PATH=/usr/bin:/bin:/Users/fly1400/var/megalib/bin
Start 2013-09-11T01:03:04
ActivePerl-1400 CPAN-2.00
Reading '/Users/fly1400/var/cpan/Metadata'
  Database was generated on Wed, 11 Sep 2013 06:53:03 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.921.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.921.tar.gz ok
BioPerl-1.6.921
BioPerl-1.6.921/.travis.yml
BioPerl-1.6.921/AUTHORS
BioPerl-1.6.921/BioPerl.pm
BioPerl-1.6.921/BUGS
BioPerl-1.6.921/Build.PL
BioPerl-1.6.921/Changes
BioPerl-1.6.921/DEPENDENCIES
BioPerl-1.6.921/DEPRECATED
BioPerl-1.6.921/INSTALL
BioPerl-1.6.921/INSTALL.SKIP
BioPerl-1.6.921/INSTALL.WIN
BioPerl-1.6.921/LICENSE
BioPerl-1.6.921/MANIFEST
BioPerl-1.6.921/META.json
BioPerl-1.6.921/META.yml
BioPerl-1.6.921/README
BioPerl-1.6.921/README.md
BioPerl-1.6.921/Bio
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BioPerl-1.6.921/examples
BioPerl-1.6.921/examples/bioperl.pl
BioPerl-1.6.921/examples/generate_random_seq.pl
BioPerl-1.6.921/examples/longorf.pl
BioPerl-1.6.921/examples/make_primers.pl
BioPerl-1.6.921/examples/rev_and_trans.pl
BioPerl-1.6.921/examples/revcom_dir.pl
BioPerl-1.6.921/examples/subsequence.cgi
BioPerl-1.6.921/examples/align
BioPerl-1.6.921/examples/align/align_on_codons.pl
BioPerl-1.6.921/examples/align/aligntutorial.pl
BioPerl-1.6.921/examples/align/clustalw.pl
BioPerl-1.6.921/examples/align/FastAlign.pl
BioPerl-1.6.921/examples/align/simplealign.pl
BioPerl-1.6.921/examples/Bio-DB-GFF
BioPerl-1.6.921/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.921/examples/cluster
BioPerl-1.6.921/examples/cluster/dbsnp.pl
BioPerl-1.6.921/examples/contributed
BioPerl-1.6.921/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.921/examples/contributed/prosite2perl.pl
BioPerl-1.6.921/examples/contributed/rebase2list.pl
BioPerl-1.6.921/examples/db
BioPerl-1.6.921/examples/db/dbfetch
BioPerl-1.6.921/examples/db/est_tissue_query.pl
BioPerl-1.6.921/examples/db/gb2features.pl
BioPerl-1.6.921/examples/db/get_seqs.pl
BioPerl-1.6.921/examples/db/getGenBank.pl
BioPerl-1.6.921/examples/db/rfetch.pl
BioPerl-1.6.921/examples/db/use_registry.pl
BioPerl-1.6.921/examples/liveseq
BioPerl-1.6.921/examples/liveseq/change_gene.pl
BioPerl-1.6.921/examples/popgen
BioPerl-1.6.921/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.921/examples/quality
BioPerl-1.6.921/examples/quality/svgtrace.pl
BioPerl-1.6.921/examples/root
BioPerl-1.6.921/examples/root/exceptions1.pl
BioPerl-1.6.921/examples/root/exceptions2.pl
BioPerl-1.6.921/examples/root/exceptions3.pl
BioPerl-1.6.921/examples/root/exceptions4.pl
BioPerl-1.6.921/examples/root/README
BioPerl-1.6.921/examples/root/lib
BioPerl-1.6.921/examples/root/lib/TestInterface.pm
BioPerl-1.6.921/examples/root/lib/TestObject.pm
BioPerl-1.6.921/examples/searchio
BioPerl-1.6.921/examples/searchio/blast_example.pl
BioPerl-1.6.921/examples/searchio/custom_writer.pl
BioPerl-1.6.921/examples/searchio/hitwriter.pl
BioPerl-1.6.921/examples/searchio/hspwriter.pl
BioPerl-1.6.921/examples/searchio/htmlwriter.pl
BioPerl-1.6.921/examples/searchio/psiblast_features.pl
BioPerl-1.6.921/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.921/examples/searchio/rawwriter.pl
BioPerl-1.6.921/examples/searchio/resultwriter.pl
BioPerl-1.6.921/examples/searchio/waba2gff.pl
BioPerl-1.6.921/examples/searchio/waba2gff3.pl
BioPerl-1.6.921/examples/sirna
BioPerl-1.6.921/examples/sirna/rnai_finder.cgi
BioPerl-1.6.921/examples/sirna/TAG
BioPerl-1.6.921/examples/structure
BioPerl-1.6.921/examples/structure/structure-io.pl
BioPerl-1.6.921/examples/tk
BioPerl-1.6.921/examples/tk/gsequence.pl
BioPerl-1.6.921/examples/tk/hitdisplay.pl
BioPerl-1.6.921/examples/tools
BioPerl-1.6.921/examples/tools/extract_genes.pl
BioPerl-1.6.921/examples/tools/gb_to_gff.pl
BioPerl-1.6.921/examples/tools/gff2ps.pl
BioPerl-1.6.921/examples/tools/parse_codeml.pl
BioPerl-1.6.921/examples/tools/psw.pl
BioPerl-1.6.921/examples/tools/reverse-translate.pl
BioPerl-1.6.921/examples/tools/run_genscan.pl
BioPerl-1.6.921/examples/tools/run_primer3.pl
BioPerl-1.6.921/examples/tools/seq_pattern.pl
BioPerl-1.6.921/examples/tools/standaloneblast.pl
BioPerl-1.6.921/examples/tree
BioPerl-1.6.921/examples/tree/paup2phylip.pl
BioPerl-1.6.921/ide
BioPerl-1.6.921/ide/bioperl.komodo
BioPerl-1.6.921/ide/bioperl-mode
BioPerl-1.6.921/ide/bioperl-mode/README
BioPerl-1.6.921/ide/bioperl-mode/dist
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BioPerl-1.6.921/ide/bioperl-mode/dist/Changes
BioPerl-1.6.921/ide/bioperl-mode/dist/package-me
BioPerl-1.6.921/ide/bioperl-mode/dist/SKIP
BioPerl-1.6.921/ide/bioperl-mode/etc
BioPerl-1.6.921/ide/bioperl-mode/etc/images
BioPerl-1.6.921/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.6.921/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.6.921/ide/bioperl-mode/site-lisp
BioPerl-1.6.921/ide/bioperl-mode/site-lisp/bioperl-init.el
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BioPerl-1.6.921/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.6.921/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.6.921/maintenance
BioPerl-1.6.921/maintenance/authors.pl
BioPerl-1.6.921/maintenance/check_NAME.pl
BioPerl-1.6.921/maintenance/check_URLs.pl
BioPerl-1.6.921/maintenance/cvs2cl_by_file.pl
BioPerl-1.6.921/maintenance/dependencies.pl
BioPerl-1.6.921/maintenance/deprecated.pl
BioPerl-1.6.921/maintenance/find_mod_deps.pl
BioPerl-1.6.921/maintenance/module_usage.pl
BioPerl-1.6.921/maintenance/modules.pl
BioPerl-1.6.921/maintenance/ncbi_blast_switches.pl
BioPerl-1.6.921/maintenance/perltidy.conf
BioPerl-1.6.921/maintenance/pod.pl
BioPerl-1.6.921/maintenance/README
BioPerl-1.6.921/maintenance/symlink_script.pl
BioPerl-1.6.921/maintenance/version.pl
BioPerl-1.6.921/maintenance/big_split
BioPerl-1.6.921/maintenance/big_split/file_classification.csv
BioPerl-1.6.921/maintenance/big_split/rbuels_notes.txt
BioPerl-1.6.921/models
BioPerl-1.6.921/models/biblio.dia
BioPerl-1.6.921/models/bio_liveseq_variation.dia
BioPerl-1.6.921/models/bio_map.dia
BioPerl-1.6.921/models/bio_restriction.dia
BioPerl-1.6.921/models/bioperl.dia
BioPerl-1.6.921/models/coordinatemapper.dia
BioPerl-1.6.921/models/map_proposal.txt
BioPerl-1.6.921/models/maps_and_markers.dia
BioPerl-1.6.921/models/popgen.dia
BioPerl-1.6.921/models/population_proposal.txt
BioPerl-1.6.921/models/README
BioPerl-1.6.921/scripts
BioPerl-1.6.921/scripts/README
BioPerl-1.6.921/scripts/Bio-DB-GFF
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.6.921/scripts/Bio-DB-GFF/README
BioPerl-1.6.921/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.6.921/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.6.921/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.6.921/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.6.921/scripts/das
BioPerl-1.6.921/scripts/das/bp_das_server.pl
BioPerl-1.6.921/scripts/das/README
BioPerl-1.6.921/scripts/das/TAG
BioPerl-1.6.921/scripts/DB
BioPerl-1.6.921/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.6.921/scripts/DB/bp_bioflat_index.pl
BioPerl-1.6.921/scripts/DB/bp_biogetseq.pl
BioPerl-1.6.921/scripts/DB/bp_flanks.pl
BioPerl-1.6.921/scripts/DB/TAG
BioPerl-1.6.921/scripts/DB-HIV
BioPerl-1.6.921/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.6.921/scripts/index
BioPerl-1.6.921/scripts/index/bp_fetch.pl
BioPerl-1.6.921/scripts/index/bp_index.pl
BioPerl-1.6.921/scripts/index/bp_seqret.pl
BioPerl-1.6.921/scripts/index/TAG
BioPerl-1.6.921/scripts/popgen
BioPerl-1.6.921/scripts/popgen/bp_composite_LD.pl
BioPerl-1.6.921/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.6.921/scripts/searchio
BioPerl-1.6.921/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.6.921/scripts/searchio/bp_filter_search.pl
BioPerl-1.6.921/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.6.921/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.6.921/scripts/searchio/bp_search2table.pl
BioPerl-1.6.921/scripts/searchio/README
BioPerl-1.6.921/scripts/searchio/TAG
BioPerl-1.6.921/scripts/seq
BioPerl-1.6.921/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.6.921/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.6.921/scripts/seq/bp_seqconvert.pl
BioPerl-1.6.921/scripts/seq/bp_seqcut.pl
BioPerl-1.6.921/scripts/seq/bp_seqpart.pl
BioPerl-1.6.921/scripts/seq/bp_seqretsplit.pl
BioPerl-1.6.921/scripts/seq/bp_split_seq.pl
BioPerl-1.6.921/scripts/seq/bp_translate_seq.pl
BioPerl-1.6.921/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.6.921/scripts/seq/TAG
BioPerl-1.6.921/scripts/seqstats
BioPerl-1.6.921/scripts/seqstats/bp_aacomp.pl
BioPerl-1.6.921/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.6.921/scripts/seqstats/bp_gccalc.pl
BioPerl-1.6.921/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.6.921/scripts/seqstats/TAG
BioPerl-1.6.921/scripts/taxa
BioPerl-1.6.921/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.6.921/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.6.921/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.6.921/scripts/taxa/bp_taxid4species.pl
BioPerl-1.6.921/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.6.921/scripts/taxa/TAG
BioPerl-1.6.921/scripts/tree
BioPerl-1.6.921/scripts/tree/bp_blast2tree.pl
BioPerl-1.6.921/scripts/tree/bp_nexus2nh.pl
BioPerl-1.6.921/scripts/tree/bp_tree2pag.pl
BioPerl-1.6.921/scripts/tree/TAG
BioPerl-1.6.921/scripts/utilities
BioPerl-1.6.921/scripts/utilities/bp_dbsplit.pl
BioPerl-1.6.921/scripts/utilities/bp_download_query_genbank.pl
BioPerl-1.6.921/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.6.921/scripts/utilities/bp_mrtrans.pl
BioPerl-1.6.921/scripts/utilities/bp_mutate.pl
BioPerl-1.6.921/scripts/utilities/bp_netinstall.pl
BioPerl-1.6.921/scripts/utilities/bp_nrdb.pl
BioPerl-1.6.921/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.6.921/scripts/utilities/bp_remote_blast.pl
BioPerl-1.6.921/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.6.921/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.6.921/scripts/utilities/bp_search2BSML.pl
BioPerl-1.6.921/scripts/utilities/bp_search2gff.pl
