy
ok 9 - blastxml for f.blastxml
ok 10 - fasta for f.fa
ok 11 - fasta for f.ssearch
ok 12 - fasta for f.psearch
ok 13 - exonerate for f.exonerate
ok 14 - fasta for f.SSEARCH.m9
ok 15 - fasta for f.fasta
ok 16 - blast for filename.blast
ok 17 - blast for fast.bls
ok 18 - fasta for f.fx
ok 19 - fasta for f.m9
ok
t/SearchIO/SimilarityPair.t ............ 
1..12
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 5
ok 6 - An object of class 'Bio::SearchIO::blast' isa 'Bio::SearchIO'
ok 7
ok 8 - An object of class 'Bio::Search::Hit::BlastHit' isa 'Bio::Search::Hit::HitI'
ok 9
ok 10 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::SeqFeatureI'
ok 11
ok 12
ok
t/SearchIO/Tiling.t .................... 
1..1141
ok 1 - use Bio::Search::Tiling::MapTiling;
ok 2 - use Bio::Search::Tiling::MapTileUtils;
ok 3 - use Bio::SearchIO;
ok 4 - use Bio::Search::Hit::BlastHit;
ok 5 - use File::Spec;
ok 6 - parse data file
ok 7 - got test hit
ok 8 - create tiling
ok 9 - An object of class 'Bio::Search::Tiling::MapTiling' isa 'Bio::Search::Tiling::TilingI'
ok 10 - implements 'next_tiling'
ok 11 - implements 'rewind_tilings'
ok 12 - implements 'identities'
ok 13 - implements 'conserved'
ok 14 - implements 'length'
ok 15 - identities regression test
ok 16 - conserved regression test
ok 17 - tiling iterator regression test(1)
ok 18 - tiling iterator regression test(2)
ok 19 - tiling iterator regression test(3, rewind)
ok 20 - ecolitst.wublastp
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - dnaEbsub_ecoli.wublastx
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36 - tricky.wublast
ok 37 - tricky.wublast(1)
ok 38 - tricky.wublast(2)
ok 39 - tricky.wublast(3)
ok 40 - tricky.wublast(4)
ok 41 - ecolitst.bls
ok 42 - tile ecolitst.bls hit 1 \#hsps 1
ok 43 - q id: est (0.98293) = fast (0.98293)
ok 44 - q cn: est (0.98293) = fast (0.98293)
ok 45 - h id: est (0.98293) = fast (0.98293)
ok 46 - h cn: est (0.98293) = fast (0.98293)
ok 47 - tile ecolitst.bls hit 2 \#hsps 1
ok 48 - q id: est (0.30074) = fast (0.30074)
ok 49 - q cn: est (0.49876) = fast (0.49876)
ok 50 - h id: est (0.30759) = fast (0.30759)
ok 51 - h cn: est (0.51013) = fast (0.51013)
ok 52 - tile ecolitst.bls hit 3 \#hsps 1
ok 53 - q id: est (0.31004) = fast (0.31004)
ok 54 - q cn: est (0.49782) = fast (0.49782)
ok 55 - h id: est (0.32054) = fast (0.32054)
ok 56 - h cn: est (0.51467) = fast (0.51467)
ok 57 - tile ecolitst.bls hit 4 \#hsps 1
ok 58 - q id: est (0.30435) = fast (0.30435)
ok 59 - q cn: est (0.47826) = fast (0.47826)
ok 60 - h id: est (0.29787) = fast (0.29787)
ok 61 - h cn: est (0.46809) = fast (0.46809)
ok 62 - tricky.wublast
ok 63 - tile tricky.wublast hit 1 \#hsps 7
ok 64 - q id: exact (0.22153) ~ est (0.22153)
ok 65 - q id: exact (0.22153) <= max (0.22153)
ok 66 - q cn: exact (0.42760) ~ est (0.42760)
ok 67 - q cn: exact (0.42760) <= max (0.42760)
ok 68 - h id: exact (0.22704) ~ est (0.22704)
ok 69 - h id: exact (0.22704) <= max (0.22704)
ok 70 - h cn: exact (0.43335) ~ est (0.43335)
ok 71 - h cn: exact (0.43335) <= max (0.43335)
ok 72 - a_thaliana.blastn
ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1
ok 74 - q id: est (0.96667) = fast (0.96667)
ok 75 - q cn: est (0.96667) = fast (0.96667)
ok 76 - h id: est (0.98305) = fast (0.98305)
ok 77 - h cn: est (0.98305) = fast (0.98305)
ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1
ok 79 - q id: est (0.96667) = fast (0.96667)
ok 80 - q cn: est (0.96667) = fast (0.96667)
ok 81 - h id: est (0.98305) = fast (0.98305)
ok 82 - h cn: est (0.98305) = fast (0.98305)
ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1
ok 84 - q id: est (1.00000) = fast (1.00000)
ok 85 - q cn: est (1.00000) = fast (1.00000)
ok 86 - h id: est (1.00000) = fast (1.00000)
ok 87 - h cn: est (1.00000) = fast (1.00000)
ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1
ok 89 - q id: est (1.00000) = fast (1.00000)
ok 90 - q cn: est (1.00000) = fast (1.00000)
ok 91 - h id: est (1.00000) = fast (1.00000)
ok 92 - h cn: est (1.00000) = fast (1.00000)
ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1
ok 94 - q id: est (0.92308) = fast (0.92308)
ok 95 - q cn: est (0.92308) = fast (0.92308)
ok 96 - h id: est (0.92308) = fast (0.92308)
ok 97 - h cn: est (0.92308) = fast (0.92308)
ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1
ok 99 - q id: est (1.00000) = fast (1.00000)
ok 100 - q cn: est (1.00000) = fast (1.00000)
ok 101 - h id: est (1.00000) = fast (1.00000)
ok 102 - h cn: est (1.00000) = fast (1.00000)
ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1
ok 104 - q id: est (1.00000) = fast (1.00000)
ok 105 - q cn: est (1.00000) = fast (1.00000)
ok 106 - h id: est (1.00000) = fast (1.00000)
ok 107 - h cn: est (1.00000) = fast (1.00000)
ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1
ok 109 - q id: est (1.00000) = fast (1.00000)
ok 110 - q cn: est (1.00000) = fast (1.00000)
ok 111 - h id: est (1.00000) = fast (1.00000)
ok 112 - h cn: est (1.00000) = fast (1.00000)
ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1
ok 114 - q id: est (1.00000) = fast (1.00000)
ok 115 - q cn: est (1.00000) = fast (1.00000)
ok 116 - h id: est (1.00000) = fast (1.00000)
ok 117 - h cn: est (1.00000) = fast (1.00000)
ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1
ok 119 - q id: est (1.00000) = fast (1.00000)
ok 120 - q cn: est (1.00000) = fast (1.00000)
ok 121 - h id: est (1.00000) = fast (1.00000)
ok 122 - h cn: est (1.00000) = fast (1.00000)
ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1
ok 124 - q id: est (1.00000) = fast (1.00000)
ok 125 - q cn: est (1.00000) = fast (1.00000)
ok 126 - h id: est (1.00000) = fast (1.00000)
ok 127 - h cn: est (1.00000) = fast (1.00000)
ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1
ok 129 - q id: est (1.00000) = fast (1.00000)
ok 130 - q cn: est (1.00000) = fast (1.00000)
ok 131 - h id: est (1.00000) = fast (1.00000)
ok 132 - h cn: est (1.00000) = fast (1.00000)
ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1
ok 134 - q id: est (1.00000) = fast (1.00000)
ok 135 - q cn: est (1.00000) = fast (1.00000)
ok 136 - h id: est (1.00000) = fast (1.00000)
ok 137 - h cn: est (1.00000) = fast (1.00000)
ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1
ok 139 - q id: est (1.00000) = fast (1.00000)
ok 140 - q cn: est (1.00000) = fast (1.00000)
ok 141 - h id: est (1.00000) = fast (1.00000)
ok 142 - h cn: est (1.00000) = fast (1.00000)
ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1
ok 144 - q id: est (1.00000) = fast (1.00000)
ok 145 - q cn: est (1.00000) = fast (1.00000)
ok 146 - h id: est (1.00000) = fast (1.00000)
ok 147 - h cn: est (1.00000) = fast (1.00000)
ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1
ok 149 - q id: est (1.00000) = fast (1.00000)
ok 150 - q cn: est (1.00000) = fast (1.00000)
ok 151 - h id: est (1.00000) = fast (1.00000)
ok 152 - h cn: est (1.00000) = fast (1.00000)
ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1
ok 154 - q id: est (1.00000) = fast (1.00000)
ok 155 - q cn: est (1.00000) = fast (1.00000)
ok 156 - h id: est (1.00000) = fast (1.00000)
ok 157 - h cn: est (1.00000) = fast (1.00000)
ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1
ok 159 - q id: est (1.00000) = fast (1.00000)
ok 160 - q cn: est (1.00000) = fast (1.00000)
ok 161 - h id: est (1.00000) = fast (1.00000)
ok 162 - h cn: est (1.00000) = fast (1.00000)
ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1
ok 164 - q id: est (1.00000) = fast (1.00000)
ok 165 - q cn: est (1.00000) = fast (1.00000)
ok 166 - h id: est (1.00000) = fast (1.00000)
ok 167 - h cn: est (1.00000) = fast (1.00000)
ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1
ok 169 - q id: est (0.95238) = fast (0.95238)
ok 170 - q cn: est (0.95238) = fast (0.95238)
ok 171 - h id: est (0.95238) = fast (0.95238)
ok 172 - h cn: est (0.95238) = fast (0.95238)
ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1
ok 174 - q id: est (1.00000) = fast (1.00000)
ok 175 - q cn: est (1.00000) = fast (1.00000)
ok 176 - h id: est (1.00000) = fast (1.00000)
ok 177 - h cn: est (1.00000) = fast (1.00000)
ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1
ok 179 - q id: est (0.95238) = fast (0.95238)
ok 180 - q cn: est (0.95238) = fast (0.95238)
ok 181 - h id: est (0.95238) = fast (0.95238)
ok 182 - h cn: est (0.95238) = fast (0.95238)
ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1
ok 184 - q id: est (1.00000) = fast (1.00000)
ok 185 - q cn: est (1.00000) = fast (1.00000)
ok 186 - h id: est (1.00000) = fast (1.00000)
ok 187 - h cn: est (1.00000) = fast (1.00000)
ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1
ok 189 - q id: est (0.95238) = fast (0.95238)
ok 190 - q cn: est (0.95238) = fast (0.95238)
ok 191 - h id: est (0.95238) = fast (0.95238)
ok 192 - h cn: est (0.95238) = fast (0.95238)
ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1
ok 194 - q id: est (1.00000) = fast (1.00000)
ok 195 - q cn: est (1.00000) = fast (1.00000)
ok 196 - h id: est (1.00000) = fast (1.00000)
ok 197 - h cn: est (1.00000) = fast (1.00000)
ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1
ok 199 - q id: est (1.00000) = fast (1.00000)
ok 200 - q cn: est (1.00000) = fast (1.00000)
ok 201 - h id: est (1.00000) = fast (1.00000)
ok 202 - h cn: est (1.00000) = fast (1.00000)
ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1
ok 204 - q id: est (1.00000) = fast (1.00000)
ok 205 - q cn: est (1.00000) = fast (1.00000)
ok 206 - h id: est (1.00000) = fast (1.00000)
ok 207 - h cn: est (1.00000) = fast (1.00000)
ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1
ok 209 - q id: est (1.00000) = fast (1.00000)
ok 210 - q cn: est (1.00000) = fast (1.00000)
ok 211 - h id: est (1.00000) = fast (1.00000)
ok 212 - h cn: est (1.00000) = fast (1.00000)
ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1
ok 214 - q id: est (1.00000) = fast (1.00000)
ok 215 - q cn: est (1.00000) = fast (1.00000)
ok 216 - h id: est (1.00000) = fast (1.00000)
ok 217 - h cn: est (1.00000) = fast (1.00000)
ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1
ok 219 - q id: est (1.00000) = fast (1.00000)
ok 220 - q cn: est (1.00000) = fast (1.00000)
ok 221 - h id: est (1.00000) = fast (1.00000)
ok 222 - h cn: est (1.00000) = fast (1.00000)
ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1
ok 224 - q id: est (1.00000) = fast (1.00000)
ok 225 - q cn: est (1.00000) = fast (1.00000)
ok 226 - h id: est (1.00000) = fast (1.00000)
ok 227 - h cn: est (1.00000) = fast (1.00000)
ok 228 - brassica_ATH.WUBLASTN
ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3
ok 230 - q id: exact (0.82465) ~ est (0.82343)
ok 231 - q id: exact (0.82465) <= max (0.83333)
ok 232 - q cn: exact (0.85590) ~ est (0.85312)
ok 233 - q cn: exact (0.85590) <= max (0.86458)
ok 234 - h id: exact (0.83920) ~ est (0.83920)
ok 235 - h id: exact (0.83920) <= max (0.83920)
ok 236 - h cn: exact (0.86935) ~ est (0.86935)
ok 237 - h cn: exact (0.86935) <= max (0.86935)
ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2
ok 239 - q id: exact (0.82486) ~ est (0.82486)
ok 240 - q id: exact (0.82486) <= max (0.82486)
ok 241 - q cn: exact (0.85122) ~ est (0.85122)
ok 242 - q cn: exact (0.85122) <= max (0.85122)
ok 243 - h id: exact (0.82955) ~ est (0.82955)
ok 244 - h id: exact (0.82955) <= max (0.82955)
ok 245 - h cn: exact (0.85606) ~ est (0.85606)
ok 246 - h cn: exact (0.85606) <= max (0.85606)
ok 247 - no_hsps.blastp
ok 248 - tile no_hsps.blastp hit 1 \#hsps 0
ok 249 - tile no_hsps.blastp hit 2 \#hsps 0
ok 250 - tile no_hsps.blastp hit 3 \#hsps 0
ok 251 - tile no_hsps.blastp hit 4 \#hsps 0
ok 252 - tile no_hsps.blastp hit 5 \#hsps 0
ok 253 - tile no_hsps.blastp hit 6 \#hsps 0
ok 254 - tile no_hsps.blastp hit 7 \#hsps 0
ok 255 - tile no_hsps.blastp hit 8 \#hsps 0
ok 256 - tile no_hsps.blastp hit 9 \#hsps 0
ok 257 - tile no_hsps.blastp hit 10 \#hsps 0
ok 258 - tile no_hsps.blastp hit 11 \#hsps 0
ok 259 - tile no_hsps.blastp hit 12 \#hsps 0
ok 260 - tile no_hsps.blastp hit 13 \#hsps 0
ok 261 - tile no_hsps.blastp hit 14 \#hsps 0
ok 262 - tile no_hsps.blastp hit 15 \#hsps 0
ok 263 - tile no_hsps.blastp hit 16 \#hsps 0
ok 264 - tile no_hsps.blastp hit 17 \#hsps 0
ok 265 - tile no_hsps.blastp hit 18 \#hsps 0
ok 266 - tile no_hsps.blastp hit 19 \#hsps 0
ok 267 - tile no_hsps.blastp hit 20 \#hsps 0
ok 268 - tile no_hsps.blastp hit 21 \#hsps 0
ok 269 - tile no_hsps.blastp hit 22 \#hsps 0
ok 270 - tile no_hsps.blastp hit 23 \#hsps 0
ok 271 - tile no_hsps.blastp hit 24 \#hsps 0
ok 272 - tile no_hsps.blastp hit 25 \#hsps 0
ok 273 - tile no_hsps.blastp hit 26 \#hsps 0
ok 274 - tile no_hsps.blastp hit 27 \#hsps 0
ok 275 - tile no_hsps.blastp hit 28 \#hsps 0
ok 276 - tile no_hsps.blastp hit 29 \#hsps 0
ok 277 - tile no_hsps.blastp hit 30 \#hsps 0
ok 278 - tile no_hsps.blastp hit 31 \#hsps 0
ok 279 - tile no_hsps.blastp hit 32 \#hsps 0
ok 280 - tile no_hsps.blastp hit 33 \#hsps 0
ok 281 - tile no_hsps.blastp hit 34 \#hsps 0
ok 282 - tile no_hsps.blastp hit 35 \#hsps 0
ok 283 - tile no_hsps.blastp hit 36 \#hsps 0
ok 284 - tile no_hsps.blastp hit 37 \#hsps 0
ok 285 - tile no_hsps.blastp hit 38 \#hsps 0
ok 286 - tile no_hsps.blastp hit 39 \#hsps 0
ok 287 - tile no_hsps.blastp hit 40 \#hsps 0
ok 288 - tile no_hsps.blastp hit 41 \#hsps 0
ok 289 - tile no_hsps.blastp hit 42 \#hsps 0
ok 290 - tile no_hsps.blastp hit 43 \#hsps 0
ok 291 - tile no_hsps.blastp hit 44 \#hsps 0
ok 292 - tile no_hsps.blastp hit 45 \#hsps 0
ok 293 - tile no_hsps.blastp hit 46 \#hsps 0
ok 294 - tile no_hsps.blastp hit 47 \#hsps 0
ok 295 - tile no_hsps.blastp hit 48 \#hsps 0
ok 296 - tile no_hsps.blastp hit 49 \#hsps 0
ok 297 - tile no_hsps.blastp hit 50 \#hsps 0
ok 298 - tile no_hsps.blastp hit 51 \#hsps 0
ok 299 - tile no_hsps.blastp hit 52 \#hsps 0
ok 300 - tile no_hsps.blastp hit 53 \#hsps 0
ok 301 - tile no_hsps.blastp hit 54 \#hsps 0
ok 302 - tile no_hsps.blastp hit 55 \#hsps 0
ok 303 - tile no_hsps.blastp hit 56 \#hsps 0
ok 304 - tile no_hsps.blastp hit 57 \#hsps 0
ok 305 - tile no_hsps.blastp hit 58 \#hsps 0
ok 306 - tile no_hsps.blastp hit 59 \#hsps 0
ok 307 - tile no_hsps.blastp hit 60 \#hsps 0
ok 308 - tile no_hsps.blastp hit 61 \#hsps 0
ok 309 - tile no_hsps.blastp hit 62 \#hsps 0
ok 310 - tile no_hsps.blastp hit 63 \#hsps 0
ok 311 - tile no_hsps.blastp hit 64 \#hsps 0
ok 312 - tile no_hsps.blastp hit 65 \#hsps 0
ok 313 - tile no_hsps.blastp hit 66 \#hsps 0
ok 314 - tile no_hsps.blastp hit 67 \#hsps 0
ok 315 - tile no_hsps.blastp hit 68 \#hsps 0
ok 316 - tile no_hsps.blastp hit 69 \#hsps 0
ok 317 - tile no_hsps.blastp hit 70 \#hsps 0
ok 318 - tile no_hsps.blastp hit 71 \#hsps 0
ok 319 - tile no_hsps.blastp hit 72 \#hsps 0
ok 320 - tile no_hsps.blastp hit 73 \#hsps 0
ok 321 - tile no_hsps.blastp hit 74 \#hsps 0
ok 322 - tile no_hsps.blastp hit 75 \#hsps 0
ok 323 - tile no_hsps.blastp hit 76 \#hsps 0
ok 324 - tile no_hsps.blastp hit 77 \#hsps 0
ok 325 - tile no_hsps.blastp hit 78 \#hsps 0
ok 326 - tile no_hsps.blastp hit 79 \#hsps 0
ok 327 - tile no_hsps.blastp hit 80 \#hsps 0
ok 328 - tile no_hsps.blastp hit 81 \#hsps 0
ok 329 - tile no_hsps.blastp hit 82 \#hsps 0
ok 330 - tile no_hsps.blastp hit 83 \#hsps 0
ok 331 - tile no_hsps.blastp hit 84 \#hsps 0
ok 332 - tile no_hsps.blastp hit 85 \#hsps 0
ok 333 - tile no_hsps.blastp hit 86 \#hsps 0
ok 334 - tile no_hsps.blastp hit 87 \#hsps 0
ok 335 - tile no_hsps.blastp hit 88 \#hsps 0
ok 336 - tile no_hsps.blastp hit 89 \#hsps 0
ok 337 - tile no_hsps.blastp hit 90 \#hsps 0
ok 338 - tile no_hsps.blastp hit 91 \#hsps 0
ok 339 - tile no_hsps.blastp hit 92 \#hsps 0
ok 340 - tile no_hsps.blastp hit 93 \#hsps 0
ok 341 - tile no_hsps.blastp hit 94 \#hsps 0
ok 342 - tile no_hsps.blastp hit 95 \#hsps 0
ok 343 - tile no_hsps.blastp hit 96 \#hsps 0
ok 344 - tile no_hsps.blastp hit 97 \#hsps 0
ok 345 - tile no_hsps.blastp hit 98 \#hsps 0
ok 346 - tile no_hsps.blastp hit 99 \#hsps 0
ok 347 - tile no_hsps.blastp hit 100 \#hsps 0
ok 348 - tile no_hsps.blastp hit 101 \#hsps 0
ok 349 - tile no_hsps.blastp hit 102 \#hsps 0
ok 350 - tile no_hsps.blastp hit 103 \#hsps 0
ok 351 - tile no_hsps.blastp hit 104 \#hsps 0
ok 352 - tile no_hsps.blastp hit 105 \#hsps 0
ok 353 - tile no_hsps.blastp hit 106 \#hsps 0
ok 354 - tile no_hsps.blastp hit 107 \#hsps 0
ok 355 - tile no_hsps.blastp hit 108 \#hsps 0
ok 356 - tile no_hsps.blastp hit 109 \#hsps 0
ok 357 - tile no_hsps.blastp hit 110 \#hsps 0
ok 358 - tile no_hsps.blastp hit 111 \#hsps 0
ok 359 - tile no_hsps.blastp hit 112 \#hsps 0
ok 360 - tile no_hsps.blastp hit 113 \#hsps 0
ok 361 - tile no_hsps.blastp hit 114 \#hsps 0
ok 362 - tile no_hsps.blastp hit 115 \#hsps 0
ok 363 - tile no_hsps.blastp hit 116 \#hsps 0
ok 364 - tile no_hsps.blastp hit 117 \#hsps 0
ok 365 - tile no_hsps.blastp hit 118 \#hsps 0
ok 366 - tile no_hsps.blastp hit 119 \#hsps 0
ok 367 - tile no_hsps.blastp hit 120 \#hsps 0
ok 368 - tile no_hsps.blastp hit 121 \#hsps 0
ok 369 - tile no_hsps.blastp hit 122 \#hsps 0
ok 370 - tile no_hsps.blastp hit 123 \#hsps 0
ok 371 - tile no_hsps.blastp hit 124 \#hsps 0
ok 372 - tile no_hsps.blastp hit 125 \#hsps 0
ok 373 - tile no_hsps.blastp hit 126 \#hsps 0
ok 374 - tile no_hsps.blastp hit 127 \#hsps 0
ok 375 - tile no_hsps.blastp hit 128 \#hsps 0
ok 376 - tile no_hsps.blastp hit 129 \#hsps 0
ok 377 - tile no_hsps.blastp hit 130 \#hsps 0
ok 378 - tile no_hsps.blastp hit 131 \#hsps 0
ok 379 - tile no_hsps.blastp hit 132 \#hsps 0
ok 380 - tile no_hsps.blastp hit 133 \#hsps 0
ok 381 - tile no_hsps.blastp hit 134 \#hsps 0
ok 382 - tile no_hsps.blastp hit 135 \#hsps 0
ok 383 - tile no_hsps.blastp hit 136 \#hsps 0
ok 384 - tile no_hsps.blastp hit 137 \#hsps 0
ok 385 - tile no_hsps.blastp hit 138 \#hsps 0
ok 386 - tile no_hsps.blastp hit 139 \#hsps 0
ok 387 - tile no_hsps.blastp hit 140 \#hsps 0
ok 388 - tile no_hsps.blastp hit 141 \#hsps 0
ok 389 - tile no_hsps.blastp hit 142 \#hsps 0
ok 390 - tile no_hsps.blastp hit 143 \#hsps 0
ok 391 - tile no_hsps.blastp hit 144 \#hsps 0
ok 392 - tile no_hsps.blastp hit 145 \#hsps 0
ok 393 - tile no_hsps.blastp hit 146 \#hsps 0
ok 394 - tile no_hsps.blastp hit 147 \#hsps 0
ok 395 - tile no_hsps.blastp hit 148 \#hsps 0
ok 396 - tile no_hsps.blastp hit 149 \#hsps 0
ok 397 - tile no_hsps.blastp hit 150 \#hsps 0
ok 398 - tile no_hsps.blastp hit 151 \#hsps 0
ok 399 - tile no_hsps.blastp hit 152 \#hsps 0
ok 400 - tile no_hsps.blastp hit 153 \#hsps 0
ok 401 - tile no_hsps.blastp hit 154 \#hsps 0
ok 402 - tile no_hsps.blastp hit 155 \#hsps 0
ok 403 - tile no_hsps.blastp hit 156 \#hsps 0
ok 404 - tile no_hsps.blastp hit 157 \#hsps 0
ok 405 - tile no_hsps.blastp hit 158 \#hsps 0
ok 406 - tile no_hsps.blastp hit 159 \#hsps 0
ok 407 - tile no_hsps.blastp hit 160 \#hsps 0
ok 408 - tile no_hsps.blastp hit 161 \#hsps 0
ok 409 - tile no_hsps.blastp hit 162 \#hsps 0
ok 410 - tile no_hsps.blastp hit 163 \#hsps 0
ok 411 - tile no_hsps.blastp hit 164 \#hsps 0
ok 412 - tile no_hsps.blastp hit 165 \#hsps 0
ok 413 - tile no_hsps.blastp hit 166 \#hsps 0
ok 414 - tile no_hsps.blastp hit 167 \#hsps 0
ok 415 - tile no_hsps.blastp hit 168 \#hsps 0
ok 416 - tile no_hsps.blastp hit 169 \#hsps 0
ok 417 - tile no_hsps.blastp hit 170 \#hsps 0
ok 418 - tile no_hsps.blastp hit 171 \#hsps 0
ok 419 - tile no_hsps.blastp hit 172 \#hsps 0
ok 420 - tile no_hsps.blastp hit 173 \#hsps 0
ok 421 - tile no_hsps.blastp hit 174 \#hsps 0
ok 422 - tile no_hsps.blastp hit 175 \#hsps 0
ok 423 - tile no_hsps.blastp hit 176 \#hsps 0
ok 424 - tile no_hsps.blastp hit 177 \#hsps 0
ok 425 - tile no_hsps.blastp hit 178 \#hsps 0
ok 426 - tile no_hsps.blastp hit 179 \#hsps 0
ok 427 - tile no_hsps.blastp hit 180 \#hsps 0
ok 428 - tile no_hsps.blastp hit 181 \#hsps 0
ok 429 - tile no_hsps.blastp hit 182 \#hsps 0
ok 430 - tile no_hsps.blastp hit 183 \#hsps 0
ok 431 - tile no_hsps.blastp hit 184 \#hsps 0
ok 432 - tile no_hsps.blastp hit 185 \#hsps 0
ok 433 - tile no_hsps.blastp hit 186 \#hsps 0
ok 434 - tile no_hsps.blastp hit 187 \#hsps 0
ok 435 - tile no_hsps.blastp hit 188 \#hsps 0
ok 436 - tile no_hsps.blastp hit 189 \#hsps 0
ok 437 - tile no_hsps.blastp hit 190 \#hsps 0
ok 438 - tile no_hsps.blastp hit 191 \#hsps 0
ok 439 - tile no_hsps.blastp hit 192 \#hsps 0
ok 440 - tile no_hsps.blastp hit 193 \#hsps 0
ok 441 - tile no_hsps.blastp hit 194 \#hsps 0
ok 442 - tile no_hsps.blastp hit 195 \#hsps 0
ok 443 - tile no_hsps.blastp hit 196 \#hsps 0
ok 444 - tile no_hsps.blastp hit 197 \#hsps 0
ok 445 - tile no_hsps.blastp hit 198 \#hsps 0
ok 446 - tile no_hsps.blastp hit 199 \#hsps 0
ok 447 - tile no_hsps.blastp hit 200 \#hsps 0
ok 448 - tile no_hsps.blastp hit 201 \#hsps 0
ok 449 - tile no_hsps.blastp hit 202 \#hsps 0
ok 450 - tile no_hsps.blastp hit 203 \#hsps 0
ok 451 - tile no_hsps.blastp hit 204 \#hsps 0
ok 452 - tile no_hsps.blastp hit 205 \#hsps 0
ok 453 - tile no_hsps.blastp hit 206 \#hsps 0
ok 454 - tile no_hsps.blastp hit 207 \#hsps 0
ok 455 - tile no_hsps.blastp hit 208 \#hsps 0
ok 456 - tile no_hsps.blastp hit 209 \#hsps 0
ok 457 - tile no_hsps.blastp hit 210 \#hsps 0
ok 458 - tile no_hsps.blastp hit 211 \#hsps 0
ok 459 - tile no_hsps.blastp hit 212 \#hsps 0
ok 460 - tile no_hsps.blastp hit 213 \#hsps 0
ok 461 - tile no_hsps.blastp hit 214 \#hsps 0
ok 462 - tile no_hsps.blastp hit 215 \#hsps 0
ok 463 - tile no_hsps.blastp hit 216 \#hsps 0
ok 464 - tile no_hsps.blastp hit 217 \#hsps 0
ok 465 - tile no_hsps.blastp hit 218 \#hsps 0
ok 466 - tile no_hsps.blastp hit 219 \#hsps 0
ok 467 - tile no_hsps.blastp hit 220 \#hsps 0
ok 468 - tile no_hsps.blastp hit 221 \#hsps 0
ok 469 - tile no_hsps.blastp hit 222 \#hsps 0
ok 470 - tile no_hsps.blastp hit 223 \#hsps 0
ok 471 - tile no_hsps.blastp hit 224 \#hsps 0
ok 472 - tile no_hsps.blastp hit 225 \#hsps 0
ok 473 - tile no_hsps.blastp hit 226 \#hsps 0
ok 474 - tile no_hsps.blastp hit 227 \#hsps 0
ok 475 - tile no_hsps.blastp hit 228 \#hsps 0
ok 476 - tile no_hsps.blastp hit 229 \#hsps 0
ok 477 - tile no_hsps.blastp hit 230 \#hsps 0
ok 478 - tile no_hsps.blastp hit 231 \#hsps 0
ok 479 - tile no_hsps.blastp hit 232 \#hsps 0
ok 480 - tile no_hsps.blastp hit 233 \#hsps 0
ok 481 - tile no_hsps.blastp hit 234 \#hsps 0
ok 482 - tile no_hsps.blastp hit 235 \#hsps 0
ok 483 - tile no_hsps.blastp hit 236 \#hsps 0
ok 484 - tile no_hsps.blastp hit 237 \#hsps 0
ok 485 - tile no_hsps.blastp hit 238 \#hsps 0
ok 486 - tile no_hsps.blastp hit 239 \#hsps 0
ok 487 - tile no_hsps.blastp hit 240 \#hsps 0
ok 488 - tile no_hsps.blastp hit 241 \#hsps 0
ok 489 - tile no_hsps.blastp hit 242 \#hsps 0
ok 490 - tile no_hsps.blastp hit 243 \#hsps 0
ok 491 - tile no_hsps.blastp hit 244 \#hsps 0
ok 492 - tile no_hsps.blastp hit 245 \#hsps 0
ok 493 - tile no_hsps.blastp hit 246 \#hsps 0
ok 494 - tile no_hsps.blastp hit 247 \#hsps 0
ok 495 - tile no_hsps.blastp hit 248 \#hsps 0
ok 496 - tile no_hsps.blastp hit 249 \#hsps 0
ok 497 - tile no_hsps.blastp hit 250 \#hsps 0
ok 498 - tile no_hsps.blastp hit 251 \#hsps 0
ok 499 - tile no_hsps.blastp hit 252 \#hsps 0
ok 500 - tile no_hsps.blastp hit 253 \#hsps 0
ok 501 - tile no_hsps.blastp hit 254 \#hsps 0
ok 502 - tile no_hsps.blastp hit 255 \#hsps 0
ok 503 - tile no_hsps.blastp hit 256 \#hsps 0
ok 504 - tile no_hsps.blastp hit 257 \#hsps 0
ok 505 - tile no_hsps.blastp hit 258 \#hsps 0
ok 506 - tile no_hsps.blastp hit 259 \#hsps 0
ok 507 - tile no_hsps.blastp hit 260 \#hsps 0
ok 508 - tile no_hsps.blastp hit 261 \#hsps 0
ok 509 - tile no_hsps.blastp hit 262 \#hsps 0
ok 510 - tile no_hsps.blastp hit 263 \#hsps 0
ok 511 - tile no_hsps.blastp hit 264 \#hsps 0
ok 512 - tile no_hsps.blastp hit 265 \#hsps 0
ok 513 - tile no_hsps.blastp hit 266 \#hsps 0
ok 514 - tile no_hsps.blastp hit 267 \#hsps 0
ok 515 - tile no_hsps.blastp hit 268 \#hsps 0
ok 516 - tile no_hsps.blastp hit 269 \#hsps 0
ok 517 - tile no_hsps.blastp hit 270 \#hsps 0
ok 518 - tile no_hsps.blastp hit 271 \#hsps 0
ok 519 - tile no_hsps.blastp hit 272 \#hsps 0
ok 520 - tile no_hsps.blastp hit 273 \#hsps 0
ok 521 - tile no_hsps.blastp hit 274 \#hsps 0
ok 522 - tile no_hsps.blastp hit 275 \#hsps 0
ok 523 - tile no_hsps.blastp hit 276 \#hsps 0
ok 524 - tile no_hsps.blastp hit 277 \#hsps 0
ok 525 - tile no_hsps.blastp hit 278 \#hsps 0
ok 526 - tile no_hsps.blastp hit 279 \#hsps 0
ok 527 - tile no_hsps.blastp hit 280 \#hsps 0
ok 528 - tile no_hsps.blastp hit 281 \#hsps 0
ok 529 - tile no_hsps.blastp hit 282 \#hsps 0
ok 530 - tile no_hsps.blastp hit 283 \#hsps 0
ok 531 - tile no_hsps.blastp hit 284 \#hsps 0
ok 532 - tile no_hsps.blastp hit 285 \#hsps 0
ok 533 - tile no_hsps.blastp hit 286 \#hsps 0
ok 534 - tile no_hsps.blastp hit 287 \#hsps 0
ok 535 - tile no_hsps.blastp hit 288 \#hsps 0
ok 536 - tile no_hsps.blastp hit 289 \#hsps 0
ok 537 - tile no_hsps.blastp hit 290 \#hsps 0
ok 538 - tile no_hsps.blastp hit 291 \#hsps 0
ok 539 - tile no_hsps.blastp hit 292 \#hsps 0
ok 540 - tile no_hsps.blastp hit 293 \#hsps 0
ok 541 - tile no_hsps.blastp hit 294 \#hsps 0
ok 542 - tile no_hsps.blastp hit 295 \#hsps 0
ok 543 - tile no_hsps.blastp hit 296 \#hsps 0
ok 544 - tile no_hsps.blastp hit 297 \#hsps 0
ok 545 - tile no_hsps.blastp hit 298 \#hsps 0
ok 546 - tile no_hsps.blastp hit 299 \#hsps 0
ok 547 - tile no_hsps.blastp hit 300 \#hsps 0
ok 548 - tile no_hsps.blastp hit 301 \#hsps 0
ok 549 - tile no_hsps.blastp hit 302 \#hsps 0
ok 550 - tile no_hsps.blastp hit 303 \#hsps 0
ok 551 - tile no_hsps.blastp hit 304 \#hsps 0
ok 552 - tile no_hsps.blastp hit 305 \#hsps 0
ok 553 - tile no_hsps.blastp hit 306 \#hsps 0
ok 554 - tile no_hsps.blastp hit 307 \#hsps 0
ok 555 - tile no_hsps.blastp hit 308 \#hsps 0
ok 556 - tile no_hsps.blastp hit 309 \#hsps 0
ok 557 - tile no_hsps.blastp hit 310 \#hsps 0
ok 558 - tile no_hsps.blastp hit 311 \#hsps 0
ok 559 - tile no_hsps.blastp hit 312 \#hsps 0
ok 560 - tile no_hsps.blastp hit 313 \#hsps 0
ok 561 - tile no_hsps.blastp hit 314 \#hsps 0
ok 562 - tile no_hsps.blastp hit 315 \#hsps 0
ok 563 - tile no_hsps.blastp hit 316 \#hsps 0
ok 564 - tile no_hsps.blastp hit 317 \#hsps 0
ok 565 - tile no_hsps.blastp hit 318 \#hsps 0
ok 566 - tile no_hsps.blastp hit 319 \#hsps 0
ok 567 - tile no_hsps.blastp hit 320 \#hsps 0
ok 568 - tile no_hsps.blastp hit 321 \#hsps 0
ok 569 - tile no_hsps.blastp hit 322 \#hsps 0
ok 570 - tile no_hsps.blastp hit 323 \#hsps 0
ok 571 - tile no_hsps.blastp hit 324 \#hsps 0
ok 572 - tile no_hsps.blastp hit 325 \#hsps 0
ok 573 - tile no_hsps.blastp hit 326 \#hsps 0
ok 574 - tile no_hsps.blastp hit 327 \#hsps 0
ok 575 - tile no_hsps.blastp hit 328 \#hsps 0
ok 576 - tile no_hsps.blastp hit 329 \#hsps 0
ok 577 - tile no_hsps.blastp hit 330 \#hsps 0
ok 578 - tile no_hsps.blastp hit 331 \#hsps 0
ok 579 - tile no_hsps.blastp hit 332 \#hsps 0
ok 580 - tile no_hsps.blastp hit 333 \#hsps 0
ok 581 - tile no_hsps.blastp hit 334 \#hsps 0
ok 582 - tile no_hsps.blastp hit 335 \#hsps 0
ok 583 - tile no_hsps.blastp hit 336 \#hsps 0
ok 584 - tile no_hsps.blastp hit 337 \#hsps 0
ok 585 - tile no_hsps.blastp hit 338 \#hsps 0
ok 586 - tile no_hsps.blastp hit 339 \#hsps 0
ok 587 - tile no_hsps.blastp hit 340 \#hsps 0
ok 588 - tile no_hsps.blastp hit 341 \#hsps 0
ok 589 - tile no_hsps.blastp hit 342 \#hsps 0
ok 590 - tile no_hsps.blastp hit 343 \#hsps 0
ok 591 - tile no_hsps.blastp hit 344 \#hsps 0
ok 592 - tile no_hsps.blastp hit 345 \#hsps 0
ok 593 - tile no_hsps.blastp hit 346 \#hsps 0
ok 594 - tile no_hsps.blastp hit 347 \#hsps 0
ok 595 - tile no_hsps.blastp hit 348 \#hsps 0
ok 596 - tile no_hsps.blastp hit 349 \#hsps 0
ok 597 - tile no_hsps.blastp hit 350 \#hsps 0
ok 598 - tile no_hsps.blastp hit 351 \#hsps 0
ok 599 - tile no_hsps.blastp hit 352 \#hsps 0
ok 600 - tile no_hsps.blastp hit 353 \#hsps 0
ok 601 - tile no_hsps.blastp hit 354 \#hsps 0
ok 602 - tile no_hsps.blastp hit 355 \#hsps 0
ok 603 - tile no_hsps.blastp hit 356 \#hsps 0
ok 604 - tile no_hsps.blastp hit 357 \#hsps 0
ok 605 - tile no_hsps.blastp hit 358 \#hsps 0
ok 606 - tile no_hsps.blastp hit 359 \#hsps 0
ok 607 - tile no_hsps.blastp hit 360 \#hsps 0
ok 608 - tile no_hsps.blastp hit 361 \#hsps 0
ok 609 - tile no_hsps.blastp hit 362 \#hsps 0
ok 610 - tile no_hsps.blastp hit 363 \#hsps 0
ok 611 - tile no_hsps.blastp hit 364 \#hsps 0
ok 612 - tile no_hsps.blastp hit 365 \#hsps 0
ok 613 - tile no_hsps.blastp hit 366 \#hsps 0
ok 614 - tile no_hsps.blastp hit 367 \#hsps 0
ok 615 - tile no_hsps.blastp hit 368 \#hsps 0
ok 616 - tile no_hsps.blastp hit 369 \#hsps 0
ok 617 - tile no_hsps.blastp hit 370 \#hsps 0
ok 618 - tile no_hsps.blastp hit 371 \#hsps 0
ok 619 - tile no_hsps.blastp hit 372 \#hsps 0
ok 620 - tile no_hsps.blastp hit 373 \#hsps 0
ok 621 - tile no_hsps.blastp hit 374 \#hsps 0
ok 622 - tile no_hsps.blastp hit 375 \#hsps 0
ok 623 - tile no_hsps.blastp hit 376 \#hsps 0
ok 624 - tile no_hsps.blastp hit 377 \#hsps 0
ok 625 - tile no_hsps.blastp hit 378 \#hsps 0
ok 626 - tile no_hsps.blastp hit 379 \#hsps 0
ok 627 - tile no_hsps.blastp hit 380 \#hsps 0
ok 628 - tile no_hsps.blastp hit 381 \#hsps 0
ok 629 - tile no_hsps.blastp hit 382 \#hsps 0
ok 630 - tile no_hsps.blastp hit 383 \#hsps 0
ok 631 - tile no_hsps.blastp hit 384 \#hsps 0
ok 632 - tile no_hsps.blastp hit 385 \#hsps 0
ok 633 - tile no_hsps.blastp hit 386 \#hsps 0
ok 634 - tile no_hsps.blastp hit 387 \#hsps 0
ok 635 - tile no_hsps.blastp hit 388 \#hsps 0
ok 636 - tile no_hsps.blastp hit 389 \#hsps 0
ok 637 - tile no_hsps.blastp hit 390 \#hsps 0
ok 638 - tile no_hsps.blastp hit 391 \#hsps 0
ok 639 - tile no_hsps.blastp hit 392 \#hsps 0
ok 640 - tile no_hsps.blastp hit 393 \#hsps 0
ok 641 - tile no_hsps.blastp hit 394 \#hsps 0
ok 642 - tile no_hsps.blastp hit 395 \#hsps 0
ok 643 - tile no_hsps.blastp hit 396 \#hsps 0
ok 644 - tile no_hsps.blastp hit 397 \#hsps 0
ok 645 - tile no_hsps.blastp hit 398 \#hsps 0
ok 646 - tile no_hsps.blastp hit 399 \#hsps 0
ok 647 - tile no_hsps.blastp hit 400 \#hsps 0
ok 648 - tile no_hsps.blastp hit 401 \#hsps 0
ok 649 - tile no_hsps.blastp hit 402 \#hsps 0
ok 650 - tile no_hsps.blastp hit 403 \#hsps 0
ok 651 - tile no_hsps.blastp hit 404 \#hsps 0
ok 652 - tile no_hsps.blastp hit 405 \#hsps 0
ok 653 - tile no_hsps.blastp hit 406 \#hsps 0
ok 654 - tile no_hsps.blastp hit 407 \#hsps 0
ok 655 - tile no_hsps.blastp hit 408 \#hsps 0
ok 656 - tile no_hsps.blastp hit 409 \#hsps 0
ok 657 - tile no_hsps.blastp hit 410 \#hsps 0
ok 658 - tile no_hsps.blastp hit 411 \#hsps 0
ok 659 - tile no_hsps.blastp hit 412 \#hsps 0
ok 660 - tile no_hsps.blastp hit 413 \#hsps 0
ok 661 - tile no_hsps.blastp hit 414 \#hsps 0
ok 662 - tile no_hsps.blastp hit 415 \#hsps 0
ok 663 - catalase-webblast.BLASTP
ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1
ok 665 - q id: est (1.00000) = fast (1.00000)
ok 666 - q cn: est (1.00000) = fast (1.00000)
ok 667 - h id: est (1.00000) = fast (1.00000)
ok 668 - h cn: est (1.00000) = fast (1.00000)
ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1
ok 670 - q id: est (0.80973) = fast (0.80973)
ok 671 - q cn: est (0.89006) = fast (0.89006)
ok 672 - h id: est (0.82543) = fast (0.82543)
ok 673 - h cn: est (0.90733) = fast (0.90733)
ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1
ok 675 - q id: est (0.71670) = fast (0.71670)
ok 676 - q cn: est (0.84144) = fast (0.84144)
ok 677 - h id: est (0.72747) = fast (0.72747)
ok 678 - h cn: est (0.85408) = fast (0.85408)
ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1
ok 680 - q id: est (0.58910) = fast (0.58910)
ok 681 - q cn: est (0.70860) = fast (0.70860)
ok 682 - h id: est (0.65654) = fast (0.65654)
ok 683 - h cn: est (0.78972) = fast (0.78972)
ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1
ok 685 - q id: est (0.49245) = fast (0.49245)
ok 686 - q cn: est (0.65257) = fast (0.65257)
ok 687 - h id: est (0.49544) = fast (0.49544)
ok 688 - h cn: est (0.65653) = fast (0.65653)
ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1
ok 690 - q id: est (0.44366) = fast (0.44366)
ok 691 - q cn: est (0.58920) = fast (0.58920)
ok 692 - h id: est (0.44787) = fast (0.44787)
ok 693 - h cn: est (0.59479) = fast (0.59479)
ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1
ok 695 - q id: est (0.42564) = fast (0.42564)
ok 696 - q cn: est (0.61282) = fast (0.61282)
ok 697 - h id: est (0.43229) = fast (0.43229)
ok 698 - h cn: est (0.62240) = fast (0.62240)
ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1
ok 700 - q id: est (0.48358) = fast (0.48358)
ok 701 - q cn: est (0.63881) = fast (0.63881)
ok 702 - h id: est (0.48943) = fast (0.48943)
ok 703 - h cn: est (0.64653) = fast (0.64653)
ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1
ok 705 - q id: est (0.42308) = fast (0.42308)
ok 706 - q cn: est (0.61282) = fast (0.61282)
ok 707 - h id: est (0.42969) = fast (0.42969)
ok 708 - h cn: est (0.62240) = fast (0.62240)
ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1
ok 710 - q id: est (0.39675) = fast (0.39675)
ok 711 - q cn: est (0.58933) = fast (0.58933)
ok 712 - h id: est (0.39767) = fast (0.39767)
ok 713 - h cn: est (0.59070) = fast (0.59070)
ok 714 - dcr1_sp.WUBLASTP
ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1
ok 716 - q id: est (1.00000) = fast (1.00000)
ok 717 - q cn: est (1.00000) = fast (1.00000)
ok 718 - h id: est (1.00000) = fast (1.00000)
ok 719 - h cn: est (1.00000) = fast (1.00000)
ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4
ok 721 - q id: exact (0.36876) ~ est (0.36973)
ok 722 - q id: exact (0.36876) <= max (0.37070)
ok 723 - q cn: exact (0.55022) ~ est (0.55041)
ok 724 - q cn: exact (0.55022) <= max (0.55105)
ok 725 - h id: exact (0.35111) ~ est (0.35111)
ok 726 - h id: exact (0.35111) <= max (0.35111)
ok 727 - h cn: exact (0.52305) ~ est (0.52305)
ok 728 - h cn: exact (0.52305) <= max (0.52305)
ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1
ok 730 - q id: est (0.38685) = fast (0.38685)
ok 731 - q cn: est (0.55397) = fast (0.55397)
ok 732 - h id: est (0.37613) = fast (0.37613)
ok 733 - h cn: est (0.53863) = fast (0.53863)
ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1
ok 735 - q id: est (0.38247) = fast (0.38247)
ok 736 - q cn: est (0.55068) = fast (0.55068)
ok 737 - h id: est (0.37306) = fast (0.37306)
ok 738 - h cn: est (0.53715) = fast (0.53715)
ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5
ok 740 - q id: exact (0.35010) ~ est (0.35010)
ok 741 - q id: exact (0.35010) <= max (0.35010)
ok 742 - q cn: exact (0.53183) ~ est (0.53183)
ok 743 - q cn: exact (0.53183) <= max (0.53183)
ok 744 - h id: exact (0.35082) ~ est (0.35082)
ok 745 - h id: exact (0.35082) <= max (0.35082)
ok 746 - h cn: exact (0.53292) ~ est (0.53292)
ok 747 - h cn: exact (0.53292) <= max (0.53292)
ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8
ok 749 - q id: exact (0.30547) ~ est (0.30659)
ok 750 - q id: exact (0.30547) <= max (0.30623)
ok 751 - q cn: exact (0.50076) ~ est (0.50205)
ok 752 - q cn: exact (0.50076) <= max (0.50076)
ok 753 - h id: exact (0.31390) ~ est (0.31179)
ok 754 - h id: exact (0.31390) <= max (0.31795)
ok 755 - h cn: exact (0.50531) ~ est (0.50557)
ok 756 - h cn: exact (0.50531) <= max (0.51091)
ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7
ok 758 - q id: exact (0.30136) ~ est (0.30184)
ok 759 - q id: exact (0.30136) <= max (0.30498)
ok 760 - q cn: exact (0.48688) ~ est (0.48742)
ok 761 - q cn: exact (0.48688) <= max (0.49140)
ok 762 - h id: exact (0.30944) ~ est (0.31034)
ok 763 - h id: exact (0.30944) <= max (0.30988)
ok 764 - h cn: exact (0.50178) ~ est (0.50277)
ok 765 - h cn: exact (0.50178) <= max (0.50223)
ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10
ok 767 - q id: exact (0.28918) ~ est (0.28961)
ok 768 - q id: exact (0.28918) <= max (0.28955)
ok 769 - q cn: exact (0.46418) ~ est (0.46247)
ok 770 - q cn: exact (0.46418) <= max (0.46866)
ok 771 - h id: exact (0.30166) ~ est (0.30299)
ok 772 - h id: exact (0.30166) <= max (0.30800)
ok 773 - h cn: exact (0.48179) ~ est (0.48439)
ok 774 - h cn: exact (0.48179) <= max (0.48535)
ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8
ok 776 - q id: exact (0.30289) ~ est (0.30238)
ok 777 - q id: exact (0.30289) <= max (0.30651)
ok 778 - q cn: exact (0.49955) ~ est (0.49787)
ok 779 - q cn: exact (0.49955) <= max (0.50362)
ok 780 - h id: exact (0.31395) ~ est (0.31347)
ok 781 - h id: exact (0.31395) <= max (0.31721)
ok 782 - h cn: exact (0.51535) ~ est (0.51578)
ok 783 - h cn: exact (0.51535) <= max (0.51814)
ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5
ok 785 - q id: exact (0.29334) ~ est (0.29534)
ok 786 - q id: exact (0.29334) <= max (0.29810)
ok 787 - q cn: exact (0.46617) ~ est (0.46719)
ok 788 - q cn: exact (0.46617) <= max (0.47040)
ok 789 - h id: exact (0.31176) ~ est (0.31176)
ok 790 - h id: exact (0.31176) <= max (0.31176)
ok 791 - h cn: exact (0.49299) ~ est (0.49299)
ok 792 - h cn: exact (0.49299) <= max (0.49299)
ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7
ok 794 - q id: exact (0.30456) ~ est (0.30514)
ok 795 - q id: exact (0.30456) <= max (0.30650)
ok 796 - q cn: exact (0.48739) ~ est (0.48879)
ok 797 - q cn: exact (0.48739) <= max (0.49370)
ok 798 - h id: exact (0.32062) ~ est (0.31987)
ok 799 - h id: exact (0.32062) <= max (0.32932)
ok 800 - h cn: exact (0.51071) ~ est (0.51306)
ok 801 - h cn: exact (0.51071) <= max (0.52410)
ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8
ok 803 - q id: exact (0.29615) ~ est (0.29879)
ok 804 - q id: exact (0.29615) <= max (0.30009)
ok 805 - q cn: exact (0.47419) ~ est (0.47394)
ok 806 - q cn: exact (0.47419) <= max (0.48119)
ok 807 - h id: exact (0.31611) ~ est (0.31482)
ok 808 - h id: exact (0.31611) <= max (0.32227)
ok 809 - h cn: exact (0.49779) ~ est (0.49788)
ok 810 - h cn: exact (0.49779) <= max (0.50616)
ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8
ok 812 - q id: exact (0.30390) ~ est (0.30440)
ok 813 - q id: exact (0.30390) <= max (0.30701)
ok 814 - q cn: exact (0.45874) ~ est (0.45993)
ok 815 - q cn: exact (0.45874) <= max (0.45963)
ok 816 - h id: exact (0.32282) ~ est (0.32324)
ok 817 - h id: exact (0.32282) <= max (0.32560)
ok 818 - h cn: exact (0.48052) ~ est (0.48136)
ok 819 - h cn: exact (0.48052) <= max (0.48330)
ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6
ok 821 - q id: exact (0.29769) ~ est (0.29851)
ok 822 - q id: exact (0.29769) <= max (0.29769)
ok 823 - q cn: exact (0.48480) ~ est (0.48628)
ok 824 - q cn: exact (0.48480) <= max (0.48637)
ok 825 - h id: exact (0.30704) ~ est (0.30810)
ok 826 - h id: exact (0.30704) <= max (0.30917)
ok 827 - h cn: exact (0.50107) ~ est (0.50292)
ok 828 - h cn: exact (0.50107) <= max (0.50320)
ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6
ok 830 - q id: exact (0.27854) ~ est (0.27854)
ok 831 - q id: exact (0.27854) <= max (0.27854)
ok 832 - q cn: exact (0.48174) ~ est (0.48174)
ok 833 - q cn: exact (0.48174) <= max (0.48174)
ok 834 - h id: exact (0.28514) ~ est (0.28623)
ok 835 - h id: exact (0.28514) <= max (0.28594)
ok 836 - h cn: exact (0.49197) ~ est (0.49154)
ok 837 - h cn: exact (0.49197) <= max (0.49237)
ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8
ok 839 - q id: exact (0.30362) ~ est (0.30824)
ok 840 - q id: exact (0.30362) <= max (0.30852)
ok 841 - q cn: exact (0.47111) ~ est (0.47587)
ok 842 - q cn: exact (0.47111) <= max (0.47405)
ok 843 - h id: exact (0.32347) ~ est (0.32392)
ok 844 - h id: exact (0.32347) <= max (0.32643)
ok 845 - h cn: exact (0.49310) ~ est (0.49360)
ok 846 - h cn: exact (0.49310) <= max (0.49606)
ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4
ok 848 - q id: exact (0.29174) ~ est (0.29174)
ok 849 - q id: exact (0.29174) <= max (0.29174)
ok 850 - q cn: exact (0.46230) ~ est (0.46230)
ok 851 - q cn: exact (0.46230) <= max (0.46230)
ok 852 - h id: exact (0.30204) ~ est (0.30204)
ok 853 - h id: exact (0.30204) <= max (0.30204)
ok 854 - h cn: exact (0.47862) ~ est (0.47862)
ok 855 - h cn: exact (0.47862) <= max (0.47862)
ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6
ok 857 - q id: exact (0.29064) ~ est (0.29089)
ok 858 - q id: exact (0.29064) <= max (0.29115)
ok 859 - q cn: exact (0.48765) ~ est (0.48670)
ok 860 - q cn: exact (0.48765) <= max (0.48868)
ok 861 - h id: exact (0.29848) ~ est (0.29887)
ok 862 - h id: exact (0.29848) <= max (0.29902)
ok 863 - h cn: exact (0.50108) ~ est (0.50116)
ok 864 - h cn: exact (0.50108) <= max (0.50163)
ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5
ok 866 - q id: exact (0.29510) ~ est (0.29505)
ok 867 - q id: exact (0.29510) <= max (0.29510)
ok 868 - q cn: exact (0.48982) ~ est (0.49039)
ok 869 - q cn: exact (0.48982) <= max (0.49029)
ok 870 - h id: exact (0.30019) ~ est (0.30019)
ok 871 - h id: exact (0.30019) <= max (0.30019)
ok 872 - h cn: exact (0.49906) ~ est (0.49906)
ok 873 - h cn: exact (0.49906) <= max (0.49906)
ok 874 - 503384.MEGABLAST.2
ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5
ok 876 - q id: exact (0.91435) ~ est (0.91435)
ok 877 - q id: exact (0.91435) <= max (0.91435)
ok 878 - q cn: exact (0.91435) ~ est (0.91435)
ok 879 - q cn: exact (0.91435) <= max (0.91435)
ok 880 - h id: exact (0.91157) ~ est (0.91157)
ok 881 - h id: exact (0.91157) <= max (0.91157)
ok 882 - h cn: exact (0.91157) ~ est (0.91157)
ok 883 - h cn: exact (0.91157) <= max (0.91157)
ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9
ok 885 - q id: exact (0.92895) ~ est (0.92895)
ok 886 - q id: exact (0.92895) <= max (0.92895)
ok 887 - q cn: exact (0.92895) ~ est (0.92895)
ok 888 - q cn: exact (0.92895) <= max (0.92895)
ok 889 - h id: exact (0.92854) ~ est (0.92854)
ok 890 - h id: exact (0.92854) <= max (0.92854)
ok 891 - h cn: exact (0.92854) ~ est (0.92854)
ok 892 - h cn: exact (0.92854) <= max (0.92854)
ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3
ok 894 - q id: exact (0.93516) ~ est (0.93516)
ok 895 - q id: exact (0.93516) <= max (0.93516)
ok 896 - q cn: exact (0.93516) ~ est (0.93516)
ok 897 - q cn: exact (0.93516) <= max (0.93516)
ok 898 - h id: exact (0.93651) ~ est (0.93651)
ok 899 - h id: exact (0.93651) <= max (0.93651)
ok 900 - h cn: exact (0.93651) ~ est (0.93651)
ok 901 - h cn: exact (0.93651) <= max (0.93651)
ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3
ok 903 - q id: exact (0.93064) ~ est (0.93064)
ok 904 - q id: exact (0.93064) <= max (0.93064)
ok 905 - q cn: exact (0.93064) ~ est (0.93064)
ok 906 - q cn: exact (0.93064) <= max (0.93064)
ok 907 - h id: exact (0.92885) ~ est (0.92885)
ok 908 - h id: exact (0.92885) <= max (0.92885)
ok 909 - h cn: exact (0.92885) ~ est (0.92885)
ok 910 - h cn: exact (0.92885) <= max (0.92885)
ok 911 - bl2seq.blastx.out
ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6
ok 913 - q id: est (0.71429) = fast (0.71429)
ok 914 - q cn: est (1.00000) = fast (1.00000)
ok 915 - q id: est (0.35714) = fast (0.35714)
ok 916 - q cn: est (0.57143) = fast (0.57143)
ok 917 - q id: exact (0.70536) ~ est (0.70495)
ok 918 - q id: exact (0.70536) <= max (0.94286)
ok 919 - q cn: exact (0.78810) ~ est (0.78803)
ok 920 - q cn: exact (0.78810) <= max (0.96429)
ok 921 - h id: exact (0.61923) ~ est (0.61955)
ok 922 - h id: exact (0.61923) <= max (0.64231)
ok 923 - h cn: exact (0.73077) ~ est (0.73077)
ok 924 - h cn: exact (0.73077) <= max (0.75000)
ok 925 - dnaEbsub_ecoli.wublastx
ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1
ok 927 - q id: est (0.36386) = fast (0.36386)
ok 928 - q cn: est (0.53735) = fast (0.53735)
ok 929 - h id: est (0.36562) = fast (0.36562)
ok 930 - h cn: est (0.53995) = fast (0.53995)
ok 931 - tblastn.out
ok 932 - tile tblastn.out hit 1 \#hsps 2
ok 933 - q id: exact (0.31250) ~ est (0.33325)
ok 934 - q id: exact (0.31250) <= max (0.33333)
ok 935 - q cn: exact (0.44792) ~ est (0.47055)
ok 936 - q cn: exact (0.44792) <= max (0.45833)
ok 937 - h id: exact (0.33333) ~ est (0.33333)
ok 938 - h id: exact (0.33333) <= max (0.33333)
ok 939 - h cn: exact (0.47059) ~ est (0.47059)
ok 940 - h cn: exact (0.47059) <= max (0.47059)
ok 941 - tile tblastn.out hit 2 \#hsps 2
ok 942 - q id: exact (0.68750) ~ est (0.68750)
ok 943 - q id: exact (0.68750) <= max (0.68750)
ok 944 - q cn: exact (0.81250) ~ est (0.81250)
ok 945 - q cn: exact (0.81250) <= max (0.81250)
ok 946 - h id: est (0.66667) = fast (0.66667)
ok 947 - h cn: est (0.77778) = fast (0.77778)
ok 948 - h id: est (0.71429) = fast (0.71429)
ok 949 - h cn: est (0.85714) = fast (0.85714)
ok 950 - dnaEbsub_ecoli.wutblastn
ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1
ok 952 - q id: est (0.36386) = fast (0.36386)
ok 953 - q cn: est (0.53735) = fast (0.53735)
ok 954 - h id: est (0.36562) = fast (0.36562)
ok 955 - h cn: est (0.53995) = fast (0.53995)
ok 956 - HUMBETGLOA.tblastx
ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1
ok 958 - q id: est (0.42308) = fast (0.42308)
ok 959 - q cn: est (0.61538) = fast (0.61538)
ok 960 - h id: est (0.42308) = fast (0.42308)
ok 961 - h cn: est (0.61538) = fast (0.61538)
ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1
ok 963 - q id: est (0.47059) = fast (0.47059)
ok 964 - q cn: est (0.76471) = fast (0.76471)
ok 965 - h id: est (0.47059) = fast (0.47059)
ok 966 - h cn: est (0.76471) = fast (0.76471)
ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1
ok 968 - q id: est (0.36000) = fast (0.36000)
ok 969 - q cn: est (0.56000) = fast (0.56000)
ok 970 - h id: est (0.36000) = fast (0.36000)
ok 971 - h cn: est (0.56000) = fast (0.56000)
ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1
ok 973 - q id: est (0.29268) = fast (0.29268)
ok 974 - q cn: est (0.58537) = fast (0.58537)
ok 975 - h id: est (0.29268) = fast (0.29268)
ok 976 - h cn: est (0.58537) = fast (0.58537)
ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1
ok 978 - q id: est (0.38889) = fast (0.38889)
ok 979 - q cn: est (0.55556) = fast (0.55556)
ok 980 - h id: est (0.38889) = fast (0.38889)
ok 981 - h cn: est (0.55556) = fast (0.55556)
ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1
ok 983 - q id: est (0.43590) = fast (0.43590)
ok 984 - q cn: est (0.51282) = fast (0.51282)
ok 985 - h id: est (0.43590) = fast (0.43590)
ok 986 - h cn: est (0.51282) = fast (0.51282)
ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1
ok 988 - q id: est (0.35714) = fast (0.35714)
ok 989 - q cn: est (0.42857) = fast (0.42857)
ok 990 - h id: est (0.35714) = fast (0.35714)
ok 991 - h cn: est (0.42857) = fast (0.42857)
ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1
ok 993 - q id: est (0.33333) = fast (0.33333)
ok 994 - q cn: est (0.66667) = fast (0.66667)
ok 995 - h id: est (0.33333) = fast (0.33333)
ok 996 - h cn: est (0.66667) = fast (0.66667)
ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2
ok 998 - q id: exact (0.40541) ~ est (0.40541)
ok 999 - q id: exact (0.40541) <= max (0.40541)
ok 1000 - q cn: exact (0.56757) ~ est (0.56757)
ok 1001 - q cn: exact (0.56757) <= max (0.56757)
ok 1002 - h id: est (0.42308) = fast (0.42308)
ok 1003 - h cn: est (0.53846) = fast (0.53846)
ok 1004 - h id: est (0.36364) = fast (0.36364)
ok 1005 - h cn: est (0.63636) = fast (0.63636)
ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1
ok 1007 - q id: est (0.29167) = fast (0.29167)
ok 1008 - q cn: est (0.39583) = fast (0.39583)
ok 1009 - h id: est (0.29167) = fast (0.29167)
ok 1010 - h cn: est (0.39583) = fast (0.39583)
ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1
ok 1012 - q id: est (0.60000) = fast (0.60000)
ok 1013 - q cn: est (0.65000) = fast (0.65000)
ok 1014 - h id: est (0.60000) = fast (0.60000)
ok 1015 - h cn: est (0.65000) = fast (0.65000)
ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1
ok 1017 - q id: est (0.50000) = fast (0.50000)
ok 1018 - q cn: est (0.68182) = fast (0.68182)
ok 1019 - h id: est (0.50000) = fast (0.50000)
ok 1020 - h cn: est (0.68182) = fast (0.68182)
ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1
ok 1022 - q id: est (0.29630) = fast (0.29630)
ok 1023 - q cn: est (0.48148) = fast (0.48148)
ok 1024 - h id: est (0.29630) = fast (0.29630)
ok 1025 - h cn: est (0.48148) = fast (0.48148)
ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1
ok 1027 - q id: est (0.47826) = fast (0.47826)