BioPerl-1.6.921/scripts/utilities/bp_search2tribe.pl
BioPerl-1.6.921/scripts/utilities/bp_seq_length.pl
BioPerl-1.6.921/scripts/utilities/bp_sreformat.pl
BioPerl-1.6.921/scripts/utilities/README
BioPerl-1.6.921/scripts/utilities/TAG
BioPerl-1.6.921/t
BioPerl-1.6.921/t/Alphabet.t
BioPerl-1.6.921/t/nexml.t
BioPerl-1.6.921/t/Perl.t
BioPerl-1.6.921/t/PodSyntax.t
BioPerl-1.6.921/t/SearchDist.t
BioPerl-1.6.921/t/SeqEvolution.t
BioPerl-1.6.921/t/Species.t
BioPerl-1.6.921/t/Symbol.t
BioPerl-1.6.921/t/TaxonTree.t
BioPerl-1.6.921/t/Align
BioPerl-1.6.921/t/Align/AlignStats.t
BioPerl-1.6.921/t/Align/AlignUtil.t
BioPerl-1.6.921/t/Align/Graphics.t
BioPerl-1.6.921/t/Align/SimpleAlign.t
BioPerl-1.6.921/t/Align/TreeBuild.t
BioPerl-1.6.921/t/Align/Utilities.t
BioPerl-1.6.921/t/AlignIO
BioPerl-1.6.921/t/AlignIO/AlignIO.t
BioPerl-1.6.921/t/AlignIO/arp.t
BioPerl-1.6.921/t/AlignIO/bl2seq.t
BioPerl-1.6.921/t/AlignIO/clustalw.t
BioPerl-1.6.921/t/AlignIO/emboss.t
BioPerl-1.6.921/t/AlignIO/fasta.t
BioPerl-1.6.921/t/AlignIO/largemultifasta.t
BioPerl-1.6.921/t/AlignIO/maf.t
BioPerl-1.6.921/t/AlignIO/mase.t
BioPerl-1.6.921/t/AlignIO/mega.t
BioPerl-1.6.921/t/AlignIO/meme.t
BioPerl-1.6.921/t/AlignIO/metafasta.t
BioPerl-1.6.921/t/AlignIO/msf.t
BioPerl-1.6.921/t/AlignIO/nexml.t
BioPerl-1.6.921/t/AlignIO/nexus.t
BioPerl-1.6.921/t/AlignIO/pfam.t
BioPerl-1.6.921/t/AlignIO/phylip.t
BioPerl-1.6.921/t/AlignIO/po.t
BioPerl-1.6.921/t/AlignIO/prodom.t
BioPerl-1.6.921/t/AlignIO/psi.t
BioPerl-1.6.921/t/AlignIO/selex.t
BioPerl-1.6.921/t/AlignIO/stockholm.t
BioPerl-1.6.921/t/AlignIO/xmfa.t
BioPerl-1.6.921/t/Annotation
BioPerl-1.6.921/t/Annotation/Annotation.t
BioPerl-1.6.921/t/Annotation/AnnotationAdaptor.t
BioPerl-1.6.921/t/Assembly
BioPerl-1.6.921/t/Assembly/ContigSpectrum.t
BioPerl-1.6.921/t/Assembly/core.t
BioPerl-1.6.921/t/Assembly/IO
BioPerl-1.6.921/t/Assembly/IO/bowtie.t
BioPerl-1.6.921/t/Assembly/IO/sam.t
BioPerl-1.6.921/t/Cluster
BioPerl-1.6.921/t/Cluster/UniGene.t
BioPerl-1.6.921/t/ClusterIO
BioPerl-1.6.921/t/ClusterIO/ClusterIO.t
BioPerl-1.6.921/t/ClusterIO/SequenceFamily.t
BioPerl-1.6.921/t/ClusterIO/unigene.t
BioPerl-1.6.921/t/Coordinate
BioPerl-1.6.921/t/Coordinate/CoordinateBoundaryTest.t
BioPerl-1.6.921/t/Coordinate/CoordinateGraph.t
BioPerl-1.6.921/t/Coordinate/CoordinateMapper.t
BioPerl-1.6.921/t/Coordinate/GeneCoordinateMapper.t
BioPerl-1.6.921/t/data
BioPerl-1.6.921/t/data/01_basic.xml
BioPerl-1.6.921/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/02_dogfish_no_taxrefs.xml
BioPerl-1.6.921/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/02_mackerel_no_taxrefs.xml
BioPerl-1.6.921/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
BioPerl-1.6.921/t/data/03_bootstraps.xml
BioPerl-1.6.921/t/data/03_bootstraps_in_tag.xml
BioPerl-1.6.921/t/data/04_labeled_ancestors.xml
BioPerl-1.6.921/t/data/05_ancestral_states.xml
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BioPerl-1.6.921/t/data/1A3I.pdb
BioPerl-1.6.921/t/data/1BPT.pdb
BioPerl-1.6.921/t/data/1ZZ19XR301R-Alignment.tblastn
BioPerl-1.6.921/t/data/2008.blasttable
BioPerl-1.6.921/t/data/27-contig_Newbler.ace
BioPerl-1.6.921/t/data/503384.MEGABLAST.0
BioPerl-1.6.921/t/data/503384.MEGABLAST.2
BioPerl-1.6.921/t/data/5X_1895.FASTXY
BioPerl-1.6.921/t/data/8HVP.pdb
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BioPerl-1.6.921/t/data/aaml.mlc
BioPerl-1.6.921/t/data/aaml_pairwise.mlc
BioPerl-1.6.921/t/data/AB077698.gb
BioPerl-1.6.921/t/data/acefile.ace.1
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BioPerl-1.6.921/t/data/adh.mb_tree.nexus
BioPerl-1.6.921/t/data/AE003528_ecoli.bls
BioPerl-1.6.921/t/data/AE003644_Adh-genomic.gb
BioPerl-1.6.921/t/data/AF032047.gbk
BioPerl-1.6.921/t/data/AF165282.gb
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BioPerl-1.6.921/t/data/ATF14F8.gbk
BioPerl-1.6.921/t/data/atp1.matrix
BioPerl-1.6.921/t/data/ay007676.gb
BioPerl-1.6.921/t/data/AY095303S1.gbk
BioPerl-1.6.921/t/data/ay116458.gb
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BioPerl-1.6.921/t/data/badfasta.fa
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BioPerl-1.6.921/t/data/Bird_Ovomucoids.nex
BioPerl-1.6.921/t/data/BK000016-tpa.gbk
BioPerl-1.6.921/t/data/bl2seq.blastn
BioPerl-1.6.921/t/data/bl2seq.blastn.rev
BioPerl-1.6.921/t/data/bl2seq.blastx.out
BioPerl-1.6.921/t/data/bl2seq.bug940.out
BioPerl-1.6.921/t/data/bl2seq.out
BioPerl-1.6.921/t/data/bl2seq.tblastx.out
BioPerl-1.6.921/t/data/blast.report
BioPerl-1.6.921/t/data/blast_no_hit_desc.txt
BioPerl-1.6.921/t/data/blast_plus.blastp
BioPerl-1.6.921/t/data/blastp2215.blast
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BioPerl-1.6.921/t/data/bug1986.blastp
BioPerl-1.6.921/t/data/bug2120.phd
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BioPerl-1.6.921/t/data/bug3086.embl
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BioPerl-1.6.921/t/data/c200-vs-yeast.BLASTN
BioPerl-1.6.921/t/data/c200-vs-yeast.BLASTN.m8
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BioPerl-1.6.921/t/data/catalase-webblast.BLASTP
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BioPerl-1.6.921/t/data/cds_sample.embl
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BioPerl-1.6.921/t/data/CG2865.fasaln
BioPerl-1.6.921/t/data/chad100.scf
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BioPerl-1.6.921/t/data/characters+trees.nexml.xml
BioPerl-1.6.921/t/data/characters.nexml.old.xml
BioPerl-1.6.921/t/data/codeml.mlc
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BioPerl-1.6.921/t/data/codeml45.mlc
BioPerl-1.6.921/t/data/codeml45b.mlc
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BioPerl-1.6.921/t/data/codeml_nssites.mlc
BioPerl-1.6.921/t/data/compLD_missingtest.prettybase
BioPerl-1.6.921/t/data/compLD_test.prettybase
BioPerl-1.6.921/t/data/component.ontology.test
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BioPerl-1.6.921/t/data/contig-by-hand.wublastp
BioPerl-1.6.921/t/data/contigspectrumtest.tigr
BioPerl-1.6.921/t/data/crab.dat.cn
BioPerl-1.6.921/t/data/crab.nj
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BioPerl-1.6.921/t/data/ctgdemo.fpc
BioPerl-1.6.921/t/data/cys1_dicdi.water
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BioPerl-1.6.921/t/data/cysprot1a.fa
BioPerl-1.6.921/t/data/cysprot1a.msf
BioPerl-1.6.921/t/data/cysprot1b.fa
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BioPerl-1.6.921/t/data/cysprot1b.msf
BioPerl-1.6.921/t/data/cysprot1b.newick
BioPerl-1.6.921/t/data/cysprot_vs_gadfly.FASTA
BioPerl-1.6.921/t/data/D10483.gbk
BioPerl-1.6.921/t/data/D12555.gbk
BioPerl-1.6.921/t/data/dcr1_sp.WUBLASTP
BioPerl-1.6.921/t/data/dmel_2Lchunk.gb
BioPerl-1.6.921/t/data/dna1.fa
BioPerl-1.6.921/t/data/dna2.fa
BioPerl-1.6.921/t/data/dnaE-bsub-prot.fa
BioPerl-1.6.921/t/data/dnaE-bsub.fa
BioPerl-1.6.921/t/data/dnaEbsub_ecoli.wublastx
BioPerl-1.6.921/t/data/dnaEbsub_ecoli.wutblastn
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BioPerl-1.6.921/t/Ontology/IO/obo.t
BioPerl-1.6.921/t/Phenotype
BioPerl-1.6.921/t/Phenotype/Correlate.t
BioPerl-1.6.921/t/Phenotype/Measure.t
BioPerl-1.6.921/t/Phenotype/MeSH.t
BioPerl-1.6.921/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.921/t/Phenotype/OMIMentry.t
BioPerl-1.6.921/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.921/t/Phenotype/OMIMparser.t
BioPerl-1.6.921/t/Phenotype/Phenotype.t
BioPerl-1.6.921/t/PopGen
BioPerl-1.6.921/t/PopGen/Coalescent.t
BioPerl-1.6.921/t/PopGen/HtSNP.t
BioPerl-1.6.921/t/PopGen/MK.t
BioPerl-1.6.921/t/PopGen/PopGen.t
BioPerl-1.6.921/t/PopGen/PopGenSims.t
BioPerl-1.6.921/t/PopGen/TagHaplotype.t
BioPerl-1.6.921/t/RemoteDB
BioPerl-1.6.921/t/RemoteDB/BioFetch.t
BioPerl-1.6.921/t/RemoteDB/CUTG.t
BioPerl-1.6.921/t/RemoteDB/EMBL.t
BioPerl-1.6.921/t/RemoteDB/EntrezGene.t
BioPerl-1.6.921/t/RemoteDB/GenBank.t
BioPerl-1.6.921/t/RemoteDB/GenPept.t
BioPerl-1.6.921/t/RemoteDB/MeSH.t
BioPerl-1.6.921/t/RemoteDB/RefSeq.t
BioPerl-1.6.921/t/RemoteDB/SeqHound.t
BioPerl-1.6.921/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.921/t/RemoteDB/SeqVersion.t
BioPerl-1.6.921/t/RemoteDB/SwissProt.t
BioPerl-1.6.921/t/RemoteDB/Taxonomy.t
BioPerl-1.6.921/t/RemoteDB/HIV
BioPerl-1.6.921/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.921/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.921/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.921/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.921/t/RemoteDB/Query
BioPerl-1.6.921/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.921/t/Restriction
BioPerl-1.6.921/t/Restriction/Analysis-refac.t
BioPerl-1.6.921/t/Restriction/Analysis.t
BioPerl-1.6.921/t/Restriction/Gel.t
BioPerl-1.6.921/t/Restriction/IO.t
BioPerl-1.6.921/t/Root
BioPerl-1.6.921/t/Root/Exception.t
BioPerl-1.6.921/t/Root/HTTPget.t
BioPerl-1.6.921/t/Root/RootI.t
BioPerl-1.6.921/t/Root/RootIO.t
BioPerl-1.6.921/t/Root/Storable.t
BioPerl-1.6.921/t/Root/Tempfile.t
BioPerl-1.6.921/t/Root/Utilities.t
BioPerl-1.6.921/t/SearchIO
BioPerl-1.6.921/t/SearchIO/axt.t
BioPerl-1.6.921/t/SearchIO/blast.t
BioPerl-1.6.921/t/SearchIO/blast_pull.t
BioPerl-1.6.921/t/SearchIO/blasttable.t
BioPerl-1.6.921/t/SearchIO/blastxml.t
BioPerl-1.6.921/t/SearchIO/CigarString.t
BioPerl-1.6.921/t/SearchIO/cross_match.t
BioPerl-1.6.921/t/SearchIO/erpin.t
BioPerl-1.6.921/t/SearchIO/exonerate.t
BioPerl-1.6.921/t/SearchIO/fasta.t
BioPerl-1.6.921/t/SearchIO/gmap_f9.t
BioPerl-1.6.921/t/SearchIO/hmmer.t
BioPerl-1.6.921/t/SearchIO/hmmer_pull.t
BioPerl-1.6.921/t/SearchIO/infernal.t
BioPerl-1.6.921/t/SearchIO/megablast.t
BioPerl-1.6.921/t/SearchIO/psl.t
BioPerl-1.6.921/t/SearchIO/rnamotif.t
BioPerl-1.6.921/t/SearchIO/SearchIO.t
BioPerl-1.6.921/t/SearchIO/sim4.t
BioPerl-1.6.921/t/SearchIO/SimilarityPair.t
BioPerl-1.6.921/t/SearchIO/Tiling.t
BioPerl-1.6.921/t/SearchIO/waba.t
BioPerl-1.6.921/t/SearchIO/wise.t
BioPerl-1.6.921/t/SearchIO/Writer
BioPerl-1.6.921/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.921/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.921/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.921/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.921/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.921/t/Seq