ok 1028 - q cn: est (0.52174) = fast (0.52174)
ok 1029 - h id: est (0.47826) = fast (0.47826)
ok 1030 - h cn: est (0.52174) = fast (0.52174)
ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1
ok 1032 - q id: est (0.47368) = fast (0.47368)
ok 1033 - q cn: est (0.63158) = fast (0.63158)
ok 1034 - h id: est (0.47368) = fast (0.47368)
ok 1035 - h cn: est (0.63158) = fast (0.63158)
ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1
ok 1037 - q id: est (0.44444) = fast (0.44444)
ok 1038 - q cn: est (0.55556) = fast (0.55556)
ok 1039 - h id: est (0.44444) = fast (0.44444)
ok 1040 - h cn: est (0.55556) = fast (0.55556)
ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1
ok 1042 - q id: est (0.47059) = fast (0.47059)
ok 1043 - q cn: est (0.70588) = fast (0.70588)
ok 1044 - h id: est (0.47059) = fast (0.47059)
ok 1045 - h cn: est (0.70588) = fast (0.70588)
ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1
ok 1047 - q id: est (0.38889) = fast (0.38889)
ok 1048 - q cn: est (0.66667) = fast (0.66667)
ok 1049 - h id: est (0.38889) = fast (0.38889)
ok 1050 - h cn: est (0.66667) = fast (0.66667)
ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1
ok 1052 - q id: est (0.27660) = fast (0.27660)
ok 1053 - q cn: est (0.48936) = fast (0.48936)
ok 1054 - h id: est (0.27660) = fast (0.27660)
ok 1055 - h cn: est (0.48936) = fast (0.48936)
ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1
ok 1057 - q id: est (0.40000) = fast (0.40000)
ok 1058 - q cn: est (0.60000) = fast (0.60000)
ok 1059 - h id: est (0.40000) = fast (0.40000)
ok 1060 - h cn: est (0.60000) = fast (0.60000)
ok 1061 - dnaEbsub_ecoli.wutblastx
ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12
ok 1063 - q id: est (0.37500) = fast (0.37500)
ok 1064 - q cn: est (0.62500) = fast (0.62500)
ok 1065 - q id: est (0.25352) = fast (0.25352)
ok 1066 - q cn: est (0.47887) = fast (0.47887)
ok 1067 - q id: exact (0.40224) ~ est (0.40912)
ok 1068 - q id: exact (0.40224) <= max (0.42628)
ok 1069 - q cn: exact (0.58494) ~ est (0.58968)
ok 1070 - q cn: exact (0.58494) <= max (0.62179)
ok 1071 - q id: exact (0.44118) ~ est (0.44118)
ok 1072 - q id: exact (0.44118) <= max (0.44118)
ok 1073 - q cn: exact (0.54412) ~ est (0.54412)
ok 1074 - q cn: exact (0.54412) <= max (0.54412)
ok 1075 - h id: exact (0.39848) ~ est (0.40304)
ok 1076 - h id: exact (0.39848) <= max (0.40355)
ok 1077 - h cn: exact (0.58376) ~ est (0.58889)
ok 1078 - h cn: exact (0.58376) <= max (0.58883)
ok 1079 - h id: exact (0.44118) ~ est (0.44118)
ok 1080 - h id: exact (0.44118) <= max (0.44118)
ok 1081 - h cn: exact (0.54412) ~ est (0.54412)
ok 1082 - h cn: exact (0.54412) <= max (0.54412)
ok 1083 - h id: est (0.25352) = fast (0.25352)
ok 1084 - h cn: est (0.47887) = fast (0.47887)
ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2
ok 1086 - q id: exact (0.41818) ~ est (0.41818)
ok 1087 - q id: exact (0.41818) <= max (0.41818)
ok 1088 - q cn: exact (0.52727) ~ est (0.52727)
ok 1089 - q cn: exact (0.52727) <= max (0.52727)
ok 1090 - h id: est (0.37500) = fast (0.37500)
ok 1091 - h cn: est (0.47500) = fast (0.47500)
ok 1092 - h id: est (0.53333) = fast (0.53333)
ok 1093 - h cn: est (0.66667) = fast (0.66667)
ok 1094 - bug2942: query m0: range correct
ok 1095 - bug2942: query m1: range correct
ok 1096 - bug2942: query m2: range correct
ok 1097 - bug2942: subject all : range correct
ok 1098 - get_tiled_alns
ok 1099 - got all alns
ok 1100
ok 1101 - aln and qfeat lengths correspond
ok 1102 - q length correct
ok 1103
ok 1104 - features on q and s correspond
ok 1105 - aln and hfeat lengths correspond
ok 1106 - s length correct
ok 1107
ok 1108 - aln and qfeat lengths correspond
ok 1109 - q length correct
ok 1110
ok 1111 - features on q and s correspond
ok 1112 - aln and hfeat lengths correspond
ok 1113 - s length correct
ok 1114
ok 1115 - aln and qfeat lengths correspond
ok 1116 - q length correct
ok 1117
ok 1118 - features on q and s correspond
ok 1119 - aln and hfeat lengths correspond
ok 1120 - s length correct
ok 1121
ok 1122 - aln and qfeat lengths correspond
ok 1123 - q length correct
ok 1124
ok 1125 - features on q and s correspond
ok 1126 - aln and hfeat lengths correspond
ok 1127 - s length correct
ok 1128
ok 1129 - aln and qfeat lengths correspond
ok 1130 - q length correct
ok 1131
ok 1132 - features on q and s correspond
ok 1133 - aln and hfeat lengths correspond
ok 1134 - s length correct
ok 1135
ok 1136 - aln and qfeat lengths correspond
ok 1137 - q length correct
ok 1138
ok 1139 - features on q and s correspond
ok 1140 - aln and hfeat lengths correspond
ok 1141 - s length correct
ok
t/SearchIO/Writer/GbrowseGFF.t ......... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
t/SearchIO/Writer/HSPTableWriter.t ..... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HSPTableWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
t/SearchIO/Writer/HTMLWriter.t ......... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HTMLResultWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
t/SearchIO/Writer/HitTableWriter.t ..... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HitTableWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
t/SearchIO/Writer/TextWriter.t ......... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::TextResultWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
t/SearchIO/axt.t ....................... 
1..19
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
t/SearchIO/blast.t ..................... 
1..1389
ok 1 - use Bio::SearchIO;
ok 2 - Bio::SearchIO->new can handle a Path::Class object
ok 3 - An object of class 'Bio::SearchIO::blast' isa 'Bio::Root::IO'
ok 4 - Bio::SearchIO->new can handle a Path::Class object
ok 5 - An object of class 'Bio::SearchIO::blast' isa 'Bio::Root::IO'
ok 6
ok 7 - database_name()
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
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ok 414
not ok 415 # TODO frac_identical & frac_conserved are still too wrong

#   Failed (TODO) test at t/SearchIO/blast.t line 668.
#     '0.852'
#         >
#     '0.9'
not ok 416 # TODO frac_identical & frac_conserved are still too wrong

#   Failed (TODO) test at t/SearchIO/blast.t line 669.
#     '1.599'
#         <=
#     '1'
ok 417
ok 418
ok 419
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ok 594
ok 595
ok 596
ok 597 - Multiblast query test
ok 598
ok 599 - Multiblast query test
ok 600
ok 601 - Multiblast query test
ok 602
ok 603 - Multiblast query test
ok 604
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ok 885 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 886
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ok 905 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 906
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ok 929 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 930
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ok 953 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 954
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ok 982 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 983
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ok 1007 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 1008
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ok 1035 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 1036
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ok 1064 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 1065
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ok 1080
ok 1081
ok 1082
ok 1083 - fasta for f.SSEARCH.m9
ok 1084 - fasta for f.fasta
ok 1085 - blast for f.tblx
ok 1086 - fasta for f.fx
ok 1087 - blast for filename.bls
ok 1088 - blast for f.blx
ok 1089 - blast for filename.blast
ok 1090 - exonerate for f.exonerate
ok 1091 - fasta for f.ssearch
ok 1092 - blastxml for f.blastxml
ok 1093 - fasta for f.fy
ok 1094 - blastxml for f.xml
ok 1095 - fasta for f.psearch
ok 1096 - fasta for f.osearch
ok 1097 - exonerate for f.exon
ok 1098 - fasta for f.fa
ok 1099 - fasta for f.m9
ok 1100 - blast for fast.bls
ok 1101
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ok 1111
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ok 1116 - full hit name
ok 1117 - hit accession
ok 1118
ok 1119
ok 1120 - query start
ok 1121 - query start
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ok 1384 - testing Bug 3298
ok 1385 - testing Bug 3298
ok 1386 - testing Bug 3298
ok 1387 - testing Bug 3251
ok 1388 - testing Bug 3251
ok 1389 - testing Bug 3251
ok
t/SearchIO/blast_pull.t ................ 
1..289
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
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ok 57
ok 58
ok 59 - database_name()
ok 60
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not ok 191 # TODO frac_identical failing!

#   Failed (TODO) test at t/SearchIO/blast_pull.t line 260.
#          got: '0.946'
#     expected: '0.943'
ok 192
ok 193
ok 194
ok 195
ok 196 - Multiblast query test
ok 197 - Multiblast query test
ok 198 - Multiblast query test
ok 199 - Multiblast query test
ok 200
ok 201
ok 202
ok 203 - full hit name
ok 204 - hit accession
ok 205
ok 206 - query start
ok 207 - query start
ok 208
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ok
t/SearchIO/blasttable.t ................ 
1..166
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::Search::SearchUtils;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6 - hit1_bits
ok 7 - hit1_name
ok 8 - hsp1_bits
ok 9 - hsp1_gaps
ok 10 - hsp1_he
ok 11 - hsp1_hs
ok 12 - hsp1_hstr
ok 13 - hsp1_qe
ok 14 - hsp1_qs
ok 15 - hsp1_qstr
ok 16 - hsp2_bits
ok 17 - hsp2_gaps
ok 18 - hsp2_he
ok 19 - hsp2_hs
ok 20 - hsp2_hstr
ok 21 - hsp2_qe
ok 22 - hsp2_qs
ok 23 - hsp2_qstr
ok 24 - hsp3_bits
ok 25 - hsp3_gaps
ok 26 - hsp3_he
ok 27 - hsp3_hs
ok 28 - hsp3_hstr
ok 29 - hsp3_qe
ok 30 - hsp3_qs
ok 31 - hsp3_qstr
ok 32 - hsp4_bits
ok 33 - hsp4_gaps
ok 34 - hsp4_he
ok 35 - hsp4_hs
ok 36 - hsp4_hstr
ok 37 - hsp4_qe
ok 38 - hsp4_qs
ok 39 - hsp4_qstr
ok 40 - hsp5_bits
ok 41 - hsp5_gaps
ok 42 - hsp5_he
ok 43 - hsp5_hs
ok 44 - hsp5_hstr
ok 45 - hsp5_qe
ok 46 - hsp5_qs
ok 47 - hsp5_qstr
ok 48 - hsp6_bits
ok 49 - hsp6_gaps
ok 50 - hsp6_he
ok 51 - hsp6_hs
ok 52 - hsp6_hstr
ok 53 - hsp6_qe
ok 54 - hsp6_qs
ok 55 - hsp6_qstr
ok 56 - hsp7_bits
ok 57 - hsp7_gaps
ok 58 - hsp7_he
ok 59 - hsp7_hs
ok 60 - hsp7_hstr
ok 61 - hsp7_qe
ok 62 - hsp7_qs
ok 63 - hsp7_qstr
ok 64 - hsp8_bits
ok 65 - hsp8_gaps
ok 66 - hsp8_he
ok 67 - hsp8_hs
ok 68 - hsp8_hstr
ok 69 - hsp8_qe
ok 70 - hsp8_qs
ok 71 - hsp8_qstr
ok 72 - query_name
ok 73 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 74
ok 75
ok 76 - hit1_bits
ok 77 - hit1_name
ok 78 - hsp1_bits
ok 79 - hsp1_gaps
ok 80 - hsp1_he
ok 81 - hsp1_hs
ok 82 - hsp1_hstr
ok 83 - hsp1_qe
ok 84 - hsp1_qs
ok 85 - hsp1_qstr
ok 86 - hsp2_bits
ok 87 - hsp2_gaps
ok 88 - hsp2_he
ok 89 - hsp2_hs
ok 90 - hsp2_hstr
ok 91 - hsp2_qe
ok 92 - hsp2_qs
ok 93 - hsp2_qstr
ok 94 - hsp3_bits
ok 95 - hsp3_gaps
ok 96 - hsp3_he
ok 97 - hsp3_hs
ok 98 - hsp3_hstr
ok 99 - hsp3_qe
ok 100 - hsp3_qs
ok 101 - hsp3_qstr
ok 102 - hsp4_bits
ok 103 - hsp4_gaps
ok 104 - hsp4_he
ok 105 - hsp4_hs
ok 106 - hsp4_hstr
ok 107 - hsp4_qe
ok 108 - hsp4_qs
ok 109 - hsp4_qstr
ok 110 - hsp5_bits
ok 111 - hsp5_gaps
ok 112 - hsp5_he
ok 113 - hsp5_hs
ok 114 - hsp5_hstr
ok 115 - hsp5_qe
ok 116 - hsp5_qs
ok 117 - hsp5_qstr
ok 118 - hsp6_bits
ok 119 - hsp6_gaps
ok 120 - hsp6_he
ok 121 - hsp6_hs
ok 122 - hsp6_hstr
ok 123 - hsp6_qe
ok 124 - hsp6_qs
ok 125 - hsp6_qstr
ok 126 - hsp7_bits
ok 127 - hsp7_gaps
ok 128 - hsp7_he
ok 129 - hsp7_hs
ok 130 - hsp7_hstr
ok 131 - hsp7_qe
ok 132 - hsp7_qs
ok 133 - hsp7_qstr
ok 134 - hsp8_bits
ok 135 - hsp8_gaps
ok 136 - hsp8_he
ok 137 - hsp8_hs
ok 138 - hsp8_hstr
ok 139 - hsp8_qe
ok 140 - hsp8_qs
ok 141 - hsp8_qstr
ok 142 - query_name
ok 143
ok 144
ok 145
ok 146
ok 147 - hit score
ok 148 - hit raw_score
ok 149 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::SeqFeatureI'
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157 - fixed bug 3343 (percent identity)
ok 158 - side effect of fixing bug 3343 (number of gaps)
ok 159 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeatureI'
ok 160
ok 161
ok 162
ok 163 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeatureI'
ok 164
ok 165
ok 166
ok
t/SearchIO/cross_match.t ............... 
1..15
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/SearchIO/erpin.t ..................... 
1..91
ok 1 - use Bio::SearchIO;
ok 2 - An object of class 'Bio::Search::Result::GenericResult' isa 'Bio::Search::Result::ResultI'
ok 3 - Result ERPIN
ok 4 - Result ERPIN reference
ok 5 - Result ERPIN version
ok 6 - Result parameters
ok 7 - Result statistics
ok 8 - Result entries
ok 9 - Result letters
ok 10 - Result database_name
ok 11 - Result num_hits
ok 12 - Result program_reference
ok 13 - Result query_accession
ok 14 - Result query_description
ok 15 - Result query_name
ok 16 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 17 - Hit accession
ok 18 - Hit GI
ok 19 - Hit algorithm
ok 20 - Hit bits
ok 21 - Hit description
ok 22 - Hit length
ok 23 - Hit locus
ok 24 - Hit n
ok 25 - Hit name
ok 26 - Hit num_hsps
ok 27 - Hit overlap
ok 28 - Hit query_length
ok 29 - Hit rank
ok 30 - Hit raw_score
ok 31 - Hit score
ok 32
ok 33 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 34 - HSP algorithm
ok 35
ok 36 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 37 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 38 - HSP frame
ok 39 - HSP gaps
ok 40 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 41 - HSP hit_string
ok 42 - HSP homology_string
ok 43 - HSP hsp_group
ok 44 - HSP hsp_length
ok 45 - HSP length
ok 46 - HSP links
ok 47 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 48 - HSP query_string
ok 49 - HSP range
ok 50 - HSP rank
ok 51
ok 52 - HSP expect
ok 53 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58
ok 59
ok 60 - HSP strand
ok 61
ok 62
ok 63 - ERPIN get_aln warning
ok 64 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 65 - HSP algorithm
ok 66
ok 67 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 68 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 69 - HSP frame
ok 70 - HSP gaps
ok 71 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 72 - HSP hit_string
ok 73 - HSP homology_string
ok 74 - HSP query_string
ok 75 - HSP hsp_group
ok 76 - HSP hsp_length
ok 77 - HSP length
ok 78 - HSP links
ok 79 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 80 - HSP range
ok 81 - HSP rank
ok 82
ok 83 - HSP end
ok 84 - HSP expect
ok 85 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 86 - HSP seq_str
ok 87 - HSP start
ok 88 - HSP custom_score
ok 89
ok 90
ok 91 - HSP strand
ok
t/SearchIO/exonerate.t ................. 
1..52
ok 1 - use Bio::SearchIO;
ok 2
ok 3 # skip no query length available in default output
ok 4
ok 5 # skip no hit length available in default output
ok 6
ok 7
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ok 24
ok 25 # skip no query length available in default output
ok 26
ok 27 # skip no hit length available in default output
ok 28
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ok 45
ok 46 - query_name
ok 47
ok 48 - query_name
ok 49
ok 50 - query_name
ok 51
ok 52
ok
t/SearchIO/fasta.t ..................... 
1..299
ok 1 - use Bio::SearchIO;
ok 2
ok 3
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ok 266
ok 267 - TFASTXY
ok 268
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ok 275
ok 276
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ok 282
ok 283
ok 284
ok 285
ok 286 - num_identical()
ok 287 - num_conserved()
ok 288 - bug 2937 and FASTA version 3.5
ok 289 - algorithm version
ok 290 - query name
ok 291 - query description
ok 292 - query length
ok 293 - algorithm
ok 294 - num_identical()
ok 295 - num_conserved()
ok 296 - hsp->strand(hit)
ok 297 - hsp->hit->strand
ok 298 - hsp->strand(query)
ok 299 - hsp->query->strand
ok
t/SearchIO/gmap_f9.t ................... 
1..54
ok 1 - use Bio::SearchIO;
ok 2 - 'Did we get a Result?' isa 'Bio::Search::Result::GenericResult'
ok 3 - Did we get the expected number of hits?
ok 4 - Did we get the expected algorithm?
ok 5 - Did we get the expected query_name?
ok 6 - 'Did we get a Hit?' isa 'Bio::Search::Hit::GenericHit'
ok 7 - An object of class 'Bio::Search::Hit::GenericHit' isa 'Bio::Search::Hit::HitI'
ok 8 - Check the name
ok 9 - Check the hit length
ok 10 - Check the number of hsps
ok 11 - Check the query length
ok 12 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::Search::HSP::HSPI'
ok 13 - Check the algorithm
ok 14 - Count gaps in the query
ok 15 - Count gaps in the hit
ok 16 - Length of the query
ok 17 - Length of the hit
ok 18 - Query sequence
ok 19 - Hit sequence
ok 20 - Check query start
ok 21 - Check query end
ok 22 - Check query end
ok 23 - Check the homology string
ok 24 - Check seq_inds
ok 25 - Check hit start
ok 26 - Check hit end
ok 27 - Check hit end
ok 28 - 'Did we get a Result?' isa 'Bio::Search::Result::GenericResult'
ok 29 - Did we get the expected number of hits?
ok 30 - Did we get the expected algorithm?
ok 31 - Did we get the expected query_name?
ok 32 - An object of class 'Bio::Search::Hit::GenericHit' isa 'Bio::Search::Hit::HitI'
ok 33 - Check the name
ok 34 - Check the hit length
ok 35 - Check the number of hsps
ok 36 - Check the query length
ok 37 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::Search::HSP::HSPI'
ok 38 - Check the algorithm
ok 39 - Count gaps in the query
ok 40 - Count gaps in the hit
ok 41 - Length of the query
ok 42 - Length of the hit
ok 43 - Query sequence
ok 44 - Hit sequence
ok 45 - Check query start
ok 46 - Check query end
ok 47 - Check query end
ok 48 - Check the homology string
ok 49 - Check seq_inds
ok 50 - Check hit start
ok 51 - Check hit end
ok 52 - Check hit end
ok 53 - Can we loop over multiple results properly (expecting 58)?
ok 54 - simple query_name now caught, bug 3021
ok
t/SearchIO/hmmer.t ..................... 
1..824
ok 1 - use Bio::SearchIO;
ok 2 - Check for the correct result reference type
ok 3 - Check algorithm
ok 4 - Check algorithm version
ok 5 - Check hmm_name
ok 6 - Check sequence_file
ok 7 - Check query_name
ok 8 - Check query_length absence
ok 9 - Check query_description
ok 10 - Check num_hits
ok 11 - Check for the correct hit reference type
ok 12 - Check hit name
ok 13 - Check for hit description
ok 14 - Check hit raw_score
ok 15 - Check hit bits (0)
ok 16 - Check hit significance
ok 17 - Check num_hsps
ok 18 - Check hit length
ok 19
ok 20
ok 21 - Check hit total conserved residues
ok 22 - Check hit total identical residues
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - Check for correct hsp reference type
ok 30 - Check for query seq_id
ok 31 - Check for hit seq_id
ok 32 - Check for hit hmmfrom value
ok 33 - Check for hit hmm to value
ok 34 - Check for query alifrom value
ok 35 - Check for query ali to value
ok 36 - Check for hsp score
ok 37 - Check for hsp bits (0)
ok 38 - Check for hsp c-Evalue
ok 39 - Check for hsp query length
ok 40 - Check for hsp hit length
ok 41 - Check for hsp total length
ok 42 - Check for hsp query gaps
ok 43 - Check for hsp hit gaps
ok 44 - Check for hsp total gaps
ok 45 - Check hit length consistency
ok 46 - Check query length consistency
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - Check for query string
ok 57 - Check for hit string
ok 58 - Check for homology string
ok 59 - Check if homology string and hit string have an equal length
ok 60 - Check if query string and homology string have an equal length
ok 61
ok 62
ok 63 - Check for the correct hit reference type
ok 64 - Check hit name
ok 65 - Check for hit description
ok 66 - Check hit raw_score
ok 67 - Check hit bits (0)
ok 68 - Check hit significance
ok 69 - Check num_hsps
ok 70 - Check hit length
ok 71
ok 72
ok 73 - Check hit total conserved residues
ok 74 - Check hit total identical residues
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81 - Check for correct hsp reference type
ok 82 - Check for query seq_id
ok 83 - Check for hit seq_id
ok 84 - Check for hit hmmfrom value
ok 85 - Check for hit hmm to value
ok 86 - Check for query alifrom value
ok 87 - Check for query ali to value
ok 88 - Check for hsp score
ok 89 - Check for hsp bits (0)
ok 90 - Check for hsp c-Evalue
ok 91 - Check for hsp query length
ok 92 - Check for hsp hit length
ok 93 - Check for hsp total length
ok 94 - Check for hsp query gaps
ok 95 - Check for hsp hit gaps
ok 96 - Check for hsp total gaps
ok 97 - Check hit length consistency
ok 98 - Check query length consistency
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108 - Check for query string
ok 109 - Check for hit string
ok 110 - Check for homology string
ok 111 - Check if homology string and hit string have an equal length
ok 112 - Check if query string and homology string have an equal length
ok 113 - Check for the correct result reference type
ok 114 - Check algorithm
ok 115 - Check algorithm version
ok 116 - Check hmm_name
ok 117 - Check sequence_file
ok 118 - Check database_name
ok 119 - Check query_name
ok 120 - Check query_length
ok 121 - Check query_description
ok 122 - Check num_hits
ok 123 - Check for the correct hit reference type
ok 124 - Check hit name
ok 125 - Check for hit description
ok 126 - Check hit raw_score
ok 127 - Check hit bits (0)
ok 128 - Check hit significance
ok 129 - Check num_hsps
ok 130 - Check hit length
ok 131 - Check for correct hsp reference type
ok 132 - Check for query seq_id
ok 133 - Check for hit seq_id
ok 134 - Check for hit hmmfrom value
ok 135 - Check for hit hmm to value
ok 136 - Check for query alifrom value
ok 137 - Check for query ali to value
ok 138 - Check for hsp score
ok 139 - Check for hsp bits (0)
ok 140 - Check for hsp c-Evalue
ok 141 - Check for hsp query length
ok 142 - Check for hsp hit length
ok 143 - Check for hsp total length
ok 144 - Check for hsp query gaps
ok 145 - Check for hsp hit gaps
ok 146 - Check for hsp total gaps
ok 147 - Check hit length
ok 148
ok 149
ok 150 - Check for query seq_id
ok 151 - Check for hit seq_id
ok 152 - Check for hit hmmfrom value
ok 153 - Check for hit hmm to value
ok 154 - Check for query alifrom value
ok 155 - Check for query ali to value
ok 156 - Check for hsp score
ok 157 - Check for hsp bits (0)
ok 158 - Check for hsp c-Evalue
ok 159 - Check for hsp query length
ok 160 - Check for hsp hit length
ok 161 - Check for hsp total length
ok 162 - Check for hsp query gaps
ok 163 - Check for hsp hit gaps
ok 164 - Check for hsp total gaps
ok 165 - Check hit length
ok 166
ok 167
ok 168 - Check for query seq_id
ok 169 - Check for hit seq_id
ok 170 - Check for hit hmmfrom value
ok 171 - Check for hit hmm to value
ok 172 - Check for query alifrom value
ok 173 - Check for query ali to value
ok 174 - Check for hsp score
ok 175 - Check for hsp bits (0)
ok 176 - Check for hsp c-Evalue
ok 177 - Check for hsp query length
ok 178 - Check for hsp hit length
ok 179 - Check for hsp total length
ok 180 - Check for hsp query gaps
ok 181 - Check for hsp hit gaps
ok 182 - Check for hsp total gaps
ok 183 - Check for the correct result reference type
ok 184 - Check algorithm
ok 185 - Check algorithm version
ok 186 - Check hmm_name
ok 187 - Check sequence_file
ok 188 - Check query_name
ok 189 - Check query_length absence
ok 190 - Check query_description
ok 191 - Check num_hits
ok 192 - Check for the correct hit reference type
ok 193 - Check hit name
ok 194 - Check for hit description
ok 195 - Check hit raw_score
ok 196 - Check hit bits (0)
ok 197 - Check hit significance
ok 198 - Check num_hsps
ok 199 - Check hit length
ok 200
ok 201
ok 202 - Check hit total conserved residues
ok 203 - Check hit total identical residues
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210 - Check for correct hsp reference type
ok 211 - Check for query seq_id
ok 212 - Check for hit seq_id
ok 213 - Check for hit hmmfrom value
ok 214 - Check for hit hmm to value
ok 215 - Check for query alifrom value
ok 216 - Check for query ali to value
ok 217 - Check for hsp score
ok 218 - Check for hsp bits (0)
ok 219 - Check for hsp evalue
ok 220 - Check for hsp query length
ok 221 - Check for hsp hit length
ok 222 - Check for hsp total length
ok 223 - Check for hsp query gaps
ok 224 - Check for hsp hit gaps
ok 225 - Check for hsp total gaps
ok 226 - Check hit length consistency
ok 227 - Check query length consistency
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238 - Check for hiy string
ok 239 - Check for query string
ok 240 - Check for homology string
ok 241 - Check for nomatch indices in query
ok 242 - Check for nomatch indices in hit
ok 243 - Check for gap indices in query
ok 244 - Check for gap indices in hit
ok 245 - Check for the correct result reference type
ok 246 - Check algorithm
ok 247 - Check algorithm version
ok 248 - Check hmm_name
ok 249 - Check database_name
ok 250 - Check sequence_file
ok 251 - Check query_name
ok 252 - Check query_length
ok 253 - Check query_accession
ok 254 - Check query_description
ok 255 - Check num_hits
ok 256 - Check for the correct hit reference type
ok 257 - Check hit name
ok 258 - Check for hit description
ok 259 - Check hit raw_score
ok 260 - Check hit bits (0)
ok 261 - Check hit significance
ok 262 - Check num_hsps
ok 263 - Check hit length absence
ok 264
ok 265
ok 266 - Check hit total conserved residues
ok 267 - Check hit total identical residues
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274 - Check for correct hsp reference type
ok 275 - Check for query seq_id
ok 276 - Check for hit seq_id
ok 277 - Check for hit hmmfrom value
ok 278 - Check for hit hmm to value
ok 279 - Check for query alifrom value
ok 280 - Check for query ali to value
ok 281 - Check for hsp score
ok 282 - Check for hsp bits (0)
ok 283 - Check for hsp evalue
ok 284 - Check for hsp query length
ok 285 - Check for hsp hit length
ok 286 - Check for hsp total length
ok 287 - Check for hsp query gaps
ok 288 - Check for hsp hit gaps
ok 289 - Check for hsp total gaps
ok 290 - Check hit length consistency
ok 291 - Check query length consistency
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298
ok 299
ok 300
ok 301
ok 302 - Check for hiy string
ok 303 - Check for homology string
ok 304 - Check for query string
ok 305
ok 306
ok 307 - Check hit name
ok 308 - Check for hit description
ok 309 - Check hit raw_score
ok 310 - Check hit bits (0)
ok 311 - Check hit significance
ok 312
ok 313
ok 314
ok 315
ok 316 - Check for consensus structure string
ok 317 - Check for hsp seq_str
ok 318 - Check for query string
ok 319 - Check for hit string
ok 320 - Check for homology string
ok 321 - Check if correct searchio object is returned
ok 322 - Check for the correct result reference type
ok 323 - Check algorithm
ok 324 - Check algorithm version
ok 325 - Check hmm_name
ok 326 - Check sequence_file
ok 327 - Check query_name
ok 328 - Check query_length
ok 329 - Check query_accession
ok 330 - Check query_description
ok 331 - Check num_hits
ok 332 - Check for the correct hit reference type
ok 333 - Check hit name
ok 334 - Check for hit description
ok 335 - Check hit raw_score
ok 336 - Check hit bits (0)
ok 337 - Check hit significance
ok 338 - Check num_hsps
ok 339 - Check hit length absence
ok 340
ok 341
ok 342 - Check for correct hsp reference type
ok 343 - Check for hit seq_id
ok 344 - Check for query seq_id
ok 345 - Check for hit hmmfrom value
ok 346 - Check for hit hmm to value
ok 347 - Check for query alifrom value
ok 348 - Check for query ali to value
ok 349 - Check for hsp score
ok 350 - Check for hsp bits (0)
ok 351 - Check for hsp c-Evalue
ok 352 - Check for hsp query length
ok 353 - Check for hsp hit length
ok 354 - Check for hsp total length
ok 355 - Check for hsp query gaps
ok 356 - Check for hsp hit gaps
ok 357 - Check for hsp total gaps
ok 358 - Check hit length consistency
ok 359 - Check query length consistency
ok 360
ok 361
ok 362
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369
ok 370 - Check for query string
ok 371 - Check for hit string
ok 372 - Check for homology string
ok 373 - Check for posterior probability string
ok 374 - Check algorithm
ok 375 - Check algorithm version
ok 376 - Check hmm_name
ok 377 - Check sequence_file
ok 378 - Check query_name
ok 379 - Check query_length
ok 380 - Check query_description
ok 381 - Check num_hits
ok 382 - Check for the correct hit reference type
ok 383 - Check hit name
ok 384 - Check for hit description
ok 385 - Check num_hsps
ok 386 - Check for correct hsp reference type
ok 387 - Check for hit seq_id
ok 388 - Check for query seq_id
ok 389 - Check for hit hmmfrom value
ok 390 - Check for hit hmm to value
ok 391 - Check for query alifrom value
ok 392 - Check for query ali to value
ok 393 - Check for hsp score
ok 394 - Check for hsp bits (0)
ok 395 - Check for hsp c-Evalue
ok 396 - Check for the correct hit reference type
ok 397 - Check hit name
ok 398 - Check for hit description
ok 399 - Check num_hsps
ok 400 - Check for correct hsp reference type
ok 401 - Check for hit seq_id
ok 402 - Check for query seq_id
ok 403 - Check for hit hmmfrom value
ok 404 - Check for hit hmm to value
ok 405 - Check for query alifrom value
ok 406 - Check for query ali to value
ok 407 - Check for hsp score
ok 408 - Check for hsp bits (0)
ok 409 - Check for hsp c-Evalue
ok 410 - Check for the correct result reference type
ok 411 - Check algorithm
ok 412 - Check algorithm version
ok 413 - Check hmm_name
ok 414 - Check sequence_file
ok 415 - Check query_name
ok 416 - Check query_length
ok 417 - Check query_description
ok 418 - Check num_hits
ok 419 - Check if correct searchio object is returned
ok 420 - Check for the correct result reference type
ok 421 - Check algorithm
ok 422 - Check algorithm version
ok 423 - Check hmm_name
ok 424 - Check sequence_file
ok 425 - Check query_name
ok 426 - Check query_length
ok 427 - Check query_accession
ok 428 - Check query_description
ok 429 - Check num_hits
ok 430 - Check for the correct result reference type
ok 431 - Check algorithm
ok 432 - Check algorithm version
ok 433 - Check hmm_name
ok 434 - Check sequence_file
ok 435 - Check query_name
ok 436 - Check query_length
ok 437 - Check query_accession
ok 438 - Check query_description
ok 439 - Check num_hits
ok 440 - Check for the correct hit reference type
ok 441 - Check hit name
ok 442 - Check for hit description
ok 443 - Check hit raw_score
ok 444 - Check hit bits (0)
ok 445 - Check hit significance
ok 446 - Check num_hsps
ok 447 - Check for correct hsp reference type
ok 448 - Check for hit seq_id
ok 449 - Check for query seq_id
ok 450 - Check for hit alifrom value
ok 451 - Check for hit ali to value
ok 452 - Check for query hmmfrom value
ok 453 - Check for query hmm to value
ok 454 - Check for hsp score
ok 455 - Check for hsp bits (0)
ok 456 - Check for hsp c-Evalue
ok 457 - Check for hsp query length
ok 458 - Check for hsp hit length
ok 459 - Check for hsp total length
ok 460 - Check for hsp query gaps
ok 461 - Check for hsp hit gaps
ok 462 - Check for hsp total gaps
ok 463 - Check hit length consistency
ok 464 - Check query length consistency
ok 465
ok 466
ok 467
ok 468
ok 469
ok 470
ok 471
ok 472
ok 473
ok 474
ok 475 - Check for consensus structure string
ok 476 - Check for query string
ok 477 - Check for hit string
ok 478 - Check for homology string
ok 479 - Check for posterior probability string
ok 480 - Check for the correct result reference type
ok 481 - Check algorithm
ok 482 - Check algorithm version
ok 483 - Check hmm_name
ok 484 - Check sequence_file
ok 485 - Check query_name
ok 486 - Check query_length
ok 487 - Check query_accession
ok 488 - Check query_description
ok 489 - Check num_hits
ok 490 - Check for the correct hit reference type
ok 491 - Check hit name
ok 492 - Check for hit description
ok 493 - Check hit raw_score
ok 494 - Check hit bits (0)
ok 495 - Check hit significance
ok 496 - Check num_hsps
ok 497 - Check hit length absence
ok 498
ok 499
ok 500 - Check for correct hsp reference type
ok 501 - Check for hit seq_id
ok 502 - Check for query seq_id
ok 503 - Check for hit alifrom value
ok 504 - Check for hit ali to value
ok 505 - Check for query hmmfrom value
ok 506 - Check for query hmm to value
ok 507 - Check for hsp score
ok 508 - Check for hsp bits (0)
ok 509 - Check for hsp c-Evalue
ok 510 - Check for hsp query length
ok 511 - Check for hsp hit length
ok 512 - Check for hsp total length
ok 513 - Check for hsp query gaps
ok 514 - Check for hsp hit gaps
ok 515 - Check for hsp total gaps
ok 516 - Check hit length consistency
ok 517 - Check query length consistency
ok 518
ok 519
ok 520
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528 - Check for consensus structure string
ok 529 - Check for query string
ok 530 - Check for hit string
ok 531 - Check for homology string
ok 532 - Check for posterior probability string
ok 533 - Check for the correct result reference type
ok 534 - Check algorithm
ok 535 - Check algorithm version
ok 536 - Check hmm_name
ok 537 - Check sequence_file
ok 538 - Check query_name
ok 539 - Check query_length
ok 540 - Check query_description
ok 541 - Check num_hits
ok 542 - Check for the correct hit reference type
ok 543 - Check hit name
ok 544 - Check for hit description
ok 545 - Check hit raw_score
ok 546 - Check hit significance
ok 547 - Check num_hsps
ok 548 - Check for correct hsp reference type
ok 549 - Check for hit envfrom value
ok 550 - Check for hit env to value
ok 551 - Check for query hmmfrom value
ok 552 - Check for query hmm to value
ok 553 - Check for hsp score
ok 554 - Check for hsp c-Evalue
ok 555 - Check for correct hsp reference type
ok 556 - Check for hit envfrom value
ok 557 - Check for hit env to value
ok 558 - Check for query hmmfrom value
ok 559 - Check for query hmm to value
ok 560 - Check for hsp score
ok 561 - Check for hsp c-Evalue
ok 562 - Check for correct hsp reference type
ok 563 - Check for hit envfrom value
ok 564 - Check for hit env to value
ok 565 - Check for query hmmfrom value
ok 566 - Check for query hmm to value
ok 567 - Check for hsp score
ok 568 - Check for hsp c-Evalue
ok 569 - Check for correct hsp reference type
ok 570 - Check for hit envfrom value
ok 571 - Check for hit env to value
ok 572 - Check for query hmmfrom value
ok 573 - Check for query hmm to value
ok 574 - Check for hsp score
ok 575 - Check for hsp c-Evalue
ok 576 - Check for correct hsp reference type
ok 577 - Check for hit envfrom value
ok 578 - Check for hit env to value
ok 579 - Check for query hmmfrom value
ok 580 - Check for query hmm to value
ok 581 - Check for hsp score
ok 582 - Check for hsp c-Evalue
ok 583 - Check for correct hsp reference type
ok 584 - Check for hit envfrom value
ok 585 - Check for hit env to value
ok 586 - Check for query hmmfrom value
ok 587 - Check for query hmm to value
ok 588 - Check for hsp score
ok 589 - Check for hsp c-Evalue
ok 590 - Check hit length
ok 591
ok 592
ok 593 - Check for the correct hit reference type
ok 594 - Check hit name
ok 595 - Check for hit description
ok 596 - Check hit raw_score
ok 597 - Check hit significance
ok 598 - Check num_hsps
ok 599 - Check for correct hsp reference type
ok 600 - Check for hit envfrom value
ok 601 - Check for hit env to value
ok 602 - Check for query hmmfrom value
ok 603 - Check for query hmm to value
ok 604 - Check for hsp score
ok 605 - Check for hsp c-Evalue
ok 606 - Check for correct hsp reference type
ok 607 - Check for hit envfrom value
ok 608 - Check for hit env to value
ok 609 - Check for query hmmfrom value
ok 610 - Check for query hmm to value
ok 611 - Check for hsp score
ok 612 - Check for hsp c-Evalue
ok 613 - Check for correct hsp reference type
ok 614 - Check for hit envfrom value
ok 615 - Check for hit env to value
ok 616 - Check for query hmmfrom value
ok 617 - Check for query hmm to value
ok 618 - Check for hsp score
ok 619 - Check for hsp c-Evalue
ok 620 - Check for the correct result reference type
ok 621 - Check algorithm
ok 622 - Check algorithm version
ok 623 - Check hmm_name
ok 624 - Check sequence_file
ok 625 - Check query_name
ok 626 - Check query_length
ok 627 - Check query_description
ok 628 - Check num_hits
ok 629 - Check for the correct hit reference type
ok 630 - Check hit name
ok 631 - Check for hit description
ok 632 - Check hit raw_score
ok 633 - Check hit significance
ok 634 - Check num_hsps
ok 635 - Check for correct hsp reference type
ok 636 - Check hit sequence
ok 637 - Check query sequence
ok 638 - Check for correct hsp reference type
ok 639 - Check hit sequence
ok 640 - Check query sequence
ok 641 - Check hit length
ok 642
ok 643
ok 644 - Check for the correct hit reference type
ok 645 - Check hit name
ok 646 - Check for hit description
ok 647 - Check hit raw_score
ok 648 - Check hit significance
ok 649 - Check num_hsps
ok 650 - Check for correct hsp reference type