BioPerl-1.6.921/t/Seq/DBLink.t
BioPerl-1.6.921/t/Seq/EncodedSeq.t
BioPerl-1.6.921/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.921/t/Seq/LargePSeq.t
BioPerl-1.6.921/t/Seq/LocatableSeq.t
BioPerl-1.6.921/t/Seq/MetaSeq.t
BioPerl-1.6.921/t/Seq/PrimaryQual.t
BioPerl-1.6.921/t/Seq/PrimarySeq.t
BioPerl-1.6.921/t/Seq/PrimedSeq.t
BioPerl-1.6.921/t/Seq/Quality.t
BioPerl-1.6.921/t/Seq/Seq.t
BioPerl-1.6.921/t/Seq/SimulatedRead.t
BioPerl-1.6.921/t/Seq/WithQuality.t
BioPerl-1.6.921/t/SeqFeature
BioPerl-1.6.921/t/SeqFeature/Amplicon.t
BioPerl-1.6.921/t/SeqFeature/Clone.t
BioPerl-1.6.921/t/SeqFeature/Collection.t
BioPerl-1.6.921/t/SeqFeature/Computation.t
BioPerl-1.6.921/t/SeqFeature/FeaturePair.t
BioPerl-1.6.921/t/SeqFeature/Gene.t
BioPerl-1.6.921/t/SeqFeature/Generic.t
BioPerl-1.6.921/t/SeqFeature/Location.t
BioPerl-1.6.921/t/SeqFeature/LocationFactory.t
BioPerl-1.6.921/t/SeqFeature/Primer.t
BioPerl-1.6.921/t/SeqFeature/Range.t
BioPerl-1.6.921/t/SeqFeature/RangeI.t
BioPerl-1.6.921/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.921/t/SeqFeature/SubSeq.t
BioPerl-1.6.921/t/SeqFeature/Unflattener.t
BioPerl-1.6.921/t/SeqFeature/Unflattener2.t
BioPerl-1.6.921/t/SeqIO
BioPerl-1.6.921/t/SeqIO/abi.t
BioPerl-1.6.921/t/SeqIO/ace.t
BioPerl-1.6.921/t/SeqIO/agave.t
BioPerl-1.6.921/t/SeqIO/alf.t
BioPerl-1.6.921/t/SeqIO/asciitree.t
BioPerl-1.6.921/t/SeqIO/bsml.t
BioPerl-1.6.921/t/SeqIO/bsml_sax.t
BioPerl-1.6.921/t/SeqIO/chadoxml.t
BioPerl-1.6.921/t/SeqIO/chaos.t
BioPerl-1.6.921/t/SeqIO/chaosxml.t
BioPerl-1.6.921/t/SeqIO/ctf.t
BioPerl-1.6.921/t/SeqIO/embl.t
BioPerl-1.6.921/t/SeqIO/entrezgene.t
BioPerl-1.6.921/t/SeqIO/excel.t
BioPerl-1.6.921/t/SeqIO/exp.t
BioPerl-1.6.921/t/SeqIO/fasta.t
BioPerl-1.6.921/t/SeqIO/fastq.t
BioPerl-1.6.921/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.921/t/SeqIO/game.t
BioPerl-1.6.921/t/SeqIO/gbxml.t
BioPerl-1.6.921/t/SeqIO/gcg.t
BioPerl-1.6.921/t/SeqIO/genbank.t
BioPerl-1.6.921/t/SeqIO/Handler.t
BioPerl-1.6.921/t/SeqIO/interpro.t
BioPerl-1.6.921/t/SeqIO/kegg.t
BioPerl-1.6.921/t/SeqIO/largefasta.t
BioPerl-1.6.921/t/SeqIO/lasergene.t
BioPerl-1.6.921/t/SeqIO/locuslink.t
BioPerl-1.6.921/t/SeqIO/mbsout.t
BioPerl-1.6.921/t/SeqIO/metafasta.t
BioPerl-1.6.921/t/SeqIO/msout.t
BioPerl-1.6.921/t/SeqIO/MultiFile.t
BioPerl-1.6.921/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.921/t/SeqIO/nexml.t
BioPerl-1.6.921/t/SeqIO/phd.t
BioPerl-1.6.921/t/SeqIO/pir.t
BioPerl-1.6.921/t/SeqIO/pln.t
BioPerl-1.6.921/t/SeqIO/qual.t
BioPerl-1.6.921/t/SeqIO/raw.t
BioPerl-1.6.921/t/SeqIO/scf.t
BioPerl-1.6.921/t/SeqIO/SeqBuilder.t
BioPerl-1.6.921/t/SeqIO/SeqIO.t
BioPerl-1.6.921/t/SeqIO/seqxml.t
BioPerl-1.6.921/t/SeqIO/Splicedseq.t
BioPerl-1.6.921/t/SeqIO/strider.t
BioPerl-1.6.921/t/SeqIO/swiss.t
BioPerl-1.6.921/t/SeqIO/tab.t
BioPerl-1.6.921/t/SeqIO/table.t
BioPerl-1.6.921/t/SeqIO/tigr.t
BioPerl-1.6.921/t/SeqIO/tigrxml.t
BioPerl-1.6.921/t/SeqIO/tinyseq.t
BioPerl-1.6.921/t/SeqIO/ztr.t
BioPerl-1.6.921/t/SeqTools
BioPerl-1.6.921/t/SeqTools/Backtranslate.t
BioPerl-1.6.921/t/SeqTools/CodonTable.t
BioPerl-1.6.921/t/SeqTools/ECnumber.t
BioPerl-1.6.921/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.921/t/SeqTools/OddCodes.t
BioPerl-1.6.921/t/SeqTools/SeqPattern.t
BioPerl-1.6.921/t/SeqTools/SeqStats.t
BioPerl-1.6.921/t/SeqTools/SeqUtils.t
BioPerl-1.6.921/t/SeqTools/SeqWords.t
BioPerl-1.6.921/t/Structure
BioPerl-1.6.921/t/Structure/IO.t
BioPerl-1.6.921/t/Structure/Structure.t
BioPerl-1.6.921/t/Tools
BioPerl-1.6.921/t/Tools/AmpliconSearch.t
BioPerl-1.6.921/t/Tools/ePCR.t
BioPerl-1.6.921/t/Tools/Est2Genome.t
BioPerl-1.6.921/t/Tools/FootPrinter.t
BioPerl-1.6.921/t/Tools/Geneid.t
BioPerl-1.6.921/t/Tools/Genewise.t
BioPerl-1.6.921/t/Tools/Genomewise.t
BioPerl-1.6.921/t/Tools/Genpred.t
BioPerl-1.6.921/t/Tools/GFF.t
BioPerl-1.6.921/t/Tools/GuessSeqFormat.t
BioPerl-1.6.921/t/Tools/Hmmer.t
BioPerl-1.6.921/t/Tools/IUPAC.t
BioPerl-1.6.921/t/Tools/Lucy.t
BioPerl-1.6.921/t/Tools/Match.t
BioPerl-1.6.921/t/Tools/pICalculator.t
BioPerl-1.6.921/t/Tools/Primer3.t
BioPerl-1.6.921/t/Tools/Promoterwise.t
BioPerl-1.6.921/t/Tools/Pseudowise.t
BioPerl-1.6.921/t/Tools/QRNA.t
BioPerl-1.6.921/t/Tools/RandDistFunctions.t
BioPerl-1.6.921/t/Tools/RepeatMasker.t
BioPerl-1.6.921/t/Tools/rnamotif.t
BioPerl-1.6.921/t/Tools/Seg.t
BioPerl-1.6.921/t/Tools/Sigcleave.t
BioPerl-1.6.921/t/Tools/Signalp.t
BioPerl-1.6.921/t/Tools/Sim4.t
BioPerl-1.6.921/t/Tools/SiRNA.t
BioPerl-1.6.921/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.921/t/Tools/TargetP.t
BioPerl-1.6.921/t/Tools/Tmhmm.t
BioPerl-1.6.921/t/Tools/tRNAscanSE.t
BioPerl-1.6.921/t/Tools/Alignment
BioPerl-1.6.921/t/Tools/Alignment/Consed.t
BioPerl-1.6.921/t/Tools/Analysis
BioPerl-1.6.921/t/Tools/Analysis/DNA
BioPerl-1.6.921/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.921/t/Tools/Analysis/Protein
BioPerl-1.6.921/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.921/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.921/t/Tools/EMBOSS
BioPerl-1.6.921/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.921/t/Tools/Phylo
BioPerl-1.6.921/t/Tools/Phylo/Gerp.t
BioPerl-1.6.921/t/Tools/Phylo/Molphy.t
BioPerl-1.6.921/t/Tools/Phylo/PAML.t
BioPerl-1.6.921/t/Tools/Phylo/Phylip
BioPerl-1.6.921/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.921/t/Tools/Run
BioPerl-1.6.921/t/Tools/Run/Dummy.pm
BioPerl-1.6.921/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.921/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.921/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.921/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.921/t/Tools/Run/WrapperBase.t
BioPerl-1.6.921/t/Tools/Run/Dummy
BioPerl-1.6.921/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.921/t/Tools/Signalp
BioPerl-1.6.921/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.921/t/Tools/Spidey
BioPerl-1.6.921/t/Tools/Spidey/Spidey.t
BioPerl-1.6.921/t/Tree
BioPerl-1.6.921/t/Tree/Compatible.t
BioPerl-1.6.921/t/Tree/Node.t
BioPerl-1.6.921/t/Tree/RandomTreeFactory.t
BioPerl-1.6.921/t/Tree/Tree.t
BioPerl-1.6.921/t/Tree/TreeIO.t
BioPerl-1.6.921/t/Tree/TreeStatistics.t
BioPerl-1.6.921/t/Tree/PhyloNetwork
BioPerl-1.6.921/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.921/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.921/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.921/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.921/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.921/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.921/t/Tree/TreeIO
BioPerl-1.6.921/t/Tree/TreeIO/lintree.t
BioPerl-1.6.921/t/Tree/TreeIO/newick.t
BioPerl-1.6.921/t/Tree/TreeIO/nexml.t
BioPerl-1.6.921/t/Tree/TreeIO/nexus.t
BioPerl-1.6.921/t/Tree/TreeIO/nhx.t
BioPerl-1.6.921/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.921/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.921/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.921/t/Variation
BioPerl-1.6.921/t/Variation/AAChange.t
BioPerl-1.6.921/t/Variation/AAReverseMutate.t
BioPerl-1.6.921/t/Variation/Allele.t
BioPerl-1.6.921/t/Variation/DNAMutation.t
BioPerl-1.6.921/t/Variation/RNAChange.t
BioPerl-1.6.921/t/Variation/SeqDiff.t
BioPerl-1.6.921/t/Variation/SNP.t
BioPerl-1.6.921/t/Variation/Variation_IO.t
BioPerl-1.6.921/travis_scripts
BioPerl-1.6.921/travis_scripts/dependency_installs

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.921.tar.gz

>>> /Users/fly1400/ap1400/bin/perl Build.PL
could not find ParserDetails.ini in /Users/fly1400/var/megalib/XML/SAX
Checking prerequisites...
  recommends:
    *  GraphViz is not installed

Checking optional features...
MySQL Tests...........disabled
  requires:
    ! DBD::mysql 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 '1.006921'
>>> ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.921.tar.gz
  ./Build -- OK
Running Build test
>>> ./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 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
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ok 16
ok 17 - The object isa Bio::Align::AlignI
ok 18
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ok 23
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ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok 44 - Warn if seqs don't overlap
ok 45
ok
t/Align/AlignUtil.t .................... 
1..47
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 42
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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 - The object isa Bio::AlignIO
ok 7 - alignment is there and defined
ok 8 - all starts are present
ok 9 - all ends are present
ok 10 - all colors are present
ok 11 - first end is further than first start
ok 12 - second end is further than second start
ok 13 - third end is further than third start
ok 14 - domain labels are present
ok 15 - domain starts are present
ok 16 - domain ends are present
ok 17 - domain colors are present
ok 18 - label - first end is further than first start
ok 19 - label - second end is further than second start
ok 20 - label - third end is further than third start
ok 21 - first label start is within domain range
ok 22 - second label start is within domain range
ok 23 - third label start is within domain range
ok 24 - first label end is within domain range
ok 25 - second label end is within domain range
ok 26 - third label end is within domain range
ok 27 - individual labels work
ok 28 - The object isa Bio::Align::Graphics
ok 29 - new object is defined
ok 30 -   pad_bottom is right
ok 31 -   default pad_top is right
ok 32 -   start point loaded
ok 33 -   end point loaded
ok 34 -   color of domain loaded
ok 35 -   domain labels loaded
ok 36 -   label starts loaded
ok 37 -   label ends loaded
ok 38 -   label colors loaded
ok 39 -   labels loaded
ok 40 -   output file is png
ok 41 -   wrapping length is not zero
ok
t/Align/SimpleAlign.t .................. 
1..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 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object isa Bio::Align::AlignI
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - 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 - The object isa Bio::AnnotatableI
ok 95 - added 3 seqs
ok 96 - first 2 features added
ok 97 - 3rd feature added
not ok 98 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.  
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 99 - slice 1 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 104 - slice 2 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 109 - slice 3 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
not ok 113 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
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 - The object isa Bio::SimpleAlign
ok 200 - consensus string looks ok
ok 201 - conservation length
ok 202 - conservation scores
ok 203 - looks like correct unmasked alignment (from clustalw)
ok 204 - looks like correct masked alignment (from clustalw)
ok 205
ok 206 - align after looks ok
ok
t/Align/TreeBuild.t .................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign
ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI
ok 9 - Tree object gotten back isa Bio::Tree::TreeI
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
t/Align/Utilities.t .................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/AlignIO/AlignIO.t .................... 
1..29
ok 1 - use Bio::AlignIO;
ok 2 - The object isa Bio::AnnotatableI
ok 3 - input filehandle method test : metafasta
ok 4 - input filehandle method test : po
ok 5 - input filehandle method test : nexus
ok 6 - input filehandle method test : clustalw
ok 7 - input filehandle method test : prodom
ok 8 - input filehandle method test : fasta
ok 9 - input filehandle method test : arp
ok 10 - input filehandle method test : xmfa
ok 11 - input filehandle method test : mase
ok 12 - input filehandle method test : psi
ok 13 - input filehandle method test : phylip
ok 14 - input filehandle method test : pfam
ok 15 - input filehandle method test : selex
ok 16 - input filehandle method test : stockholm
ok 17 - input filehandle method test : msf
ok 18 - filehandle output test : metafasta
ok 19 - filehandle output test : po
ok 20 - filehandle output test : nexus
ok 21 - filehandle output test : clustalw
ok 22 - filehandle output test : fasta
ok 23 - filehandle output test : xmfa
ok 24 - filehandle output test : psi
ok 25 - filehandle output test : phylip
ok 26 - filehandle output test : pfam
ok 27 - filehandle output test : selex
ok 28 - filehandle output test : stockholm
ok 29 - filehandle output test : msf
ok
t/AlignIO/arp.t ........................ 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP num_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - The object isa Bio::AnnotationCollectionI
ok 10 - The object isa Bio::AnnotationI
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - The object isa Bio::AnnotationCollectionI
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Align::AlignI
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - The object isa Bio::AnnotationCollectionI
ok 33 - The object isa Bio::AnnotationI
ok 34
ok 35
ok 36
ok 37
ok 38 - The object isa Bio::Align::AlignI
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - The object isa Bio::AnnotationCollectionI
ok 44 - The object isa Bio::AnnotationI
ok 45
ok 46
ok 47
ok 48
ok
t/AlignIO/bl2seq.t ..................... 
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - BLAST bl2seq format test
ok
t/AlignIO/clustalw.t ................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - The object isa Bio::Align::AlignI
ok 6 - clustalw (.aln) input test
ok
t/AlignIO/emboss.t ..................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Align::AlignI
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Align::AlignI
ok 19
ok 20
ok 21 - The object isa Bio::Align::AlignI
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Align::AlignI
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/AlignIO/fasta.t ...................... 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test  
ok 10 - filehandle output test
ok
t/AlignIO/largemultifasta.t ............ 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
t/AlignIO/maf.t ........................ 
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - maf input test
ok 4
ok 5 - The object isa Bio::Align::AlignI
ok 6 - maf input test
ok 7
ok 8 - maf input test
ok 9
ok 10 - maf input test
ok 11
ok
t/AlignIO/mase.t ....................... 
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - mase input test 
ok
t/AlignIO/mega.t ....................... 
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
t/AlignIO/meme.t ....................... 
1..20
ok 1 - use Bio::AlignIO::meme;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object 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 - The object 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 - The object 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 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - nexus output test
ok 6 - The object isa Bio::AlignIO
ok 7 - The object isa Bio::Align::AlignI
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10 - The object isa Bio::AlignIO
ok 11 - The object isa Bio::Align::AlignI
ok 12 - The object isa Bio::AlignIO
ok 13 - The object isa Bio::Align::AlignI
ok 14 - The object isa Bio::AlignIO
ok 15 - The object isa Bio::Align::AlignI
ok 16 - The object isa Bio::AlignIO
ok 17 - The object isa Bio::Align::AlignI
ok 18 - The object isa Bio::AlignIO
ok 19 - The object isa Bio::Align::AlignI
ok 20 - The object isa Bio::AlignIO
ok 21 - The object isa Bio::Align::AlignI
ok 22 - The object isa Bio::AlignIO
ok 23 - The object isa Bio::Align::AlignI
ok 24 - The object isa Bio::AlignIO
ok 25 - The object isa Bio::Align::AlignI
ok 26 - The object isa Bio::AlignIO
ok 27 - The object isa Bio::Align::AlignI
ok 28 - The object isa Bio::AlignIO
ok 29 - The object isa Bio::Align::AlignI
ok 30 - The object isa Bio::AlignIO
ok 31 - The object isa Bio::Align::AlignI
ok 32 - The object isa Bio::AlignIO
ok 33 - The object isa Bio::Align::AlignI
ok 34 - The object isa Bio::AlignIO
ok 35 - The object isa Bio::Align::AlignI
ok 36 - The object isa Bio::AlignIO
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::AlignIO
ok 39 - The object isa Bio::Align::AlignI
ok 40 - The object isa Bio::AlignIO
ok 41 - The object isa Bio::Align::AlignI
ok 42 - The object isa Bio::AlignIO
ok 43 - The object isa Bio::Align::AlignI
ok
t/AlignIO/pfam.t ....................... 
1..5
ok 1 - use Bio::AlignIO::pfam;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 -  pfam output test
ok
t/AlignIO/phylip.t ..................... 
1..17
ok 1 - use Bio::AlignIO::phylip;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11 - phylip output test
ok 12
ok 13
ok 14
not ok 15 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 81.
#          got: undef
#     expected: '0'
not ok 16 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 82.
#          got: '50'
#     expected: '47'
ok 17 - newline between header and sequences is parsed correctly
ok
t/AlignIO/po.t ......................... 
1..11
ok 1 - use Bio::AlignIO::po;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - The object isa Bio::AlignIO
ok 6 - The object isa Bio::Align::AlignI
ok 7 - po output test
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok
t/AlignIO/prodom.t ..................... 
1..3
ok 1 - use Bio::AlignIO::prodom;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - prodom input test 
ok
t/AlignIO/psi.t ........................ 
1..5
ok 1 - use Bio::AlignIO::psi;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok
t/AlignIO/selex.t ...................... 
1..4
ok 1 - use Bio::AlignIO::selex;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - selex format test 
ok 4 - selex output test
ok
t/AlignIO/stockholm.t .................. 
1..87
ok 1 - use Bio::AlignIO::stockholm;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Annotation::Comment
ok 10 - Stockholm annotation
ok 11 - Stockholm annotation
ok 12 - stockholm output test
ok 13 - The object isa Bio::Align::AlignI
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20 - Stockholm annotation isa Bio::Annotation::Reference
ok 21 - Stockholm annotation
ok 22 - Stockholm annotation
ok 23 - Stockholm annotation
ok 24 - Stockholm annotation
ok 25 - The object isa Bio::Seq::MetaI
ok 26 - Rfam meta data
ok 27 - Rfam meta data
ok 28
ok 29 - The object isa Bio::Align::AlignI
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35 - The object isa Bio::Seq::MetaI
ok 36 - Rfam meta data
ok 37 - Rfam meta data
ok 38 - The object isa Bio::AlignIO
ok 39
ok 40 - The object isa Bio::Align::AlignI
ok 41
ok 42
ok 43
ok 44
ok 45 - The object isa Bio::Annotation::SimpleValue
ok 46 - Pfam annotation
ok 47
ok 48 - The object isa Bio::Align::AlignI
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::Align::AlignI
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - The object isa Bio::Seq::MetaI
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam aln meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69 - Pfam seq meta data
ok 70
ok 71 - The object isa Bio::SeqFeatureI
ok 72 - The object isa Bio::Seq::Meta
ok 73 - The object isa Bio::AnnotationI
ok 74 - The object isa Bio::Annotation::DBLink
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok
t/AlignIO/xmfa.t ....................... 
1..30
ok 1 - use Bio::AlignIO::xmfa;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - xmfa input test 
ok 4 - xmfa input test for start
ok 5 - xmfa input test for end
ok 6 - xmfa strand test
ok 7 - xmfa input test for id
ok 8 - xmfa input test for id
ok 9 - xmfa input test 
ok 10 - xmfa input test for start
ok 11 - xmfa input test for end
ok 12 - xmfa strand test
ok 13 - xmfa input test for id
ok 14 - xmfa input test for id
ok 15 - xmfa input test 
ok 16 - xmfa input test for start
ok 17 - xmfa input test for end
ok 18 - xmfa strand test
ok 19 - xmfa input test for id
ok 20 - xmfa input test for id
ok 21 - xmfa alignment score
ok 22 - The object isa Bio::Align::AlignI
ok 23 - xmfa input test 
ok 24 - xmfa strand
ok 25 - xmfa input test for description
ok 26 - xmfa input test for id
ok 27 - xmfa input test for end
ok 28 - xmfa input test for end
ok 29 - xmfa alignment score
ok 30 - xmfa output test
ok
t/Alphabet.t ........................... 
1..100
ok 1 - use Bio::Symbol::Alphabet;
ok 2 - use Bio::Symbol::Symbol;
ok 3 - use Bio::Symbol::DNAAlphabet;
ok 4 - use Bio::Symbol::ProteinAlphabet;
ok 5 - The object isa Bio::Symbol::Alphabet
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Symbol::AlphabetI
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - The object isa Bio::Symbol::AlphabetI
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok
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 - The object isa Bio::AnnotationI
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::AnnotationI
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::AnnotationCollectionI
ok 23
ok 24
ok 25 - The object isa Bio::AnnotationI
ok 26
ok 27 - The object 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 - The object 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 - The object isa Bio::AnnotationCollectionI
ok 66
ok 67
ok 68
ok 69
ok 70 - The object isa Bio::Annotation::StructuredValue
ok 71
ok 72
ok 73
ok 74
ok 75 - use Bio::Annotation::OntologyTerm;
ok 76 - The object isa Bio::Ontology::Term
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 83 - isa AnnotatableI isa Bio::AnnotatableI
ok 84 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 85 - isa AnnotatableI isa Bio::AnnotatableI
ok 86 - The object isa Bio::Factory::ObjectFactoryI
ok 87 - The object isa Bio::Annotation::SimpleValue
ok 88
ok 89 - The object isa Bio::Annotation::OntologyTerm
ok 90 - Bio::Annotation::Comment
ok 91 - The object isa Bio::Annotation::Comment
ok 92
ok 93 - Bio::Annotation::Comment
ok 94 - The object isa Bio::Annotation::Comment
ok 95 - Bio::Annotation::Comment
ok 96 - The object isa Bio::Annotation::Comment
ok 97
ok 98 - The object isa Bio::Annotation::Target
ok 99
ok 100
ok 101 - The object 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 - The object isa Bio::Annotation::Tree
ok 109 - The object isa Bio::AnnotationI
ok 110 - default itext
ok 111 - roundtrip
ok 112 - itext
ok 113 - spxr
ok 114 - indent
ok 115 - xml
ok 116 - The object isa Data::Stag::StagI
ok 117
ok 118 - child changes
ok 119 - The object isa Data::Stag::StagI
ok 120
ok 121 - child changes
ok 122 - The object 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 - The object isa Bio::AnnotationI
ok 144 - The object isa Data::Stag::StagI
ok 145 - child changes
ok 146 - The object isa Data::Stag::StagI
ok 147 - child changes
ok 148 - The object isa Data::Stag::StagI
ok 149 - child changes
ok 150
ok 151
ok 152 - The object isa Bio::Annotation::TagTree
ok
t/Annotation/AnnotationAdaptor.t ....... 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Assembly/ContigSpectrum.t ............ 