ok 651 - Check hit sequence
ok 652 - Check query sequence
ok 653 - Check for correct hsp reference type
ok 654 - Check hit sequence
ok 655 - Check query sequence
ok 656 - Check for the correct hit reference type
ok 657 - Check hit name
ok 658 - Check for hit description
ok 659 - Check hit raw_score
ok 660 - Check hit significance
ok 661 - Check num_hsps
ok 662 - Check for correct hsp reference type
ok 663 - Check hit sequence
ok 664 - Check query sequence
ok 665 - Check for correct hsp reference type
ok 666 - Check hit sequence
ok 667 - Check query sequence
ok 668 - Check for the correct result reference type
ok 669 - Check algorithm
ok 670 - Check algorithm version
ok 671 - Check query_name
ok 672 - Check query_length
ok 673 - Check query_description
ok 674 - Check num_hits
ok 675 - Check for the correct hit reference type
ok 676 - Check hit name
ok 677 - Check for hit description
ok 678 - Check hit raw_score
ok 679 - Check hit significance
ok 680 - Check num_hsps
ok 681 - Check for correct hsp reference type
ok 682 - Check for query string
ok 683 - Check for hit string
ok 684 - Check for homology string
ok 685 - Check for posterior probability string
ok 686 - Check if loading hmmpfam output via the hmm2 parser directly works
ok 687 - Check for the correct result reference type
ok 688 - Check if loading hmmsearch2 output via the hmm2 parser directly works
ok 689 - Check for the correct result reference type
ok 690 - Check if loading hmmscan output via the hmm3 parser directly works
ok 691 - Check for the correct result reference type
ok 692 - Check if loading hmmsearch3 output via the hmm3 parser directly works
ok 693 - Check for the correct result reference type
ok 694 - Check if selecting the correct hmmpfam parser using -version works
ok 695 - Check for the correct result reference type
ok 696 - Check if selecting the correct hmmsearch2 parser using -version works
ok 697 - Check for the correct result reference type
ok 698 - Check if selecting the correct hmmscan parser using -version works
ok 699 - Check for the correct result reference type
ok 700 - Check if selecting the correct hmmsearch3 parser using -version works
ok 701 - Check for the correct result reference type
ok 702 - Check if reading from a pipe works
ok 703 - Check for the correct result reference type
ok 704 - Check num_hits
ok 705 - Check query_length
ok 706 - Check hit length
ok 707 - bug3376
ok 708 - bug3421 - Check if can correctly parse an HSP with line full of dashes
ok 709 - bug3302 - Check if can parse multiresult hmmer
ok 710 - Check algorithm
ok 711 - Check nhmmer algorithm version
ok 712 - Check hmm_name
ok 713 - Check sequence_file
ok 714 - Check query_name
ok 715 - Check query_length
ok 716 - Check query_accession
ok 717 - Check query_description
ok 718 - Check num_hits
ok 719 - Check for the correct hit reference type
ok 720 - Check nhmmer hit name
ok 721 - Check nhmmer hit description
ok 722 - Check nhmmer hit score
ok 723 - Check nhmmer hit bits (0)
ok 724 - Check nhmmer hit significance
ok 725 - Check num_hsps
ok 726 - Check nhmmer hit length
ok 727
ok 728
ok 729 - Check for correct hsp reference type
ok 730 - Check for nhmmer hit seq_id
ok 731 - Check for nhmmer query seq_id
ok 732 - Check nhmmer hsp hit start
ok 733 - Check nhmmer hsp hit end
ok 734 - Check nhmmer hsp query start
ok 735 - Check nhmmer hsp query end
ok 736 - Check nhmmer hsp hit strand
ok 737 - Check nhmmer hsp query strand
ok 738 - Check nhmmer hsp score
ok 739 - Check nhmmer hsp bits (0)
ok 740 - Check nhmmer hsp evalue
ok 741 - Check for hsp query length
ok 742 - Check for hsp hit length
ok 743 - Check for hsp total length
ok 744 - Check for hsp query gaps
ok 745 - Check for hsp hit gaps
ok 746 - Check for hsp total gaps
ok 747 - Check hit length consistency
ok 748 - Check query length consistency
ok 749
ok 750
ok 751
ok 752
ok 753
ok 754
ok 755
ok 756
ok 757
ok 758 - Check for consensus structure string
ok 759 - Check for nhmmer query string
ok 760 - Check for nhmmer homology string
ok 761 - Check for nhmmer hit string
ok 762 - Check for nhmmer posterior probability string
ok 763 - Check if nhmmer homology string and hit string have an equal length
ok 764 - Check if nhmmer query string and homology string have an equal length
ok 765 - Check nhmmer hit name
ok 766 - Check nhmmer hit description
ok 767 - Check nhmmer hit score
ok 768 - Check nhmmer hit bits (0)
ok 769 - Check nhmmer hit significance
ok 770 - Check nhmmer hit length
ok 771 - Check for nhmmer hit seq_id
ok 772 - Check for nhmmer query seq_id
ok 773 - Check nhmmer hsp query start
ok 774 - Check nhmmer hsp query end
ok 775 - Check nhmmer hsp hit start
ok 776 - Check nhmmer hsp hit end
ok 777 - Check nhmmer hsp hit strand
ok 778 - Check nhmmer hsp query strand
ok 779 - Check nhmmer hsp score
ok 780 - Check nhmmer hsp bits (0)
ok 781 - Check nhmmer hsp evalue
ok 782 - Check for hsp query length
ok 783 - Check for hsp hit length
ok 784 - Check for hsp total length
ok 785 - Check for hsp query gaps
ok 786 - Check for hsp hit gaps
ok 787 - Check for hsp total gaps
ok 788 - Check hit length consistency
ok 789 - Check query length consistency
ok 790
ok 791 - Check for consensus structure string
ok 792 - Check for nhmmer query string
ok 793 - Check for nhmmer homology string
ok 794 - Check for nhmmer hit string
ok 795 - Check for nhmmer posterior probability string
ok 796 - Check if nhmmer homology string and hit string have an equal length
ok 797 - Check if nhmmer query string and homology string have an equal length
ok 798 - Check Significance filtered num_hits
ok 799 - Check Significance filtered hit ID
ok 800 - Check Significance filtered hit ID
ok 801 - Check Significance filtered hit ID
ok 802 - Check Significance filtered hit ID
ok 803 - Check Significance filtered hit ID
ok 804
ok 805 - Check Score filtered num_hits
ok 806 - Check Score filtered hit ID
ok 807 - Check Score filtered hit ID
ok 808 - Check Score filtered hit ID
ok 809 - Check Score filtered hit ID
ok 810
ok 811 - Check Bits filtered num_hits
ok 812 - Check Bits filtered num_hits
ok 813 - Check Bits filtered num_hits
ok 814 - Check Hit_filter filtered num_hits
ok 815 - Check Hit_filter filtered hits ID
ok 816
ok 817 - Correct parsing of alignments with stops
ok 818 - Check algorithm
ok 819 - Check query_name
ok 820 - Check query_length absence
ok 821 - Check query_description
ok 822 - Check num_hits
ok 823 - query name okay
ok 824 - Check num_hsps
ok
t/SearchIO/hmmer_pull.t ................ 
1..290
ok 1 - use Bio::SearchIO;
ok 2
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t/SearchIO/infernal.t .................. 
1..496
ok 1 - use Bio::SearchIO;
ok 2 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI'
ok 3 - Check for the correct Result reference type
ok 4 - Check algorithm
ok 5 - Check cmsearch algorithm version
ok 6 - Check cm_name
ok 7 - Check database_name
ok 8 - Check database_entries
ok 9 - Check database_letters
ok 10 - Check query_name
ok 11 - Check query_length
ok 12 - Check query_accession
ok 13 - Check query_description
ok 14 - Check num_hits
ok 15 - Check for the correct hit reference type
ok 16 - Hit algorithm
ok 17 - Check hit name
ok 18 - Check hit description
ok 19 - Check hit length
ok 20 - Check hit score
ok 21 - Check hit bits
ok 22 - Check number of HSPs
ok 23 - Check hit significance
ok 24 - Check hit rank
ok 25 - Check for correct hsp reference type
ok 26 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 28 - 'Check for hsp hit isa seqfeature similarity' isa 'Bio::SeqFeature::Similarity'
ok 29 - Check for HSP hit seq_id
ok 30 - Check for HSP query seq_id
ok 31 - Check hsp query start
ok 32 - Check hsp query end
ok 33 - Check hsp hit start
ok 34 - Check hsp hit end
ok 35 - Check hsp score
ok 36 - Check hsp bits
ok 37 - Check hsp evalue
ok 38 - Check for hsp query length
ok 39 - Check for hsp hit length
ok 40 - Check for hsp total length
ok 41 - Check for hsp query gaps
ok 42 - Check for hsp hit gaps
ok 43 - Check for hsp total gaps
ok 44 - Check hsp hit strand
ok 45 - Check hit name
ok 46 - Check hit description
ok 47 - Check hit score
ok 48 - Check hit raw_score
ok 49 - Check hit bits
ok 50 - Check hit significance
ok 51 - Check hit length
ok 52 - Hit rank
ok 53 - Check for hit seq_id
ok 54 - Check for query seq_id
ok 55 - Check hsp query start
ok 56 - Check hsp query end
ok 57 - Check hsp hit start
ok 58 - Check hsp hit end
ok 59 - Check hsp score
ok 60 - Check hsp bits
ok 61 - Check hsp evalue
ok 62 - Check for hsp query gaps
ok 63 - Check for hsp hit gaps
ok 64 - Check for hsp total gaps
ok 65 - Check hsp hit strand
ok 66 - Check for NC string
ok 67 - Check for CS string
ok 68 - Check for query string
ok 69 - Check for homology string
ok 70 - Check for hit string
ok 71 - Check for posterior probability string
ok 72 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 73 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 74 - Check hsp feature1 get_tag_values
ok 75 - Check hsp feature2 get_tag_values
ok 76 - Check for undefined result
ok 77 - Check result num_hits - multi report
ok 78 - Check result query_name - multi report
ok 79 - Check hit length - multi report
ok 80 - Check result\#2 num_hits - multi report
ok 81 - Check result\#2 query_name - multi report
ok 82 - Check result\#2 hit length - multi report
ok 83 - Check result\#2 hsp hit strand - multi report
ok 84 - Check cm_name
ok 85 - Check for undefined hit
ok 86 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI'
ok 87 - Result
ok 88 - Result reference
ok 89 - Result version
ok 90 - Result parameters
ok 91 - Result statistics
ok 92 - Result entries
ok 93 - Result letters
ok 94 - Result database_name
ok 95 - Result num_hits
ok 96 - Result program_reference
ok 97 - Result query_accession
ok 98 - Result query_description
ok 99 - Result query_length
ok 100 - Result query_name
ok 101 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 102 - Hit GI
ok 103 - Hit accession
ok 104 - Hit algorithm
ok 105 - Hit bits
ok 106 - Hit description
ok 107 - Hit locus
ok 108 - Hit n
ok 109 - Hit name
ok 110 - Hit num_hsps
ok 111 - Hit length_aln() not implemented
ok 112 - Hit num_unaligned_hit() not implemented
ok 113 - Hit num_unaligned_query() not implemented
ok 114 - Hit num_unaligned_sbjct() not implemented
ok 115 - Hit start not implemented
ok 116 - Hit end not implemented
ok 117 - Hit strand not implemented
ok 118 - Hit logical_length not implemented
ok 119 - Hit frac_aligned_hit not implemented
ok 120 - Hit frac_aligned_query not implemented
ok 121 - Hit frac_conserved not implemented
ok 122 - Hit frac_identical not implemented
ok 123 - Hit matches not implemented
ok 124 - Hit gaps not implemented
ok 125 - Hit frame not implemented
ok 126 - Hit range not implemented
ok 127 - Hit seq_inds not implemented
ok 128 - Hit length
ok 129 - Hit overlap
ok 130 - Hit query_length
ok 131 - Hit rank
ok 132 - Hit raw_score
ok 133 - Hit score
ok 134 - Hit p
ok 135
ok 136 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 137 - HSP algorithm
ok 138
ok 139 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 140 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 141
ok 142
ok 143 - HSP frame
ok 144 - HSP gaps
ok 145 - Hit length
ok 146 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 147 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 148 - HSP hit_string
ok 149 - HSP homology_string
ok 150 - HSP hsp_group
ok 151 - HSP hsp_length
ok 152 - HSP length
ok 153 - HSP links
ok 154 - HSP n
ok 155 - HSP pvalue
ok 156 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 157 - HSP query_string
ok 158 - HSP range
ok 159 - HSP rank
ok 160
ok 161 - HSP end
ok 162 - HSP expect
ok 163 - HSP seq_inds not implemented
ok 164 - HSP matches not implemented
ok 165 - HSP frac_conserved not implemented
ok 166 - HSP frac_identical not implemented
ok 167 - HSP num_conserved not implemented
ok 168 - HSP num_identical not implemented
ok 169 - HSP percent_identity not implemented
ok 170 - HSP cigar_string not implemented
ok 171 - HSP cigar_string not implemented
ok 172 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 173 - HSP seq_str
ok 174 - HSP start
ok 175 - HSP custom_score
ok 176 - HSP meta
ok 177 - HSP strand
ok 178 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 179 - HSP algorithm
ok 180
ok 181 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 182 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 183 - HSP frame
ok 184 - HSP gaps
ok 185 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 186 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 187 - HSP hit_string
ok 188 - HSP homology_string
ok 189 - HSP hsp_group
ok 190 - HSP hsp_length
ok 191 - HSP length
ok 192 - HSP links
ok 193 - HSP n
ok 194 - HSP pvalue
ok 195 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 196 - HSP query_string
ok 197 - HSP range
ok 198 - HSP rank
ok 199
ok 200 - HSP end
ok 201 - HSP expect
ok 202 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 203 - HSP seq_str
ok 204 - HSP start
ok 205 - HSP custom_score
ok 206 - HSP meta
ok 207 - HSP strand
ok 208 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI'
ok 209 - Result CMSEARCH
ok 210 - Result CMSEARCH reference
ok 211 - Result CMSEARCH version
ok 212 - Result parameters
ok 213 - Result statistics
ok 214 - Result entries
ok 215 - Result letters
ok 216 - Result database_name
ok 217 - Result num_hits
ok 218 - Result program_reference
ok 219 - Result query_accession
ok 220 - Result query_description
ok 221 - Result query_length
ok 222 - Result query_name
ok 223 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 224 - Hit GI
ok 225 - Hit accession
ok 226 - Hit algorithm
ok 227 - Hit bits
ok 228 - Hit description
ok 229 - Hit locus
ok 230 - Hit n
ok 231 - Hit name
ok 232 - Hit num_hsps
ok 233 - No p values
ok 234 - Hit length
ok 235 - Hit overlap
ok 236 - Hit query_length
ok 237 - Hit rank
ok 238 - Hit raw_score
ok 239 - Hit score
ok 240
ok 241 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 242 - HSP algorithm
ok 243
ok 244 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 245 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 246
ok 247
ok 248 - HSP frame
ok 249 - HSP gaps
ok 250 - Hit length
ok 251 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 252 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 253 - HSP hit_string
ok 254 - HSP homology_string
ok 255 - HSP hsp_group
ok 256 - HSP hsp_length
ok 257 - HSP length
ok 258 - HSP links
ok 259 - HSP n
ok 260 - HSP pvalue
ok 261 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 262 - HSP query_string
ok 263 - HSP range
ok 264 - HSP rank
ok 265
ok 266 - HSP end
ok 267 - HSP expect
ok 268 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 269 - HSP seq_str
ok 270 - HSP start
ok 271 - HSP custom_score
ok 272 - HSP meta
ok 273 - HSP strand
ok 274 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 275 - HSP algorithm
ok 276
ok 277 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 278 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 279 - HSP frame
ok 280 - HSP gaps
ok 281 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 282 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 283 - HSP hit_string
ok 284 - HSP homology_string
ok 285 - HSP hsp_group
ok 286 - HSP hsp_length
ok 287 - HSP length
ok 288 - HSP links
ok 289 - HSP n
ok 290 - HSP pvalue
ok 291 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 292 - HSP query_string
ok 293 - HSP range
ok 294 - HSP rank
ok 295
ok 296 - HSP end
ok 297 - HSP expect
ok 298 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 299 - HSP seq_str
ok 300 - HSP start
ok 301 - HSP custom_score
ok 302 - HSP meta
ok 303 - HSP strand
ok 304 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 305 - Hit accession
ok 306 - Hit GI
ok 307 - Hit algorithm
ok 308 - Hit bits
ok 309 - Hit description
ok 310 - Hit length
ok 311 - Hit locus
ok 312 - Hit n
ok 313 - Hit name
ok 314 - Hit num_hsps
ok 315 - Hit overlap
ok 316 - Hit query_length
ok 317 - Hit rank
ok 318 - Hit raw_score
ok 319 - Hit score
ok 320
ok 321 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 322 - HSP algorithm
ok 323
ok 324 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 325 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 326 - HSP frame
ok 327 - HSP gaps
ok 328 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 329 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 330 - HSP hit_string
ok 331 - HSP homology_string
ok 332 - HSP hsp_group
ok 333 - HSP hsp_length
ok 334 - HSP length
ok 335 - HSP links
ok 336 - HSP n
ok 337 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 338 - HSP query_string
ok 339 - HSP range
ok 340 - HSP rank
ok 341
ok 342 - HSP end
ok 343 - HSP expect
ok 344 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 345 - HSP seq_str
ok 346 - HSP start
ok 347 - HSP custom_score
ok 348 - HSP meta
ok 349 - HSP strand
ok 350 - HSP meta gap bug
ok 351 - HSP meta
ok 352 - HSP meta
ok 353
ok 354
ok 355 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI'
ok 356 - Result CMSEARCH
ok 357 - Result CMSEARCH reference
ok 358 - Result CMSEARCH version
ok 359 - Result parameters
ok 360 - Result statistics
ok 361 - Result entries
ok 362 - Result letters
ok 363 - Result database_name
ok 364 - Result num_hits
ok 365 - Result program_reference
ok 366 - Result query_accession
ok 367 - Result query_description
ok 368 - Result query_length
ok 369 - Result query_name
ok 370 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 371 - Hit GI
ok 372 - Hit accession
ok 373 - Hit algorithm
ok 374 - Hit bits
ok 375 - Hit description
ok 376 - Hit locus
ok 377 - Hit n
ok 378 - Hit name
ok 379 - Hit num_hsps
ok 380 - No p values
ok 381 - Hit length
ok 382 - Hit overlap
ok 383 - Hit query_length
ok 384 - Hit rank
ok 385 - Hit raw_score
ok 386 - Hit score
ok 387
ok 388 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 389 - HSP algorithm
ok 390
ok 391 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 392 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 393
ok 394
ok 395 - HSP frame
ok 396 - HSP gaps
ok 397 - Hit length
ok 398 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 399 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 400 - HSP hit_string
ok 401 - HSP homology_string
ok 402 - HSP hsp_group
ok 403 - HSP hsp_length
ok 404 - HSP length
ok 405 - HSP links
ok 406 - HSP n
ok 407 - HSP pvalue
ok 408 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 409 - HSP query_string
ok 410 - HSP range
ok 411 - HSP rank
ok 412
ok 413 - HSP end
ok 414 - HSP expect
ok 415 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 416 - HSP seq_str
ok 417 - HSP start
ok 418 - HSP custom_score
ok 419 - HSP meta
ok 420 - HSP strand
ok 421 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 422 - HSP algorithm
ok 423
ok 424 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 425 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 426 - HSP frame
ok 427 - HSP gaps
ok 428 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 429 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 430 - HSP hit_string
ok 431 - HSP homology_string
ok 432 - HSP hsp_group
ok 433 - HSP hsp_length
ok 434 - HSP length
ok 435 - HSP links
ok 436 - HSP n
ok 437 - HSP pvalue
ok 438 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 439 - HSP query_string
ok 440 - HSP range
ok 441 - HSP rank
ok 442
ok 443 - HSP end
ok 444 - HSP expect
ok 445 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 446 - HSP seq_str
ok 447 - HSP start
ok 448 - HSP custom_score
ok 449 - HSP meta
ok 450 - HSP strand
ok 451 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 452 - Hit accession
ok 453 - Hit GI
ok 454 - Hit algorithm
ok 455 - Hit bits
ok 456 - Hit description
ok 457 - Hit length
ok 458 - Hit locus
ok 459 - Hit n
ok 460 - Hit name
ok 461 - Hit num_hsps
ok 462 - Hit overlap
ok 463 - Hit query_length
ok 464 - Hit rank
ok 465 - Hit raw_score
ok 466 - Hit score
ok 467
ok 468 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 469 - HSP algorithm
ok 470
ok 471 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 472 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 473 - HSP frame
ok 474 - HSP gaps
ok 475 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 476 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 477 - HSP hit_string
ok 478 - HSP homology_string
ok 479 - HSP hsp_group
ok 480 - HSP hsp_length
ok 481 - HSP length
ok 482 - HSP links
ok 483 - HSP n
ok 484 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 485 - HSP query_string
ok 486 - HSP range
ok 487 - HSP rank
ok 488
ok 489 - HSP end
ok 490 - HSP expect
ok 491 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 492 - HSP seq_str
ok 493 - HSP start
ok 494 - HSP custom_score
ok 495 - HSP meta
ok 496 - HSP strand
ok
t/SearchIO/megablast.t ................. 