1..239
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
ok 3 - The object isa Bio::Assembly::IO
ok 4 - The object isa Bio::Assembly::Scaffold
ok 5 - get/set methods
ok 6 - The object isa Bio::Assembly::Tools::ContigSpectrum
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 - simple spectrum
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 - contig spectrum score
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57 - mixed contig spectrum
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 - dissolved contig spectrum
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 - cross-contig spectrum
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139 - cross-contig spectrum
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - cross-contig spectrum
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160 - contig spectrum sum
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 - average contig spectrum
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 - drop assembly
ok 190
ok 191 - The object isa Bio::Assembly::IO
ok 192 - The object isa Bio::Assembly::Scaffold
ok 193 - large contig spectrum
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 - 74.7485808732225
ok 207 - 74.7485808732225
ok 208 - large cross-contig spectrum
ok 209
ok 210 - 88.8076923076923
ok 211 - 88.8076923076923
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222 - one contig at a time
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
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
t/Assembly/core.t ...................... 
1..890
ok 1 - use Bio::Seq;
ok 2 - use Bio::LocatableSeq;
ok 3 - use Bio::Seq::Quality;
ok 4 - use Bio::Assembly::IO;
ok 5 - use Bio::Assembly::Singlet;
ok 6 - singlet from Bio::PrimarySeq
ok 7 - The object isa Bio::Assembly::Contig
ok 8 - The object isa Bio::Assembly::Singlet
ok 9
ok 10
ok 11 - The object isa Bio::LocatableSeq
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 - singlet from Bio::Seq::Quality
ok 25
ok 26
ok 27 - The object isa Bio::Seq::QualI
ok 28
ok 29 - singlet from LocatableSeq
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38 - singlet from LocatableSeq with set coordinates
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - consed
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::Assembly::IO
ok 54 - The object isa Bio::Assembly::Contig
ok 55 - The object isa Bio::Assembly::Contig
ok 56 - The object isa Bio::Assembly::Contig
ok 57 - The object isa Bio::Assembly::IO
not ok 58 # TODO phrap parser doesn't include the sequence string in the sequence objects.

#   Failed (TODO) test at t/Assembly/core.t line 126.
ok 59
ok 60 - The object isa Bio::Assembly::Scaffold
ok 61
ok 62
ok 63 - The object isa Bio::AnnotationCollectionI
ok 64 - no annotations in Annotation collection?
ok 65
ok 66
ok 67 - get_nof_singlets
ok 68 - get_contig_seq_ids
ok 69 - get_contig_ids
ok 70 - get_singlet_ids
ok 71 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 72 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 73 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet
ok 74 - get_contig_seq_ids
ok 75
ok 76
ok 77
ok 78 - get_contig_ids
ok 79
ok 80
ok 81 - get_singlet_ids
ok 82
ok 83
ok 84
ok 85 - get_all_seq_ids
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92 - contig features
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - get_nof_singlets
ok 100 - get_contig_seq_ids
ok 101 - get_contig_ids
ok 102 - get_singlet_ids
ok 103 - The object isa Bio::Assembly::Contig
ok 104 - The object isa Bio::Assembly::Contig
ok 105 - The object isa Bio::Assembly::Contig
ok 106 - The object isa Bio::Assembly::Contig
ok 107 - The object isa Bio::Assembly::Contig
ok 108 - The object isa Bio::Assembly::Contig
ok 109 - The object isa Bio::Assembly::Contig
ok 110 - The object isa Bio::Assembly::Contig
ok 111 - The object isa Bio::Assembly::Contig
ok 112 - The object isa Bio::Assembly::Contig
ok 113 - The object isa Bio::Assembly::Contig
ok 114 - The object isa Bio::Assembly::Contig
ok 115 - The object isa Bio::Assembly::Contig
ok 116 - The object isa Bio::Assembly::Contig
ok 117 - The object isa Bio::Assembly::Contig
ok 118 - The object isa Bio::Assembly::Contig
ok 119 - The object isa Bio::Assembly::Contig
ok 120 - The object isa Bio::Assembly::Contig
ok 121 - The object isa Bio::Assembly::Contig
ok 122 - The object isa Bio::Assembly::Contig
ok 123 - The object isa Bio::Assembly::Contig
ok 124 - The object isa Bio::Assembly::Contig
ok 125 - The object isa Bio::Assembly::Contig
ok 126 - The object isa Bio::Assembly::Contig
ok 127 - The object isa Bio::Assembly::Contig
ok 128 - The object isa Bio::Assembly::Contig
ok 129 - The object isa Bio::Assembly::Contig
ok 130 - The object isa Bio::Assembly::Contig
ok 131 - The object isa Bio::Assembly::Contig
ok 132 - The object isa Bio::Assembly::Contig
ok 133 - The object isa Bio::Assembly::Contig
ok 134 - The object isa Bio::Assembly::Contig
ok 135 - The object isa Bio::Assembly::Contig
ok 136 - The object isa Bio::Assembly::Contig
ok 137 - The object isa Bio::Assembly::Contig
ok 138 - The object isa Bio::Assembly::Contig
ok 139
ok 140 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146 - get_nof_singlets
ok 147 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 148 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet
ok 149 - get_contig_seq_ids
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157 - get_contig_ids
ok 158
ok 159
ok 160
ok 161
ok 162 - get_singlet_ids
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 - get_all_seq_ids
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 - 454 ACE variant coordinates check
ok 240
ok 241 - 454 ACE variant consensus check
ok 242
ok 243
ok 244
ok 245
ok 246 - writing in the ACE format
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252 - The object isa Bio::Assembly::Contig
ok 253 - The object isa Bio::Assembly::Contig
ok 254 - The object isa Bio::Assembly::Contig
ok 255 - The object isa Bio::Assembly::Contig
ok 256 - The object isa Bio::Assembly::Contig
ok 257 - The object isa Bio::Assembly::Contig
ok 258 - The object isa Bio::Assembly::Contig
ok 259 - The object isa Bio::Assembly::Contig
ok 260 - The object isa Bio::Assembly::Contig
ok 261 - The object isa Bio::Assembly::Contig
ok 262 - The object isa Bio::Assembly::Contig
ok 263 - The object isa Bio::Assembly::Contig
ok 264 - The object isa Bio::Assembly::Contig
ok 265 - The object isa Bio::Assembly::Contig
ok 266 - The object isa Bio::Assembly::Scaffold
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274 - The object isa Bio::LocatableSeq
ok 275 - The object isa Bio::Assembly::Contig
ok 276
ok 277
ok 278
ok 279 - The object isa Bio::AnnotationCollectionI
ok 280 - no annotations in Annotation collection?
ok 281 - writing in the TIGR format
ok 282 - init maq IO object
ok 283 - get maq assy
ok 284 - got all contigs
ok 285 - read test file as text
ok 286 - recorded all maq reads
ok 287 - no singlets
ok 288
ok 289 - The object isa Bio::Assembly::IO
ok 290 - The object isa Bio::Assembly::Contig
ok 291 - The object isa Bio::Assembly::Contig
ok 292 - The object isa Bio::Assembly::Contig
ok 293 - The object isa Bio::Assembly::Contig
ok 294 - The object isa Bio::Assembly::Contig
ok 295 - The object isa Bio::Assembly::Contig
ok 296 - The object isa Bio::Assembly::Contig
ok 297 - The object isa Bio::Assembly::Contig
ok 298 - The object isa Bio::Assembly::Contig
ok 299 - The object isa Bio::Assembly::Contig
ok 300 - The object isa Bio::Assembly::Contig
ok 301
ok 302 - get maq assy
ok 303 - The object isa Bio::Assembly::IO
ok 304 - get_contig_seq_ids
ok 305
ok 306
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312
ok 313
ok 314
ok 315
ok 316
ok 317
ok 318
ok 319
ok 320
ok 321
ok 322
ok 323
ok 324
ok 325
ok 326
ok 327
ok 328
ok 329
ok 330
ok 331
ok 332
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339
ok 340
ok 341
ok 342
ok 343
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353
ok 354
ok 355
ok 356
ok 357
ok 358
ok 359
ok 360
ok 361
ok 362
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369
ok 370
ok 371
ok 372
ok 373
ok 374
ok 375
ok 376
ok 377
ok 378
ok 379
ok 380
ok 381
ok 382
ok 383
ok 384
ok 385
ok 386
ok 387
ok 388
ok 389
ok 390
ok 391
ok 392
ok 393
ok 394
ok 395
ok 396
ok 397
ok 398
ok 399
ok 400
ok 401
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
ok 416
ok 417
ok 418
ok 419
ok 420
ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
ok 437
ok 438
ok 439
ok 440
ok 441
ok 442
ok 443
ok 444
ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok 451
ok 452
ok 453
ok 454
ok 455
ok 456
ok 457
ok 458
ok 459
ok 460
ok 461
ok 462
ok 463
ok 464
ok 465
ok 466
ok 467
ok 468
ok 469
ok 470
ok 471
ok 472
ok 473
ok 474
ok 475
ok 476
ok 477
ok 478
ok 479
ok 480
ok 481
ok 482
ok 483
ok 484
ok 485
ok 486
ok 487
ok 488
ok 489
ok 490
ok 491
ok 492
ok 493
ok 494
ok 495
ok 496
ok 497
ok 498
ok 499
ok 500
ok 501
ok 502
ok 503
ok 504
ok 505
ok 506
ok 507
ok 508
ok 509
ok 510
ok 511
ok 512
ok 513
ok 514
ok 515
ok 516
ok 517
ok 518
ok 519
ok 520
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528
ok 529
ok 530
ok 531
ok 532
ok 533
ok 534
ok 535
ok 536
ok 537
ok 538
ok 539
ok 540
ok 541
ok 542
ok 543
ok 544
ok 545
ok 546
ok 547
ok 548
ok 549
ok 550
ok 551
ok 552 - get_contig_ids
ok 553
ok 554
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561
ok 562
ok 563
ok 564
ok 565
ok 566
ok 567
ok 568
ok 569
ok 570
ok 571
ok 572
ok 573
ok 574
ok 575
ok 576
ok 577
ok 578
ok 579
ok 580
ok 581
ok 582
ok 583
ok 584
ok 585
ok 586
ok 587
ok 588
ok 589
ok 590
ok 591 - get_singlet_ids
ok 592
ok 593
ok 594
ok 595
ok 596
ok 597 - get_all_seq_ids
ok 598
ok 599
ok 600
ok 601
ok 602
ok 603
ok 604
ok 605
ok 606
ok 607
ok 608
ok 609
ok 610
ok 611
ok 612
ok 613
ok 614
ok 615
ok 616
ok 617
ok 618
ok 619
ok 620
ok 621
ok 622
ok 623
ok 624
ok 625
ok 626
ok 627
ok 628
ok 629
ok 630
ok 631
ok 632
ok 633
ok 634
ok 635
ok 636
ok 637
ok 638
ok 639
ok 640
ok 641
ok 642
ok 643
ok 644
ok 645
ok 646
ok 647
ok 648
ok 649
ok 650
ok 651
ok 652
ok 653
ok 654
ok 655
ok 656
ok 657
ok 658
ok 659
ok 660
ok 661
ok 662
ok 663
ok 664
ok 665
ok 666
ok 667
ok 668
ok 669
ok 670
ok 671
ok 672
ok 673
ok 674
ok 675
ok 676
ok 677
ok 678
ok 679
ok 680
ok 681
ok 682
ok 683
ok 684
ok 685
ok 686
ok 687
ok 688
ok 689
ok 690
ok 691
ok 692
ok 693
ok 694
ok 695
ok 696
ok 697
ok 698
ok 699
ok 700
ok 701
ok 702
ok 703
ok 704
ok 705
ok 706
ok 707
ok 708
ok 709
ok 710
ok 711
ok 712
ok 713
ok 714
ok 715
ok 716
ok 717
ok 718
ok 719
ok 720
ok 721
ok 722
ok 723
ok 724
ok 725
ok 726
ok 727
ok 728
ok 729
ok 730
ok 731
ok 732
ok 733
ok 734
ok 735
ok 736
ok 737
ok 738
ok 739
ok 740
ok 741
ok 742
ok 743
ok 744
ok 745
ok 746
ok 747
ok 748
ok 749
ok 750
ok 751
ok 752
ok 753
ok 754
ok 755
ok 756
ok 757
ok 758
ok 759
ok 760
ok 761
ok 762
ok 763
ok 764
ok 765
ok 766
ok 767
ok 768
ok 769
ok 770
ok 771
ok 772
ok 773
ok 774
ok 775
ok 776
ok 777
ok 778
ok 779
ok 780
ok 781
ok 782
ok 783
ok 784
ok 785
ok 786
ok 787
ok 788
ok 789
ok 790
ok 791
ok 792
ok 793
ok 794
ok 795
ok 796
ok 797
ok 798
ok 799
ok 800
ok 801
ok 802
ok 803
ok 804
ok 805
ok 806
ok 807
ok 808
ok 809
ok 810
ok 811
ok 812
ok 813
ok 814
ok 815
ok 816
ok 817
ok 818
ok 819
ok 820
ok 821
ok 822
ok 823
ok 824
ok 825
ok 826
ok 827
ok 828
ok 829
ok 830
ok 831
ok 832
ok 833
ok 834
ok 835
ok 836
ok 837
ok 838
ok 839
ok 840
ok 841
ok 842
ok 843
ok 844
ok 845
ok 846
ok 847
ok 848
ok 849
ok 850 - The object isa Bio::Assembly::Contig
ok 851 - The object isa Bio::Assembly::Contig
ok 852 - The object isa Bio::Assembly::Contig
ok 853 - The object isa Bio::Assembly::Contig
ok 854 - The object isa Bio::Assembly::Contig
ok 855 - The object isa Bio::Assembly::Contig
ok 856 - The object isa Bio::Assembly::Contig
ok 857 - The object isa Bio::Assembly::Contig
ok 858 - The object isa Bio::Assembly::Contig
ok 859 - The object isa Bio::Assembly::Contig
ok 860 - The object isa Bio::Assembly::Contig
ok 861 - The object isa Bio::Assembly::Contig
ok 862 - The object isa Bio::Assembly::Contig
ok 863 - The object isa Bio::Assembly::Contig
ok 864 - The object isa Bio::Assembly::Contig
ok 865 - The object isa Bio::Assembly::Contig
ok 866 - The object isa Bio::Assembly::Contig
ok 867 - The object isa Bio::Assembly::Contig
ok 868 - The object isa Bio::Assembly::Contig
ok 869 - The object isa Bio::Assembly::Contig
ok 870 - The object isa Bio::Assembly::Contig
ok 871 - The object isa Bio::Assembly::Contig
ok 872 - The object isa Bio::Assembly::Contig
ok 873 - The object isa Bio::Assembly::Contig
ok 874 - The object isa Bio::Assembly::Contig
ok 875 - The object isa Bio::Assembly::Contig
ok 876 - The object isa Bio::Assembly::Contig
ok 877 - The object isa Bio::Assembly::Contig
ok 878 - The object isa Bio::Assembly::Contig
ok 879 - The object isa Bio::Assembly::Contig
ok 880 - The object isa Bio::Assembly::Contig
ok 881 - The object isa Bio::Assembly::Contig
ok 882 - The object isa Bio::Assembly::Contig
ok 883 - The object isa Bio::Assembly::Contig
ok 884 - The object isa Bio::Assembly::Contig
ok 885 - The object isa Bio::Assembly::Contig
ok 886 - The object isa Bio::Assembly::Contig
ok 887 - The object isa Bio::Assembly::Contig
ok 888 - The object isa Bio::Assembly::Contig
ok 889 - The object isa Bio::Assembly::Contig
ok 890 - The object isa Bio::Assembly::Contig
ok
t/Cluster/UniGene.t .................... 