1..31
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/SearchIO/psl.t ....................... 
1..53
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50 - next_hsp should be undef
ok 51 - next_hit should be undef
not ok 52 - next_result should be undef # TODO next_result should really return undef, not empty string

#   Failed (TODO) test 'next_result should be undef'
#   at t/SearchIO/psl.t line 97.
#          got: ''
#     expected: undef
ok 53
ok
t/SearchIO/rnamotif.t .................. 
1..60
ok 1 - use Bio::SearchIO;
ok 2 - An object of class 'Bio::Search::Result::GenericResult' isa 'Bio::Search::Result::ResultI'
ok 3 - Result RNAMOTIF
ok 4 - Result RNAMOTIF reference
ok 5 - Result RNAMOTIF version
ok 6 - Result entries
ok 7 - Result letters
ok 8 - Result database_name
ok 9 - Result num_hits
ok 10 - Result program_reference
ok 11 - Result query_accession
ok 12 - Result query_description
ok 13 - Result query_length
ok 14 - Result query_name
ok 15 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI'
ok 16 - Hit accession
ok 17 - Hit GI
ok 18 - Hit algorithm
ok 19 - Hit description
ok 20 - Hit length
ok 21 - Hit locus
ok 22 - Hit n
ok 23 - Hit name
ok 24 - Hit num_hsps
ok 25 - Hit overlap
ok 26 - Hit rank
ok 27 - Hit raw_score
ok 28 - Hit score
ok 29
ok 30 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI'
ok 31 - HSP algorithm
ok 32
ok 33 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 34 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity'
ok 35 - HSP frame
ok 36 - HSP gaps
ok 37 - RNAMotif get_aln warning
ok 38 - 'HSP hit' isa 'Bio::SeqFeature::Similarity'
ok 39 - HSP hit_string
ok 40 - HSP homology_string
ok 41 - HSP hsp_group
ok 42 - HSP hsp_length
ok 43 - HSP length
ok 44 - HSP links
ok 45 - HSP n
ok 46 - 'HSP query' isa 'Bio::SeqFeature::Similarity'
ok 47 - HSP query_string
ok 48 - HSP range
ok 49 - HSP rank
ok 50
ok 51 - HSP end
ok 52 - HSP expect
ok 53 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58 - HSP strand
ok 59
ok 60
ok
t/SearchIO/sim4.t ...................... 
1..102
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/SearchIO/waba.t ...................... 
1..64
ok 1 - use Bio::SearchIO;
ok 2 - An object of class 'Bio::SearchIO::waba' isa 'Bio::SearchIO'
ok 3 - query_name
ok 4 - query database
ok 5 - database name
ok 6 - name
ok 7 - hsps
ok 8 - total length
ok 9 - start
ok 10 - end
ok 11 - strand
ok 12 - start
ok 13 - end
ok 14 - strand
ok 15 - query string
ok 16 - hit_string
ok 17 - hmmstate string
ok 18
ok 19
ok 20
ok 21 - total length
ok 22 - start
ok 23 - end
ok 24 - strand
ok 25 - start
ok 26 - end
ok 27 - strand
ok 28 - query string
ok 29 - hit_string
ok 30 - hmmstate string
ok 31
ok 32
ok 33
ok 34 - total length
ok 35 - start
ok 36 - end
ok 37 - strand
ok 38 - start
ok 39 - end
ok 40 - strand
ok 41 - query string
ok 42 - hit_string
ok 43 - hmmstate string
ok 44
ok 45
ok 46
ok 47 - query_name
ok 48 - query database
ok 49 - database name
ok 50 - name
ok 51 - hsps
ok 52 - total length
ok 53 - start
ok 54 - end
ok 55 - strand
ok 56 - start
ok 57 - end
ok 58 - strand
ok 59 - query string
ok 60 - hit_string
ok 61 - hmmstate string
ok 62
ok 63
ok 64
ok
t/SearchIO/wise.t ...................... 
1..20
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok
t/Seq/DBLink.t ......................... 
1..131
ok 1 - use Bio::SeqIO;
ok 2 - "swissprot:K1C9_HUMAN"
ok 3 - no double colon
ok 4 - no trailing colon
ok 5 - no double space
ok 6 - dblink value is splittable
ok 7 - "GenBank:Z29074.1"
ok 8 - no double colon
ok 9 - no trailing colon
ok 10 - no double space
ok 11 - dblink value is splittable
ok 12 - "GenPept:CAA82315.1"
ok 13 - no double colon
ok 14 - no trailing colon
ok 15 - no double space
ok 16 - dblink value is splittable
ok 17 - "GenBank:S69510.1"
ok 18 - no double colon
ok 19 - no trailing colon
ok 20 - no double space
ok 21 - dblink value is splittable
ok 22 - "GenPept:AAC60619.1"
ok 23 - no double colon
ok 24 - no trailing colon
ok 25 - no double space
ok 26 - dblink value is splittable
ok 27 - "GenBank:X75015.1"
ok 28 - no double colon
ok 29 - no trailing colon
ok 30 - no double space
ok 31 - dblink value is splittable
ok 32 - "GenPept:CAA52924.1"
ok 33 - no double colon
ok 34 - no trailing colon
ok 35 - no double space
ok 36 - dblink value is splittable
ok 37 - "GenBank:AB001594.1"
ok 38 - no double colon
ok 39 - no trailing colon
ok 40 - no double space
ok 41 - dblink value is splittable
ok 42 - "GenPept:BAA19418.1"
ok 43 - no double colon
ok 44 - no trailing colon
ok 45 - no double space
ok 46 - dblink value is splittable
ok 47 - "GenBank:I37984"
ok 48 - no double colon
ok 49 - no trailing colon
ok 50 - no double space
ok 51 - dblink value is splittable
ok 52 - "HSSP:P08670"
ok 53 - no double colon
ok 54 - no trailing colon
ok 55 - no double space
ok 56 - dblink value is splittable
ok 57 - "IntAct:P35527"
ok 58 - no double colon
ok 59 - no trailing colon
ok 60 - no double space
ok 61 - dblink value is splittable
ok 62 - "Ensembl:ENSG00000171403"
ok 63 - no double colon
ok 64 - no trailing colon
ok 65 - no double space
ok 66 - dblink value is splittable
ok 67 - "KEGG:hsa:3857"
ok 68 - no double colon
ok 69 - no trailing colon
ok 70 - no double space
ok 71 - dblink value is splittable
ok 72 - "HGNC:6447"
ok 73 - no double colon
ok 74 - no trailing colon
ok 75 - no double space
ok 76 - dblink value is splittable
ok 77 - "MIM:144200"
ok 78 - no double colon
ok 79 - no trailing colon
ok 80 - no double space
ok 81 - dblink value is splittable
ok 82 - "MIM:607606"
ok 83 - no double colon
ok 84 - no trailing colon
ok 85 - no double space
ok 86 - dblink value is splittable
ok 87 - "ArrayExpress:P35527"
ok 88 - no double colon
ok 89 - no trailing colon
ok 90 - no double space
ok 91 - dblink value is splittable
ok 92 - "GO:0005200"
ok 93 - no double colon
ok 94 - no trailing colon
ok 95 - no double space
ok 96 - dblink value is splittable
ok 97 - "GO:0008544"
ok 98 - no double colon
ok 99 - no trailing colon
ok 100 - no double space
ok 101 - dblink value is splittable
ok 102 - "InterPro:IPR011000"
ok 103 - no double colon
ok 104 - no trailing colon
ok 105 - no double space
ok 106 - dblink value is splittable
ok 107 - "InterPro:IPR001664"
ok 108 - no double colon
ok 109 - no trailing colon
ok 110 - no double space
ok 111 - dblink value is splittable
ok 112 - "InterPro:IPR002957"
ok 113 - no double colon
ok 114 - no trailing colon
ok 115 - no double space
ok 116 - dblink value is splittable
ok 117 - "Pfam:PF00038"
ok 118 - no double colon
ok 119 - no trailing colon
ok 120 - no double space
ok 121 - dblink value is splittable
ok 122 - "PRINTS:PR01248"
ok 123 - no double colon
ok 124 - no trailing colon
ok 125 - no double space
ok 126 - dblink value is splittable
ok 127 - "PROSITE:PS00226"
ok 128 - no double colon
ok 129 - no trailing colon
ok 130 - no double space
ok 131 - dblink value is splittable
ok
t/Seq/EncodedSeq.t ..................... 
1..37
ok 1 - use Bio::Seq::EncodedSeq;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 12
ok 13
ok 14 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/Seq/LargeLocatableSeq.t .............. 
1..8
ok 1 - use Bio::Seq::LargeLocatableSeq;
ok 2
ok 3 - An object of class 'Bio::Seq::LargeLocatableSeq' isa 'Bio::Seq::LargeSeqI'
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Seq/LargePSeq.t ...................... 
1..30
ok 1 - use Bio::Seq::LargePrimarySeq;
ok 2 - use Bio::Seq::LargeSeq;
ok 3 - use Bio::Location::Simple;
ok 4 - use Bio::Location::Fuzzy;
ok 5 - use Bio::Location::Split;
ok 6 - use Bio::SeqIO;
ok 7
ok 8
ok 9 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 10 - Subseq is GGGGT
ok 11
ok 12
ok 13
ok 14 - trunc seq was GGGGTGAA
ok 15
ok 16
ok 17
ok 18 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 19
ok 20 - output via Bio::SeqIO::fasta
ok 21 - Subseq is GGGGT
ok 22 - trunc seq was GGGGTGAA
ok 23
ok 24
ok 25
ok 26 - Sequence is ATGGGGTGGGGT
ok 27 - Subseq is GGGGT
ok 28 - trunc seq was GGGGT
ok 29
ok 30
ok
t/Seq/LocatableSeq.t ................... 
1..119
ok 1 - use Bio::LocatableSeq;
ok 2 - use Bio::AlignIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 13
ok 14
ok 15 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 16
ok 17
ok 18
ok 19
not ok 20 # TODO Need to fix columns before start of seq w/ start > 1

#   Failed (TODO) test at t/Seq/LocatableSeq.t line 47.
#          got: 'Bio::Location::Simple=HASH(0x3a20048)'
#     expected: undef
ok 21
ok 22 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
ok 23
ok 24
ok 25
ok 26
ok 27 - threw Regexp ((?^:.+))
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::Location::Simple' isa 'Bio::Location::Simple'
ok 51
ok 52
ok 53 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
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 - * is counted in length
ok 107 - * is counted in length, but end is wrong
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
not ok 118 # TODO Bio::LocatableSeq global variables have scoping issues

#   Failed (TODO) test at t/Seq/LocatableSeq.t line 307.
#          got: '\-\.=~'
#     expected: '-\?'
not ok 119 # TODO Bio::LocatableSeq global variables have scoping issues

#   Failed (TODO) test at t/Seq/LocatableSeq.t line 309.
#          got: '19'
#     expected: anything else
ok
t/Seq/MetaSeq.t ........................ 
1..132
ok 1 - use Bio::Seq::Meta;
ok 2 - use Bio::Seq::Meta::Array;
ok 3 - use Bio::SeqIO;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Seq::Quality;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - aa-bb  bb 
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
t/Seq/PrimaryQual.t .................... 
1..70
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::Quality;
ok 3 - use Bio::Seq::PrimaryQual;
ok 4
ok 5
ok 6
ok 7
ok 8 - A reference of type 'ARRAY' isa 'ARRAY'
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 - threw Regexp ((?^:.+))
ok 27 - threw Regexp ((?^:.+))
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33 - threw Regexp ((?^:EX))
ok 34
ok 35
ok 36 - threw Regexp ((?^:EX))
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
t/Seq/PrimarySeq.t ..................... 
1..312
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Location::Simple;
ok 3 - use Bio::Location::Fuzzy;
ok 4 - use Bio::Location::Split;
ok 5 - Bare object
ok 6 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
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 - An object of class 'Bio::PrimarySeq' isa 'Bio::IdentifiableI'
ok 26 - An object of class 'Bio::PrimarySeq' isa 'Bio::DescribableI'
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 - threw Regexp ((?^:.+))
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 59
ok 60 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 61
ok 62 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 63
ok 64 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76 - Translation: LVAST
ok 77 - Translation: MVAST
ok 78 - Translation: MVAST
ok 79 - Translation: MVAST*
ok 80 - Translation: M*
ok 81 - Translation: M
ok 82
ok 83 - Translation: MWP
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92 - frame 0 start, frame 1 stop < frame 0 stop
ok 93 - frame 1 start, frame 2 stop < frame 1 stop
ok 94
ok 95
ok 96
ok 97 - Alphabet
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 - Bug 2438
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140 - Bug \#2864
ok 141 - Terminator + inside sequence
ok 142
ok 143 - Length method
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 - threw Regexp ((?^:.+))
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175 - threw Regexp ((?^:.+))
ok 176 - Validation
ok 177
ok 178
ok 179 - threw Regexp ((?^:.+))
ok 180
ok 181
ok 182 - _find_orfs 1
ok 183 - orfs are sorted by descending length
ok 184 - got correct -orf => "longest" seq
ok 185 - _find_orfs 1
ok 186 - orfs are sorted by descending length
ok 187 - got correct -orf => "longest" seq
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274
ok 275
ok 276
ok 277
ok 278
ok 279
ok 280
ok 281
ok 282
ok 283
ok 284
ok 285
ok 286
ok 287
ok 288
ok 289
ok 290
ok 291
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298
ok 299
ok 300
ok 301
ok 302
ok 303
ok 304
ok 305
ok 306
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312
ok
t/Seq/PrimedSeq.t ...................... 
1..65
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::PrimedSeq;
ok 3 - Priming the target with sequence objects
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer'
ok 13
ok 14
ok 15 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer'
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26 - Priming the target with primer objects
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 - Priming the target with located primer objects
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
t/Seq/Quality.t ........................ 
1..85
ok 1 - use Bio::Seq::Quality;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - Bug 2845
ok 73
ok 74 - Bug 2845
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok
t/Seq/Seq.t ............................ 
1..76
ok 1 - use Bio::Seq;
ok 2 - use Bio::Seq::RichSeq;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Species;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7 - An object of class 'Bio::Seq' isa 'Bio::AnnotatableI'
ok 8
ok 9
ok 10
ok 11 - truncated sequence length
ok 12 - truncated sequence string
ok 13
ok 14
ok 15 - alphabet
ok 16 - id
ok 17 - accession number
ok 18 - subseq
ok 19 - An object of class 'Bio::Seq' isa 'Bio::IdentifiableI'
ok 20 - An object of class 'Bio::Seq' isa 'Bio::DescribableI'
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 - translated sequence
ok 35 - translated sequence with explicit unambiguous codons
ok 36 - translated sequence with unknown unambiguous codons
ok 37 - translated sequence with unknown unambiguous codons, completed
ok 38 - translated sequence with unambiguous codons
ok 39 - translated sequence with unambiguous codons
ok 40 - translated sequence with unknown unambiguous codons, completed
ok 41 - translated sequence with unambiguous codons
ok 42 - translated sequence with unknown unambiguous codons, completed
ok 43 - translated sequence with stop
ok 44 - translated sequence
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 - Don't use clone for trunc of Bio::Seq::RichSeq
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - Bug \#2864
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok
t/Seq/SimulatedRead.t .................. 
1..194
ok 1 - use Bio::Seq;
ok 2 - use Bio::Seq::Quality;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::Seq::SimulatedRead;
ok 6
ok 7 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::Seq::SimulatedRead'
ok 8 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::LocatableSeq'
ok 9 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::Seq::Quality'
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 - redundant errors
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114 - errors()
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 - track()
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137 - qual_levels()
ok 138
ok 139 - reference()
ok 140
ok 141 - mid()
ok 142
ok 143
ok 144
ok 145 - ACGT
ok 146
ok 147
ok 148
ok 149
ok 150 - TTTAAA
ok 151
ok 152
ok 153
ok 154
ok 155 - Bio::Seq::Quality
ok 156 - Bio::Seq
ok 157 - Bio::PrimarySeq
ok 158 - Bio::LocatableSeq
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
t/Seq/WithQuality.t .................... 
1..22
ok 1 - use Bio::Seq::SeqWithQuality;
ok 2 - use Bio::PrimarySeq;
ok 3 - use Bio::Seq::PrimaryQual;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual'
ok 20 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 21
ok 22
ok
t/SeqEvolution.t ....................... 
1..39
ok 1 - use Bio::SeqEvolution::Factory;
ok 2 - use Bio::PrimarySeq;
ok 3
ok 4 - An object of class 'Bio::SeqEvolution::DNAPoint' isa 'Bio::SeqEvolution::DNAPoint'
ok 5
ok 6 - An object of class 'Bio::SeqEvolution::DNAPoint' isa 'Bio::SeqEvolution::DNAPoint'
ok 7
ok 8 - An object of class 'Bio::SeqEvolution::DNAPoint' isa 'Bio::SeqEvolution::DNAPoint'
ok 9
ok 10
ok 11 - get rate()
ok 12 - get and set rate()
ok 13 - identity()
ok 14 - identity()
ok 15 - pam()
ok 16 - pam()
ok 17 - mutation_count()
ok 18 - mutation_count()
ok 19 - seq_type()
ok 20 - seq_type()
ok 21 - next_seq()
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27 - each_mutation()
ok 28
ok 29
ok 30 - get_alignment_identity()
ok 31
ok 32
ok 33 - get_mutation_counter()
ok 34 - get_sequence_counter()
ok 35 - reset_sequence_counter()
ok 36 - get_sequence_counter() == 0
ok 37
ok 38
ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok
t/SeqFeature/Amplicon.t ................ 
1..21
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqFeature::Primer;
ok 3 - use Bio::SeqFeature::Amplicon;
ok 4 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon'
ok 5 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::SubSeq'
ok 6
ok 7
ok 8 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 16
ok 17
ok 18
ok 19
ok 20 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 21
ok
t/SeqFeature/Clone.t ................... 