1..2
ok 1 - use Bio::Cluster::UniGene;
ok 2 - The object 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 - The object isa Bio::Cluster::UniGeneI
ok 12 - The object 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 - The object isa Bio::Cluster::UniGeneI
ok 5 - The object isa Bio::ClusterI
ok 6 - The object isa Bio::IdentifiableI
ok 7 - The object isa Bio::DescribableI
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::PrimarySeqI
ok 49
ok 50
ok 51 - annotation object defined
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66 - The object isa Bio::PrimarySeqI
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
t/Coordinate/CoordinateBoundaryTest.t .. 
1..174
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3
ok 4 - The object isa Bio::Location::Simple
ok 5
ok 6 - The object isa Bio::Location::Simple
ok 7
ok 8 - The object isa Bio::Location::Simple
ok 9
ok 10 - The object isa Bio::Coordinate::Pair
ok 11
ok 12 - The object isa Bio::Coordinate::Pair
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::LocationI
ok 33
ok 34 - The object isa Bio::Coordinate::Result
ok 35
ok 36 - The object isa Bio::Coordinate::Result
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50 - The object isa Bio::LocationI
ok 51
ok 52 - The object isa Bio::Coordinate::Result
ok 53
ok 54 - The object isa Bio::Coordinate::Result
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - The object isa Bio::LocationI
ok 69
ok 70 - The object isa Bio::Coordinate::Result
ok 71
ok 72 - The object isa Bio::Coordinate::Result
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88 - The object isa Bio::LocationI
ok 89
ok 90 - The object isa Bio::Coordinate::Result
ok 91
ok 92 - The object isa Bio::Coordinate::Result
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108 - The object isa Bio::Location::Simple
ok 109
ok 110 - The object isa Bio::Location::Simple
ok 111
ok 112 - The object isa Bio::Location::Simple
ok 113
ok 114 - The object isa Bio::Coordinate::Pair
ok 115
ok 116 - The object isa Bio::Coordinate::Pair
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132 - The object isa Bio::Coordinate::Result
ok 133
ok 134 - The object isa Bio::Coordinate::Result
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142 - The object isa Bio::Coordinate::Result
ok 143
ok 144 - The object isa Bio::Coordinate::Result
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - The object isa Bio::Coordinate::Result
ok 153
ok 154 - The object isa Bio::Coordinate::Result
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164 - The object isa Bio::Coordinate::Result
ok 165
ok 166 - The object isa Bio::Coordinate::Result
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok
t/Coordinate/CoordinateGraph.t ......... 
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
t/Coordinate/CoordinateMapper.t ........ 
1..175
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::Result::Match;
ok 4 - use Bio::Coordinate::Result::Gap;
ok 5 - use Bio::Coordinate::Chain;
ok 6 - use Bio::Coordinate::Collection;
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Coordinate::Result
ok 15 - The object isa Bio::Location::SplitLocationI
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::LocationI
ok 20 - The object isa Bio::Coordinate::Result::Match
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Coordinate::Result::Gap
ok 38 - The object isa Bio::LocationI
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106 - The object isa Bio::Coordinate::Result::Match
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138 - Match: |314696| Test: 314696|
ok 139
ok 140
ok 141
ok 142 - Match: |341| Test: 341|
ok 143
ok 144
ok 145
ok 146 - Match: |315843| Test: 315843|
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - Match: |627011| Test: 627011|
ok 153
ok 154
ok 155
ok 156 - Match: |chr1| Test: chr1|
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok
t/Coordinate/GeneCoordinateMapper.t .... 
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Location::Simple
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Location::Simple
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/Draw/Pictogram.t ..................... 
1..6
ok 1 - use Bio::Draw::Pictogram;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Matrix::PSM::IO;
ok 4 - The object isa Bio::Draw::Pictogram
ok 5
ok 6
ok
t/LiveSeq/Chain.t ...................... 
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
t/LiveSeq/LiveSeq.t .................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
t/LiveSeq/Mutation.t ................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
t/LiveSeq/Mutator.t .................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok

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
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
ok 272
ok 273
ok 274
ok 275
ok
Subroutine new redefined at Bio/DB/IndexedBase.pm line 1075.
Subroutine next_seq redefined at Bio/DB/IndexedBase.pm line 1084.
Subroutine TIEHANDLE redefined at Bio/DB/IndexedBase.pm line 1093.
Subroutine READLINE redefined at Bio/DB/IndexedBase.pm line 1098.
Subroutine new redefined at Bio/DB/Fasta.pm line 359.
Subroutine fetch_sequence redefined at Bio/DB/Fasta.pm line 372.
Subroutine seq redefined at Bio/DB/Fasta.pm line 376.
Subroutine subseq redefined at Bio/DB/Fasta.pm line 381.
Subroutine trunc redefined at Bio/DB/Fasta.pm line 386.
Subroutine is_circular redefined at Bio/DB/Fasta.pm line 401.
Subroutine display_id redefined at Bio/DB/Fasta.pm line 406.
Subroutine accession_number redefined at Bio/DB/Fasta.pm line 411.
Subroutine primary_id redefined at Bio/DB/Fasta.pm line 416.
Subroutine can_call_new redefined at Bio/DB/Fasta.pm line 423.
Subroutine alphabet redefined at Bio/DB/Fasta.pm line 427.
Subroutine revcom redefined at Bio/DB/Fasta.pm line 432.
Subroutine length redefined at Bio/DB/Fasta.pm line 438.
Subroutine description redefined at Bio/DB/Fasta.pm line 446.
Subroutine Bio::PrimarySeq::Fasta::desc redefined at Bio/DB/Fasta.pm line 452.
t/LocalDB/Fasta.t ...................... 
1..107
ok 1 - Index a directory
ok 2
ok 3 - The object 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 - The object isa Bio::PrimarySeq::Fasta
ok 29 - The object 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 - The object isa Bio::PrimarySeq::Fasta
ok 41 - The object isa Bio::PrimarySeqI
ok 42
ok 43
ok 44
ok 45 - The object isa Bio::PrimarySeq::Fasta
ok 46 - The object 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 - The object isa Bio::DB::Indexed::Stream
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88 - Make single ID
ok 89
ok 90
ok 91 - The object isa Bio::PrimarySeqI
ok 92 - Make multiple IDs, bug \#3389
ok 93
ok 94
ok 95 - The object isa Bio::PrimarySeqI
ok 96 - Index a set of files
ok 97
ok 98
ok 99
ok 100
ok 101 - threw Regexp ((?^:FASTA header doesn't match))
ok 102 - threw Regexp ((?^:Blank lines can only precede header lines))
ok 103
ok 104 - length is correct in sequences past spaces
ok 105
ok 106 - subseq is correct
ok 107 - subseq is correct
ok
t/LocalDB/Flat.t ....................... 
1..25
ok 1 - use Bio::DB::Flat;
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
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 ................ 
1..69
ok 1 - use Bio::Index::Fasta;
ok 2 - use Bio::Index::Qual;
ok 3 - use Bio::Index::SwissPfam;
ok 4 - use Bio::Index::EMBL;
ok 5 - use Bio::Index::GenBank;
ok 6 - use Bio::Index::Stockholm;
ok 7 - use Bio::Index::Swissprot;
ok 8 - use Bio::DB::InMemoryCache;
ok 9 - use Bio::DB::InMemoryCache;
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::PrimarySeqI
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::SeqI
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 - The object isa Bio::Index::Stockholm
ok 68
ok 69 - The object isa Bio::SimpleAlign
ok
t/LocalDB/Qual.t ....................... 
1..56
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5 - The object 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 - The object isa Bio::Seq::PrimaryQual::Qual
ok 23 - The object 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 - The object isa Bio::Seq::PrimaryQual::Qual
ok 38 - The object isa Bio::Seq::QualI
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Seq::PrimaryQual::Qual
ok 43 - The object isa Bio::Seq::PrimaryQual
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::DB::Indexed::Stream
ok 49
ok 50 - The object isa Bio::Seq::PrimaryQual
ok 51
ok 52 - The object 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
ok 5
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 ................. 
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;
ok 5 - use Bio::DB::Fasta;
ok 6 - use File::Copy;
ok 7
ok 8
ok 9
ok 10 - adding a feature
ok 11
ok 12
ok 13
ok 14 - adding a feature with no primary_id
ok 15
ok 16 - searching for a feature that shouldnt exist
ok 17 - simple type
ok 18 - base type with colon
ok 19 - base type alone
ok 20 - queried types are not interpolated
ok 21
ok 22
ok 23 - The object isa Bio::DB::GFF::Typename
ok 24 - feature deletion
ok 25
ok 26
ok 27 - adding subfeatures
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 - feature names should be case insensitive
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 - base type
ok 65 - base:source type
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73 - The object isa Bio::Location::Split
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 - keyword search; 1 term
ok 103 - keyword search; 2 terms
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok
t/LocalDB/Taxonomy/greengenes.t ........ 
1..38
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::greengenes
ok 5 - The object isa Bio::DB::Taxonomy::list
ok 6 - The object 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 - The object isa Bio::DB::Taxonomy::silva
ok 5 - The object isa Bio::DB::Taxonomy::list
ok 6 - The object 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/transfac_pro.t ............... 
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::Annotation::Reference
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 - The object isa Bio::Seq
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 - The object isa Bio::Matrix::PSM::SiteMatrix
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69 - The object isa Bio::SimpleAlign
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 - The object isa Bio::SeqI
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107 - The object isa Bio::Map::TranscriptionFactor
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok
t/Map/Cyto.t ........................... 
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Map::CytoPosition
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Range
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
t/Map/Linkage.t ........................ 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/Map/Map.t ............................ 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
t/Map/MapIO.t .......................... 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - The object isa Bio::Map::MapI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
t/Map/MicrosatelliteMarker.t ........... 
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Map/Physical.t ....................... 
1..40
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40 # TODO Possible hash randomization-related bug, sum of contig pos values sometimes fails with off-by-one
ok
t/Matrix/IO/masta.t .................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
t/Matrix/IO/psm.t ...................... 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
t/Matrix/InstanceSite.t ................ 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
t/Matrix/Matrix.t ...................... 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - The object isa Bio::Matrix::Scoring
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Matrix::Scoring
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
t/Matrix/ProtMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Matrix/ProtPsm.t ..................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5 # skip TODO: Module incomplete
ok 6 # skip TODO: Module incomplete
ok 7 # skip TODO: Module incomplete
ok 8 # skip TODO: Module incomplete
ok 9 # skip TODO: Module incomplete
ok 10 # skip TODO: Module incomplete
ok 11 # skip TODO: Module incomplete
ok 12 # skip TODO: Module incomplete
ok 13 # skip TODO: Module incomplete
ok 14 # skip TODO: Module incomplete
ok
t/Matrix/SiteMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::SiteMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Ontology/GOterm.t .................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::GOterm
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t .............. 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ..................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok
t/Ontology/IO/interpro.t ............... 
1..69
ok 1 - use Bio::OntologyIO;
ok 2 - The object isa Bio::OntologyIO::InterProParser
ok 3
ok 4 - get_dbxrefs on leaf terms is non-empty
ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty
ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty
ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty
ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty
ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty
ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty
ok 11 - get_members on leaf terms is non-empty
ok 12 - class_list on leaf terms is non-empty
ok 13 - get_examples on leaf terms is non-empty
ok 14 - get_external_documents on leaf terms is non-empty
ok 15 - get_references on leaf terms is non-empty
ok 16 - protein_count on leaf terms is non-empty
ok 17 - to_string looks reasonable
ok 18 - There are 8 root InterPro terms
ok 19 - The object isa Bio::Ontology::Ontology
ok 20 - term Integrins alpha chain in ontology InterPro
ok 21 - The object isa Bio::Ontology::Ontology
ok 22 - term post-translational modification in ontology InterPro
ok 23 - The object isa Bio::Ontology::Ontology
ok 24 - term Repeat in ontology InterPro
ok 25 - The object isa Bio::Ontology::Ontology
ok 26 - term Binding Site in ontology InterPro
ok 27 - The object isa Bio::Ontology::Ontology
ok 28 - term Cdc20/Fizzy in ontology InterPro
ok 29 - The object isa Bio::Ontology::Ontology
ok 30 - term Conserved Site in ontology InterPro
ok 31 - The object isa Bio::Ontology::Ontology
ok 32 - term Region in ontology InterPro
ok 33 - The object isa Bio::Ontology::Ontology
ok 34 - term Kringle in ontology InterPro
ok 35 - The object isa Bio::Ontology::Ontology
ok 36 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 37 - The object isa Bio::Ontology::Ontology
ok 38 - term Active Site in ontology InterPro
ok 39 - The object isa Bio::Ontology::Ontology
ok 40 - term Active Site in ontology InterPro
ok 41 - The object isa Bio::Ontology::Ontology
ok 42 - term Binding Site in ontology InterPro
ok 43 - The object isa Bio::Ontology::Ontology
ok 44 - term Conserved Site in ontology InterPro
ok 45 - The object isa Bio::Ontology::Ontology
ok 46 - term Domain in ontology InterPro
ok 47 - The object isa Bio::Ontology::Ontology
ok 48 - term Family in ontology InterPro
ok 49 - The object isa Bio::Ontology::Ontology
ok 50 - term Region in ontology InterPro
ok 51 - The object isa Bio::Ontology::Ontology
ok 52 - term Repeat in ontology InterPro
ok 53 - The object isa Bio::Ontology::Ontology
ok 54 - term post-translational modification in ontology InterPro
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61 - Integrins alpha chain term has one parent
ok 62 - Integrins alpha chain term has one ancestor
ok 63 - Cdc20/Fizzy term has one parent
ok 64 - Cdc20/Fizzy term has one ancestor
ok 65 - Kringle term has one parent
ok 66 - Kringle term has one ancestor
ok 67 - Helix-turn-helix, AraC type  term has one parent
ok 68 - Helix-turn-helix, AraC type  term has one ancestor
ok 69 - secondary accession map has 2 keys
ok
t/Ontology/IO/obo.t .................... 
1..92
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - got a ontology IO handler isa Bio::OntologyIO
ok 47 - got ontology parser2 isa Bio::Ontology::Ontology
ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 49 - got ontology parser2 isa Bio::Ontology::Ontology
ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 51 - got ontology parser2 isa Bio::Ontology::Ontology
ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - Got term object isa Bio::Ontology::Term
ok 70 - Got term id
ok 71 - Got term name
ok 72 - Got regulated object isa Bio::Ontology::Term
ok 73 - Got regulated term1 id
ok 74 - Got term1 object isa Bio::Ontology::Term
ok 75 - Got back the child
ok 76 - Got term object isa Bio::Ontology::Term
ok 77 - Got term id
ok 78 - Got term name
ok 79 - Got regulated object isa Bio::Ontology::Term
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - Got term1 object isa Bio::Ontology::Term
ok 83 - Got back the child
ok 84 - got a ontology IO handler isa Bio::OntologyIO
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok
t/Ontology/Ontology.t .................. 
1..55
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3 - The object isa Bio::Ontology::Ontology
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - Interpro XML file interpro.xml can be parsed
ok 54 - Interpro XML file interpro_sample.xml can be parsed
ok 55 - Interpro XML file interpro_relationship.xml can be parsed
ok
t/Ontology/OntologyEngine.t ............ 
1..31
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - The object isa Bio::Ontology::OntologyEngineI
ok 7
ok 8 - adding a relationship with an undef object term fails
ok 9 - adding a relationship with an undef object term fails
ok 10 - adding a relationship with an undef subject term fails
ok 11 - adding a relationship with an undef subject term fails
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/Ontology/OntologyStore.t ............. skipped: Network tests have not been requested
t/Ontology/Relationship.t .............. 
1..12
ok 1 - use Bio::Ontology::Relationship;
ok 2 - use Bio::Ontology::GOterm;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - The object isa Bio::Ontology::RelationshipType
ok 5 - The object isa Bio::Ontology::GOterm
ok 6 - The object isa Bio::Ontology::GOterm
ok 7 - The object isa Bio::Ontology::Relationship
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/Ontology/RelationshipType.t .......... 
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - The object isa Bio::Ontology::RelationshipType
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Ontology/Term.t ...................... 
1..54
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::TermFactory;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Ontology::TermI
ok 45
ok 46 - The object isa Bio::Ontology::TermI
ok 47 - The object isa Bio::Ontology::GOterm
ok 48
ok 49
ok 50 - The object isa Bio::Ontology::TermI
ok 51 - The object isa Bio::AnnotationI
ok 52
ok 53
ok 54
ok
t/Perl.t ............................... 
1..31
ok 1 - use Bio::Perl;
ok 2
ok 3 - The object isa Bio::SeqI
ok 4
ok 5 - The object isa Bio::SeqI
ok 6
ok 7 - The object isa Bio::SeqI
ok 8 - The object isa Bio::SeqI
ok 9
ok 10
ok 11 - The object isa Bio::SeqI
ok 12
ok 13 - The object isa Bio::SeqI
ok 14
ok 15 - The object isa Bio::PrimarySeqI
ok 16
ok 17
ok 18
ok 19
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 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 - The object isa Bio::Phenotype::Correlate
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
t/Phenotype/MeSH.t ..................... 
1..24
ok 1 - use Bio::Phenotype::MeSH::Term;
ok 2 - use Bio::Phenotype::MeSH::Twig;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/Phenotype/Measure.t .................. 
1..21
ok 1 - use Bio::Phenotype::Measure;
ok 2 - The object isa Bio::Phenotype::Measure
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok
t/Phenotype/MiniMIMentry.t ............. 
1..15
ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 2 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/Phenotype/OMIMentry.t ................ 
1..153
ok 1 - use Bio::Phenotype::OMIM::OMIMentry;
ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 3 - use Bio::Species;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Map::CytoPosition;
ok 6 - use Bio::Phenotype::Correlate;
ok 7 - use Bio::Phenotype::Measure;
ok 8 - use Bio::Annotation::DBLink;
ok 9 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - operator overloading in AnnotationI is deprecated
ok 80 - operator overloading in AnnotationI is deprecated
ok 81
ok 82
ok 83 - operator overloading in AnnotationI is deprecated
ok 84 - operator overloading in AnnotationI is deprecated
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136 - operator overloading in AnnotationI is deprecated
ok 137 - operator overloading in AnnotationI is deprecated
ok 138
ok 139
ok 140 - operator overloading in AnnotationI is deprecated
ok 141 - operator overloading in AnnotationI is deprecated
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok
t/Phenotype/OMIMentryAllelicVariant.t .. 
1..27
ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMentryAllelicVariant
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/Phenotype/OMIMparser.t ............... 
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser
ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175 - missing linebreak caught
ok
t/Phenotype/Phenotype.t ................ 
1..116
ok 1 - use Bio::Phenotype::Phenotype;
ok 2 - use Bio::Species;
ok 3 - use Bio::Annotation::Reference;
ok 4 - use Bio::Map::CytoPosition;
ok 5 - use Bio::Phenotype::Correlate;
ok 6 - use Bio::Phenotype::Measure;
ok 7 - use Bio::Annotation::DBLink;
ok 8 - The object isa Bio::Phenotype::PhenotypeI
ok 9 - The object isa Bio::Phenotype::Phenotype
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
ok 101
ok 102
ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/PodSyntax.t .......................... 
1..953
ok 1 - POD test for Bio/AlignIO.pm
ok 2 - POD test for Bio/AnalysisI.pm
ok 3 - POD test for Bio/AnalysisParserI.pm
ok 4 - POD test for Bio/AnalysisResultI.pm
ok 5 - POD test for Bio/AnnotatableI.pm
ok 6 - POD test for Bio/AnnotationCollectionI.pm
ok 7 - POD test for Bio/AnnotationI.pm
ok 8 - POD test for Bio/ClusterI.pm
ok 9 - POD test for Bio/ClusterIO.pm
ok 10 - POD test for Bio/DasI.pm
ok 11 - POD test for Bio/DBLinkContainerI.pm
ok 12 - POD test for Bio/DescribableI.pm
ok 13 - POD test for Bio/FeatureHolderI.pm
ok 14 - POD test for Bio/HandlerBaseI.pm
ok 15 - POD test for Bio/IdCollectionI.pm
ok 16 - POD test for Bio/IdentifiableI.pm
ok 17 - POD test for Bio/LocatableSeq.pm
ok 18 - POD test for Bio/LocationI.pm
ok 19 - POD test for Bio/MapIO.pm
ok 20 - POD test for Bio/NexmlIO.pm
ok 21 - POD test for Bio/OntologyIO.pm
ok 22 - POD test for Bio/ParameterBaseI.pm
ok 23 - POD test for Bio/Perl.pm
ok 24 - POD test for Bio/PhyloNetwork.pm
ok 25 - POD test for Bio/PrimarySeq.pm
ok 26 - POD test for Bio/PrimarySeqI.pm
ok 27 - POD test for Bio/PullParserI.pm
ok 28 - POD test for Bio/Range.pm
ok 29 - POD test for Bio/RangeI.pm
ok 30 - POD test for Bio/SearchDist.pm
ok 31 - POD test for Bio/SearchIO.pm
ok 32 - POD test for Bio/Seq.pm
ok 33 - POD test for Bio/SeqAnalysisParserI.pm
ok 34 - POD test for Bio/SeqFeatureI.pm
ok 35 - POD test for Bio/SeqI.pm
ok 36 - POD test for Bio/SeqIO.pm
ok 37 - POD test for Bio/SeqUtils.pm
ok 38 - POD test for Bio/SimpleAlign.pm
ok 39 - POD test for Bio/SimpleAnalysisI.pm
ok 40 - POD test for Bio/Species.pm
ok 41 - POD test for Bio/Taxon.pm
ok 42 - POD test for Bio/Taxonomy.pm
ok 43 - POD test for Bio/TreeIO.pm
ok 44 - POD test for Bio/UpdateableSeqI.pm
ok 45 - POD test for Bio/WebAgent.pm
ok 46 - POD test for Bio/Align/AlignI.pm
ok 47 - POD test for Bio/Align/DNAStatistics.pm
ok 48 - POD test for Bio/Align/Graphics.pm
ok 49 - POD test for Bio/Align/PairwiseStatistics.pm
ok 50 - POD test for Bio/Align/ProteinStatistics.pm
ok 51 - POD test for Bio/Align/StatisticsI.pm
ok 52 - POD test for Bio/Align/Utilities.pm
ok 53 - POD test for Bio/AlignIO/arp.pm
ok 54 - POD test for Bio/AlignIO/bl2seq.pm
ok 55 - POD test for Bio/AlignIO/clustalw.pm
ok 56 - POD test for Bio/AlignIO/emboss.pm
ok 57 - POD test for Bio/AlignIO/fasta.pm