1..17
ok 1 - clone()
ok 2 - start() clone set
ok 3 - start() clone get
ok 4 - start() original unchanged
ok 5 - clone() with arguments
ok 6 - start() orig get
ok 7 - end() orig get
ok 8 - start() clone get
ok 9 - end() clone get
ok 10 - start() clone set
ok 11 - start() clone get
ok 12 - start() original unchanged
ok 13 - location() Bio::Location::Split
ok 14 - clone()
ok 15 - start() clone set
ok 16 - start() clone get
ok 17 - start() original unchanged
ok
t/SeqFeature/Collection.t .............. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/SeqFeature/Computation.t ............. 
1..12
ok 1 - use Bio::SeqFeature::Computation;
ok 2
ok 3 - computation id
ok 4 - score value
ok 5
ok 6
ok 7
ok 8 - sft[0] is exon
ok 9
ok 10 - computation id
ok 11
ok 12 - score value
ok
t/SeqFeature/FeaturePair.t ............. 
1..19
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::FeaturePair;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8 - feature1 of pair stored
ok 9 - feature2 of pair stored
ok 10 - feature start
ok 11 - feature end
ok 12 - primary tag
ok 13 - source tag
ok 14 - hstart
ok 15 - hend
ok 16 - hprimary tag
ok 17 - hsource tag
ok 18
ok 19 - inverted end
ok
t/SeqFeature/Gene.t .................... 
1..28
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::SeqFeature::Gene::Transcript;
ok 3 - use Bio::SeqFeature::Gene::UTR;
ok 4 - use Bio::SeqFeature::Gene::Exon;
ok 5 - use Bio::SeqFeature::Gene::Poly_A_site;
ok 6 - use Bio::SeqFeature::Gene::GeneStructure;
ok 7 - use Bio::Location::Fuzzy;
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 - mRNA spliced length
ok 28 - has 2 UTRs
ok
t/SeqFeature/Generic.t ................. 
1..364
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - Start of feature location
ok 10 - End of feature location
ok 11 - Primary tag
ok 12 - Source tag
ok 13 - Display name
ok 14 - Undef phase by default
ok 15 - Phase accessor returns
ok 16 - Phase is persistent
ok 17
ok 18
ok 19 - Set phase from constructor
ok 20
ok 21
ok 22 - Start of first seqfeature
ok 23 - End of first seqfeature
ok 24 - Strand of first seqfeature
ok 25
ok 26 - Sequence of first seqfeature
ok 27
ok 28
ok 29
ok 30 - Start of second seqfeature
ok 31 - End of second seqfeature
ok 32 - Strand of second seqfeature
ok 33
ok 34 - Sequence of second seqfeature
ok 35
ok 36
ok 37
ok 38 - sfeat start for EXPAND-ED feature (bug \#947)
ok 39 - sfeat end for EXPAND-ED feature (bug \#947)
ok 40
ok 41
ok 42 - Can create feature starting and ending at 0
ok 43
ok 44 - Can create feature starting and ending at 0
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO'
ok 55
ok 56 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq'
ok 57
ok 58 # skip Network tests have not been requested
ok 59 # skip Network tests have not been requested
ok 60 # skip Network tests have not been requested
ok 61 # skip Network tests have not been requested
ok 62 # skip Network tests have not been requested
ok 63
ok 64 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO'
ok 65
ok 66 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq'
ok 67
ok 68 # skip Network tests have not been requested
ok 69 # skip Network tests have not been requested
ok 70
ok 71 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO'
ok 72
ok 73
ok 74 - spliced_seq translation matches expected
ok 75
ok 76 - spliced_seq translation matches expected
ok 77
ok 78 - spliced_seq translation matches expected
ok 79
ok 80 - spliced_seq translation matches expected
ok 81
ok 82 - spliced_seq translation matches expected
ok 83
ok 84 - spliced_seq translation matches expected
ok 85
ok 86 - spliced_seq translation matches expected
ok 87
ok 88 - spliced_seq translation matches expected
ok 89
ok 90 - spliced_seq translation matches expected
ok 91
ok 92 - spliced_seq translation matches expected
ok 93
ok 94 - spliced_seq translation matches expected
ok 95
ok 96 - spliced_seq translation matches expected
ok 97
ok 98 - spliced_seq translation matches expected
ok 99
ok 100 - spliced_seq translation matches expected
ok 101
ok 102 - spliced_seq translation matches expected
ok 103
ok 104 - spliced_seq translation matches expected
ok 105
ok 106 - spliced_seq translation matches expected
ok 107
ok 108 - spliced_seq translation matches expected
ok 109
ok 110 - spliced_seq translation matches expected
ok 111
ok 112 - spliced_seq translation matches expected
ok 113
ok 114 - spliced_seq translation matches expected
ok 115
ok 116 - spliced_seq translation matches expected
ok 117
ok 118 - spliced_seq translation matches expected
ok 119
ok 120 - spliced_seq translation matches expected
ok 121
ok 122 - spliced_seq translation matches expected
ok 123
ok 124 - spliced_seq translation matches expected
ok 125
ok 126 - spliced_seq translation matches expected
ok 127
ok 128 - spliced_seq translation matches expected
ok 129
ok 130 - spliced_seq translation matches expected
ok 131
ok 132 - spliced_seq translation matches expected
ok 133
ok 134 - spliced_seq translation matches expected
ok 135
ok 136 - spliced_seq translation matches expected
ok 137
ok 138 - spliced_seq translation matches expected
ok 139
ok 140 - spliced_seq translation matches expected
ok 141
ok 142 - spliced_seq translation matches expected
ok 143
ok 144 - spliced_seq translation matches expected
ok 145
ok 146 - spliced_seq translation matches expected
ok 147
ok 148 - spliced_seq translation matches expected
ok 149
ok 150 - spliced_seq translation matches expected
ok 151
ok 152 - spliced_seq translation matches expected
ok 153
ok 154 - spliced_seq translation matches expected
ok 155
ok 156 - spliced_seq translation matches expected
ok 157
ok 158 - spliced_seq translation matches expected
ok 159
ok 160 - spliced_seq translation matches expected
ok 161
ok 162 - spliced_seq translation matches expected
ok 163
ok 164 - spliced_seq translation matches expected
ok 165
ok 166 - spliced_seq translation matches expected
ok 167
ok 168 - spliced_seq translation matches expected
ok 169
ok 170 - spliced_seq translation matches expected
ok 171
ok 172 - spliced_seq translation matches expected
ok 173
ok 174 - spliced_seq translation matches expected
ok 175
ok 176 - spliced_seq translation matches expected
ok 177
ok 178 - spliced_seq translation matches expected
ok 179
ok 180 - spliced_seq translation matches expected
ok 181
ok 182 - spliced_seq translation matches expected
ok 183
ok 184 - spliced_seq translation matches expected
ok 185
ok 186 - spliced_seq translation matches expected
ok 187
ok 188 - spliced_seq translation matches expected
ok 189
ok 190 - spliced_seq translation matches expected
ok 191
ok 192 - spliced_seq translation matches expected
ok 193
ok 194 - spliced_seq translation matches expected
ok 195
ok 196 - spliced_seq translation matches expected
ok 197
ok 198 - spliced_seq translation matches expected
ok 199
ok 200 - spliced_seq translation matches expected
ok 201
ok 202 - spliced_seq translation matches expected
ok 203
ok 204 - spliced_seq translation matches expected
ok 205
ok 206 - spliced_seq translation matches expected
ok 207
ok 208 - spliced_seq translation matches expected
ok 209
ok 210 - spliced_seq translation matches expected
ok 211
ok 212 - spliced_seq translation matches expected
ok 213
ok 214 - spliced_seq translation matches expected
ok 215
ok 216 - spliced_seq translation matches expected
ok 217
ok 218 - spliced_seq translation matches expected
ok 219
ok 220 - spliced_seq translation matches expected
ok 221
ok 222 - spliced_seq translation matches expected
ok 223
ok 224 - spliced_seq translation matches expected
ok 225
ok 226 - spliced_seq translation matches expected
ok 227
ok 228 - spliced_seq translation matches expected
ok 229
ok 230 - spliced_seq translation matches expected
ok 231
ok 232 - spliced_seq translation matches expected
ok 233
ok 234 - spliced_seq translation matches expected
ok 235
ok 236 - spliced_seq translation matches expected
ok 237
ok 238 - spliced_seq translation matches expected
ok 239
ok 240 - spliced_seq translation matches expected
ok 241
ok 242 - spliced_seq translation matches expected
ok 243
ok 244 - spliced_seq translation matches expected
ok 245
ok 246 - spliced_seq translation matches expected
ok 247
ok 248 - spliced_seq translation matches expected
ok 249
ok 250 - spliced_seq translation matches expected
ok 251
ok 252 - spliced_seq translation matches expected
ok 253
ok 254 - spliced_seq translation matches expected
ok 255
ok 256 - spliced_seq translation matches expected
ok 257
ok 258 - spliced_seq translation matches expected
ok 259
ok 260 - spliced_seq translation matches expected
ok 261
ok 262 - spliced_seq translation matches expected
ok 263
ok 264 - spliced_seq translation matches expected
ok 265
ok 266 - spliced_seq translation matches expected
ok 267
ok 268 - spliced_seq translation matches expected
ok 269
ok 270 - spliced_seq translation matches expected
ok 271
ok 272 - spliced_seq translation matches expected
ok 273
ok 274 - spliced_seq translation matches expected
ok 275
ok 276 - spliced_seq translation matches expected
ok 277
ok 278 - spliced_seq translation matches expected
ok 279
ok 280 - spliced_seq translation matches expected
ok 281
ok 282 - spliced_seq translation matches expected
ok 283
ok 284 - spliced_seq translation matches expected
ok 285
ok 286 - spliced_seq translation matches expected
ok 287
ok 288 - spliced_seq translation matches expected
ok 289
ok 290 - spliced_seq translation matches expected
ok 291
ok 292 - spliced_seq translation matches expected
ok 293
ok 294 - spliced_seq translation matches expected
ok 295
ok 296 - spliced_seq translation matches expected
ok 297
ok 298 - spliced_seq translation matches expected
ok 299
ok 300 - spliced_seq translation matches expected
ok 301
ok 302 - spliced_seq translation matches expected
ok 303
ok 304 - spliced_seq translation matches expected
ok 305
ok 306 - spliced_seq translation matches expected
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312 - phase check
ok 313
ok 314
ok 315 - phase check
ok 316
ok 317
ok 318 - phase check
ok 319
ok 320
ok 321 - phase check
ok 322
ok 323
ok 324 - phase check
ok 325
ok 326
ok 327
ok 328 - Tags found
ok 329 - get_tagset_values tag values found
ok 330 - get_tagset_values tag values for multiple tags found
ok 331 - get_tag_values tag values found
ok 332 - get_tag_values lives with tag
ok 333 - get_tagset_values no tag values found
ok 334 - get_tagset_values lives with no tag
ok 335 - get_tag_values throws with no tag
ok 336 - Phi-X174 genome is circular
ok 337
ok 338 - Only 3 split locations
ok 339 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI'
ok 340
ok 341 - Feature string
ok 342 - First ten nucleotides
ok 343 - Strand
ok 344 - Start
ok 345 - End
ok 346 - Expected length
ok 347 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI'
ok 348
ok 349 - Feature string
ok 350 - First ten nucleotides
ok 351 - Strand
ok 352 - Start
ok 353 - End
ok 354 - Expected length
ok 355 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI'
ok 356
ok 357 - Feature string
ok 358 - First ten nucleotides
ok 359 - Strand
ok 360 - Start
ok 361 - End
ok 362 - Expected length
ok 363 - Reverse strand is spliced correctly
ok 364 - Reverse strand is spliced correctly
ok
t/SeqFeature/Location.t ................ 
1..109
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Location::Split;
ok 3 - use Bio::Location::Fuzzy;
ok 4 - use Bio::SeqFeature::Generic;
ok 5 - use Bio::SeqFeature::SimilarityPair;
ok 6 - use Bio::SeqFeature::FeaturePair;
ok 7 - use Bio::SeqFeature::Lite;
ok 8 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 9 - An object of class 'Bio::Location::Simple' isa 'Bio::RangeI'
ok 10 - Bio::Location::Simple tests
ok 11
ok 12
ok 13
ok 14
ok 15 - 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI'
ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::RangeI'
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 - Bio::SeqFeature::FeaturePair tests
ok 25
ok 26
ok 27
ok 28 - Bio::SeqFeature::Generic tests
ok 29
ok 30 - Bio::Location::Fuzzy tests
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 - Bio::Location::Split tests
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 - Bugfix 1074
ok 62
ok 63
ok 64
ok 65 - Positive length
ok 66
ok 67 - seq_id() on Bio::Location::Split
ok 68
ok 69
ok 70 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 71 - An object of class 'Bio::Location::Simple' isa 'Bio::RangeI'
ok 72 - Bio::Location::Simple EXACT
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78 - Bio::Location::Simple IN-BETWEEN
ok 79
ok 80
ok 81
ok 82
ok 83 - Testing error handling
ok 84
ok 85
ok 86
ok 87 - use Bio::Location::WidestCoordPolicy;
ok 88 - use Bio::Location::NarrowestCoordPolicy;
ok 89 - use Bio::Location::AvWithinCoordPolicy;
ok 90 - Default coodinate policy
ok 91
ok 92
ok 93
ok 94 - An object of class 'Bio::Location::WidestCoordPolicy' isa 'Bio::Location::WidestCoordPolicy'
ok 95 - Narrowest coodinate policy
ok 96
ok 97
ok 98
ok 99 - An object of class 'Bio::Location::NarrowestCoordPolicy' isa 'Bio::Location::NarrowestCoordPolicy'
ok 100 - Average coodinate policy
ok 101
ok 102
ok 103
ok 104 - An object of class 'Bio::Location::AvWithinCoordPolicy' isa 'Bio::Location::AvWithinCoordPolicy'
ok 105 - Widest coodinate policy
ok 106
ok 107
ok 108
ok 109 - An object of class 'Bio::Location::WidestCoordPolicy' isa 'Bio::Location::WidestCoordPolicy'
ok
t/SeqFeature/LocationFactory.t ......... 
1..325
ok 1 - use Bio::Factory::FTLocationFactory;
ok 2 - An object of class 'Bio::Factory::FTLocationFactory' isa 'Bio::Factory::LocationFactoryI'
ok 3 - Bio::Location::Fuzzy
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - Location String: 1..?
ok 13
ok 14 - Bio::Location::Fuzzy
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - Location String: ?..536
ok 24
ok 25 - Bio::Location::Fuzzy
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - Location String: <345..500
ok 35
ok 36 - Bio::Location::Split
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45 - Location String: join(1..100,J00194.1:100..202)
ok 46
ok 47 - Bio::Location::Fuzzy
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - Location String: 22..?64
ok 57
ok 58 - Bio::Location::Fuzzy
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - Location String: ?..?
ok 68
ok 69 - Bio::Location::Fuzzy
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78 - Location String: <1..?
ok 79
ok 80 - Bio::Location::Split
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
ok 90
ok 91 - Bio::Location::Fuzzy
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100 - Location String: ?..>393
ok 101
ok 102 - Bio::Location::Fuzzy
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 - Location String: 145^177
ok 112
ok 113 - Bio::Location::Fuzzy
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122 - Location String: complement(34..(122.126))
ok 123
ok 124 - Bio::Location::Fuzzy
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133 - Location String: ?22..?64
ok 134
ok 135 - Bio::Location::Split
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144 - Location String: join(12..78,134..202)
ok 145
ok 146 - Bio::Location::Split
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155 - Location String: complement(join(94468..94578,94578..>94889))
ok 156
ok 157 - Bio::Location::Split
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166 - Location String: complement(join(2691..4571,4918..5163))
ok 167
ok 168 - Bio::Location::Fuzzy
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177 - Location String: ?1..12
ok 178
ok 179 - Bio::Location::Simple
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188 - Location String: 467
ok 189
ok 190 - Bio::Location::Fuzzy
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199 - Location String: (122.133)..(204.221)
ok 200
ok 201 - Bio::Location::Fuzzy
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210 - Location String: (23.45)..600
ok 211
ok 212 - Bio::Location::Fuzzy
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221 - Location String: (102.110)
ok 222
ok 223 - Bio::Location::Fuzzy
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232 - Location String: 1..>888
ok 233
ok 234 - Bio::Location::Simple
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243 - Location String: 123^124
ok 244
ok 245 - Bio::Location::Fuzzy
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254 - Location String: (122.133)..(204.221)
ok 255
ok 256 - Bio::Location::Fuzzy
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265 - Location String: ?2465..2774
ok 266
ok 267 - Bio::Location::Simple
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274
ok 275
ok 276 - Location String: J00194:100..202
ok 277
ok 278 - Bio::Location::Fuzzy
ok 279
ok 280
ok 281
ok 282
ok 283
ok 284
ok 285
ok 286
ok 287 - Location String: <1..888
ok 288
ok 289 - Bio::Location::Simple
ok 290
ok 291
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298 - Location String: J00194:100..202
ok 299
ok 300 - Bio::Location::Simple
ok 301
ok 302
ok 303
ok 304
ok 305
ok 306
ok 307
ok 308
ok 309 - Location String: 340..565
ok 310
ok 311 - complement(join(2691..4571,4918..5163))
ok 312 - join(complement(4918..5163),complement(2691..4571))
ok 313 - equivalent remote location strings
ok 314 - complement(join(TEST0001.1:2691..4571,4918..5163))
ok 315 - join(complement(4918..5163),complement(TEST0001.1:2691..4571))
ok 316 - equivalent remote location strings
ok 317 - complement(join(TEST0001.1:2691..4571,TEST0008.1:4918..5163))
ok 318 - join(complement(TEST0008.1:4918..5163),complement(TEST0001.1:2691..4571))
ok 319 - equivalent remote location strings
ok 320 - join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294)))
ok 321 - join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))
ok 322 - join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))
ok 323 - join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669)))
ok 324 - join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)
ok 325 - order(S67862.1:72..75,join(S67863.1:1..788,1..19))
ok
t/SeqFeature/Primer.t .................. 
1..47
ok 1 - use Bio::SeqFeature::Primer;
ok 2 - use Bio::PrimarySeq;
ok 3 - Implied primer sequence
ok 4 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer'
ok 5 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::SubSeq'
ok 6
ok 7
ok 8 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 9
ok 10 - PrimarySeq primer
ok 11
ok 12
ok 13 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
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 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer'
ok 42
ok 43
ok 44 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer'
ok 45 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 46
ok 47
ok
t/SeqFeature/Range.t ................... 
1..49
ok 1 - use Bio::Range;
ok 2 - 'BioRange object' isa 'Bio::Range'
ok 3
ok 4 - 'BioRange object' isa 'Bio::Range'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - 'BioRange object' isa 'Bio::Range'
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - 'BioRange object' isa 'Bio::Range'
ok 26 - 'BioRange object' isa 'Bio::Range'
ok 27 - 'BioRange object' isa 'Bio::Range'
ok 28 -  1 & -1
ok 29 -  1 & 1 true
ok 30 -  1 & 0 true
ok 31 -  1 & -1 false
ok 32 -  1 & 1 true
ok 33 -  1 & 0 false
ok 34 -  1 & -1 false
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45 - 'Bio::Range object' isa 'Bio::Range'
ok 46
ok 47
ok 48
ok 49
ok
t/SeqFeature/RangeI.t .................. 
1..45
ok 1 - use Bio::SeqFeature::Generic;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39 - subtract() of split features
ok 40 -    0 start
ok 41 -    0 end
ok 42 -    1 start
ok 43 -    1 end
ok 44 -    2 start
ok 45 -    2 end
ok
t/SeqFeature/SeqAnalysisParser.t ....... 
1..14
ok 1 - use Bio::Factory::SeqAnalysisParserFactory;
ok 2 - use Bio::SeqIO;
ok 3 - An object of class 'Bio::SeqIO::fasta' isa 'Bio::SeqIO'
ok 4 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI'
ok 5 - An object of class 'Bio::Tools::Genscan' isa 'Bio::SeqAnalysisParserI'
ok 6
ok 7
ok 8
ok 9 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI'
ok 10 - An object of class 'Bio::Tools::MZEF' isa 'Bio::SeqAnalysisParserI'
ok 11
ok 12
ok 13 - An object of class 'Bio::Tools::EPCR' isa 'Bio::SeqAnalysisParserI'
ok 14
ok
t/SeqFeature/SubSeq.t .................. 
1..37
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqFeature::SubSeq;
ok 3 - An object of class 'Bio::SeqFeature::SubSeq' isa 'Bio::SeqFeature::SubSeq'
ok 4 - An object of class 'Bio::SeqFeature::SubSeq' isa 'Bio::SeqFeature::Generic'
ok 5
ok 6
ok 7
ok 8
ok 9 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 10
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 15
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 26
ok 27
ok 28
ok 29
ok 30 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 31
ok 32
ok 33
ok 34
ok 35 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 36
ok 37
ok

Timeout (max run time is 300s)
C:\Perl-5.24-64\bin\perl.exe exits with 37.