ok 58 - POD test for Bio/AlignIO/largemultifasta.pm
ok 59 - POD test for Bio/AlignIO/maf.pm
ok 60 - POD test for Bio/AlignIO/mase.pm
ok 61 - POD test for Bio/AlignIO/mega.pm
ok 62 - POD test for Bio/AlignIO/meme.pm
ok 63 - POD test for Bio/AlignIO/metafasta.pm
ok 64 - POD test for Bio/AlignIO/msf.pm
ok 65 - POD test for Bio/AlignIO/nexml.pm
ok 66 - POD test for Bio/AlignIO/nexus.pm
ok 67 - POD test for Bio/AlignIO/pfam.pm
ok 68 - POD test for Bio/AlignIO/phylip.pm
ok 69 - POD test for Bio/AlignIO/po.pm
ok 70 - POD test for Bio/AlignIO/proda.pm
ok 71 - POD test for Bio/AlignIO/prodom.pm
ok 72 - POD test for Bio/AlignIO/psi.pm
ok 73 - POD test for Bio/AlignIO/selex.pm
ok 74 - POD test for Bio/AlignIO/stockholm.pm
ok 75 - POD test for Bio/AlignIO/xmfa.pm
ok 76 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm
ok 77 - POD test for Bio/Annotation/AnnotationFactory.pm
ok 78 - POD test for Bio/Annotation/Collection.pm
ok 79 - POD test for Bio/Annotation/Comment.pm
ok 80 - POD test for Bio/Annotation/DBLink.pm
ok 81 - POD test for Bio/Annotation/OntologyTerm.pm
ok 82 - POD test for Bio/Annotation/Reference.pm
ok 83 - POD test for Bio/Annotation/Relation.pm
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ok 499 - POD test for Bio/Search/Result/ResultFactory.pm
ok 500 - POD test for Bio/Search/Result/ResultI.pm
ok 501 - POD test for Bio/Search/Result/WABAResult.pm
ok 502 - POD test for Bio/Search/Tiling/MapTileUtils.pm
ok 503 - POD test for Bio/Search/Tiling/MapTiling.pm
ok 504 - POD test for Bio/Search/Tiling/TilingI.pm
ok 505 - POD test for Bio/SearchIO/axt.pm
ok 506 - POD test for Bio/SearchIO/blast.pm
ok 507 - POD test for Bio/SearchIO/blast_pull.pm
ok 508 - POD test for Bio/SearchIO/blasttable.pm
ok 509 - POD test for Bio/SearchIO/blastxml.pm
ok 510 - POD test for Bio/SearchIO/cross_match.pm
ok 511 - POD test for Bio/SearchIO/erpin.pm
ok 512 - POD test for Bio/SearchIO/EventHandlerI.pm
ok 513 - POD test for Bio/SearchIO/exonerate.pm
ok 514 - POD test for Bio/SearchIO/fasta.pm
ok 515 - POD test for Bio/SearchIO/FastHitEventBuilder.pm
ok 516 - POD test for Bio/SearchIO/gmap_f9.pm
ok 517 - POD test for Bio/SearchIO/hmmer.pm
ok 518 - POD test for Bio/SearchIO/hmmer2.pm
ok 519 - POD test for Bio/SearchIO/hmmer3.pm
ok 520 - POD test for Bio/SearchIO/hmmer_pull.pm
ok 521 - POD test for Bio/SearchIO/infernal.pm
ok 522 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm
ok 523 - POD test for Bio/SearchIO/megablast.pm
ok 524 - POD test for Bio/SearchIO/psl.pm
ok 525 - POD test for Bio/SearchIO/rnamotif.pm
ok 526 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm
ok 527 - POD test for Bio/SearchIO/SearchWriterI.pm
ok 528 - POD test for Bio/SearchIO/sim4.pm
ok 529 - POD test for Bio/SearchIO/waba.pm
ok 530 - POD test for Bio/SearchIO/wise.pm
ok 531 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 532 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 533 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 534 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 535 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 536 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 537 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 538 - POD test for Bio/SearchIO/XML/BlastHandler.pm
ok 539 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm
ok 540 - POD test for Bio/Seq/BaseSeqProcessor.pm
ok 541 - POD test for Bio/Seq/EncodedSeq.pm
ok 542 - POD test for Bio/Seq/LargeLocatableSeq.pm
ok 543 - POD test for Bio/Seq/LargePrimarySeq.pm
ok 544 - POD test for Bio/Seq/LargeSeq.pm
ok 545 - POD test for Bio/Seq/LargeSeqI.pm
ok 546 - POD test for Bio/Seq/Meta.pm
ok 547 - POD test for Bio/Seq/MetaI.pm
ok 548 - POD test for Bio/Seq/PrimaryQual.pm
ok 549 - POD test for Bio/Seq/PrimedSeq.pm
ok 550 - POD test for Bio/Seq/QualI.pm
ok 551 - POD test for Bio/Seq/Quality.pm
ok 552 - POD test for Bio/Seq/RichSeq.pm
ok 553 - POD test for Bio/Seq/RichSeqI.pm
ok 554 - POD test for Bio/Seq/SeqBuilder.pm
ok 555 - POD test for Bio/Seq/SeqFactory.pm
ok 556 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm
ok 557 - POD test for Bio/Seq/SequenceTrace.pm
ok 558 - POD test for Bio/Seq/SeqWithQuality.pm
ok 559 - POD test for Bio/Seq/SimulatedRead.pm
ok 560 - POD test for Bio/Seq/TraceI.pm
ok 561 - POD test for Bio/Seq/Meta/Array.pm
ok 562 - POD test for Bio/SeqEvolution/DNAPoint.pm
ok 563 - POD test for Bio/SeqEvolution/EvolutionI.pm
ok 564 - POD test for Bio/SeqEvolution/Factory.pm
ok 565 - POD test for Bio/SeqFeature/Amplicon.pm
ok 566 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm
ok 567 - POD test for Bio/SeqFeature/Collection.pm
ok 568 - POD test for Bio/SeqFeature/CollectionI.pm
ok 569 - POD test for Bio/SeqFeature/Computation.pm
ok 570 - POD test for Bio/SeqFeature/FeaturePair.pm
ok 571 - POD test for Bio/SeqFeature/Generic.pm
ok 572 - POD test for Bio/SeqFeature/Lite.pm
ok 573 - POD test for Bio/SeqFeature/PositionProxy.pm
ok 574 - POD test for Bio/SeqFeature/Primer.pm
ok 575 - POD test for Bio/SeqFeature/Similarity.pm
ok 576 - POD test for Bio/SeqFeature/SimilarityPair.pm
ok 577 - POD test for Bio/SeqFeature/SubSeq.pm
ok 578 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm
ok 579 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 580 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 581 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 582 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 583 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 584 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 585 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 586 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 587 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 588 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 589 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 590 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 591 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 592 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 593 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 594 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 595 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 596 - POD test for Bio/SeqIO/abi.pm
ok 597 - POD test for Bio/SeqIO/ace.pm
ok 598 - POD test for Bio/SeqIO/agave.pm
ok 599 - POD test for Bio/SeqIO/alf.pm
ok 600 - POD test for Bio/SeqIO/asciitree.pm
ok 601 - POD test for Bio/SeqIO/bsml.pm
ok 602 - POD test for Bio/SeqIO/bsml_sax.pm
ok 603 - POD test for Bio/SeqIO/chadoxml.pm
ok 604 - POD test for Bio/SeqIO/chaos.pm
ok 605 - POD test for Bio/SeqIO/chaosxml.pm
ok 606 - POD test for Bio/SeqIO/ctf.pm
ok 607 - POD test for Bio/SeqIO/embl.pm
ok 608 - POD test for Bio/SeqIO/embldriver.pm
ok 609 - POD test for Bio/SeqIO/entrezgene.pm
ok 610 - POD test for Bio/SeqIO/excel.pm
ok 611 - POD test for Bio/SeqIO/exp.pm
ok 612 - POD test for Bio/SeqIO/fasta.pm
ok 613 - POD test for Bio/SeqIO/fastq.pm
ok 614 - POD test for Bio/SeqIO/flybase_chadoxml.pm
ok 615 - POD test for Bio/SeqIO/FTHelper.pm
ok 616 - POD test for Bio/SeqIO/game.pm
ok 617 - POD test for Bio/SeqIO/gbdriver.pm
ok 618 - POD test for Bio/SeqIO/gbxml.pm
ok 619 - POD test for Bio/SeqIO/gcg.pm
ok 620 - POD test for Bio/SeqIO/genbank.pm
ok 621 - POD test for Bio/SeqIO/interpro.pm
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ok 623 - POD test for Bio/SeqIO/largefasta.pm
ok 624 - POD test for Bio/SeqIO/lasergene.pm
ok 625 - POD test for Bio/SeqIO/locuslink.pm
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ok 627 - POD test for Bio/SeqIO/metafasta.pm
ok 628 - POD test for Bio/SeqIO/msout.pm
ok 629 - POD test for Bio/SeqIO/MultiFile.pm
ok 630 - POD test for Bio/SeqIO/nexml.pm
ok 631 - POD test for Bio/SeqIO/phd.pm
ok 632 - POD test for Bio/SeqIO/pir.pm
ok 633 - POD test for Bio/SeqIO/pln.pm
ok 634 - POD test for Bio/SeqIO/qual.pm
ok 635 - POD test for Bio/SeqIO/raw.pm
ok 636 - POD test for Bio/SeqIO/scf.pm
ok 637 - POD test for Bio/SeqIO/seqxml.pm
ok 638 - POD test for Bio/SeqIO/strider.pm
ok 639 - POD test for Bio/SeqIO/swiss.pm
ok 640 - POD test for Bio/SeqIO/swissdriver.pm
ok 641 - POD test for Bio/SeqIO/tab.pm
ok 642 - POD test for Bio/SeqIO/table.pm
ok 643 - POD test for Bio/SeqIO/tigr.pm
ok 644 - POD test for Bio/SeqIO/tigrxml.pm
ok 645 - POD test for Bio/SeqIO/tinyseq.pm
ok 646 - POD test for Bio/SeqIO/ztr.pm
ok 647 - POD test for Bio/SeqIO/game/featHandler.pm
ok 648 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 649 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 650 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 651 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 652 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 653 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 654 - POD test for Bio/Structure/Atom.pm
ok 655 - POD test for Bio/Structure/Chain.pm
ok 656 - POD test for Bio/Structure/Entry.pm
ok 657 - POD test for Bio/Structure/IO.pm
ok 658 - POD test for Bio/Structure/Model.pm
ok 659 - POD test for Bio/Structure/Residue.pm
ok 660 - POD test for Bio/Structure/StructureI.pm
ok 661 - POD test for Bio/Structure/IO/pdb.pm
ok 662 - POD test for Bio/Structure/SecStr/DSSP/Res.pm
ok 663 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
ok 664 - POD test for Bio/Symbol/Alphabet.pm
ok 665 - POD test for Bio/Symbol/AlphabetI.pm
ok 666 - POD test for Bio/Symbol/DNAAlphabet.pm
ok 667 - POD test for Bio/Symbol/ProteinAlphabet.pm
ok 668 - POD test for Bio/Symbol/Symbol.pm
ok 669 - POD test for Bio/Symbol/SymbolI.pm
ok 670 - POD test for Bio/Taxonomy/FactoryI.pm
ok 671 - POD test for Bio/Taxonomy/Node.pm
ok 672 - POD test for Bio/Taxonomy/Taxon.pm
ok 673 - POD test for Bio/Taxonomy/Tree.pm
ok 674 - POD test for Bio/Tools/AlignFactory.pm
ok 675 - POD test for Bio/Tools/AmpliconSearch.pm
ok 676 - POD test for Bio/Tools/AnalysisResult.pm
ok 677 - POD test for Bio/Tools/Blat.pm
ok 678 - POD test for Bio/Tools/CodonTable.pm
ok 679 - POD test for Bio/Tools/Coil.pm
ok 680 - POD test for Bio/Tools/dpAlign.pm
ok 681 - POD test for Bio/Tools/ECnumber.pm
ok 682 - POD test for Bio/Tools/EPCR.pm
ok 683 - POD test for Bio/Tools/Eponine.pm
ok 684 - POD test for Bio/Tools/ERPIN.pm
ok 685 - POD test for Bio/Tools/Est2Genome.pm
ok 686 - POD test for Bio/Tools/ESTScan.pm
ok 687 - POD test for Bio/Tools/Fgenesh.pm
ok 688 - POD test for Bio/Tools/FootPrinter.pm
ok 689 - POD test for Bio/Tools/Gel.pm
ok 690 - POD test for Bio/Tools/Geneid.pm
ok 691 - POD test for Bio/Tools/Genemark.pm
ok 692 - POD test for Bio/Tools/Genewise.pm
ok 693 - POD test for Bio/Tools/Genomewise.pm
ok 694 - POD test for Bio/Tools/Genscan.pm
ok 695 - POD test for Bio/Tools/GFF.pm
ok 696 - POD test for Bio/Tools/Glimmer.pm
ok 697 - POD test for Bio/Tools/Grail.pm
ok 698 - POD test for Bio/Tools/GuessSeqFormat.pm
ok 699 - POD test for Bio/Tools/Hmmpfam.pm
ok 700 - POD test for Bio/Tools/Infernal.pm
ok 701 - POD test for Bio/Tools/ipcress.pm
ok 702 - POD test for Bio/Tools/isPcr.pm
ok 703 - POD test for Bio/Tools/IUPAC.pm
ok 704 - POD test for Bio/Tools/Lucy.pm
ok 705 - POD test for Bio/Tools/Match.pm
ok 706 - POD test for Bio/Tools/MZEF.pm
ok 707 - POD test for Bio/Tools/OddCodes.pm
ok 708 - POD test for Bio/Tools/pICalculator.pm
ok 709 - POD test for Bio/Tools/Primer3.pm
ok 710 - POD test for Bio/Tools/Prints.pm
ok 711 - POD test for Bio/Tools/Profile.pm
ok 712 - POD test for Bio/Tools/Promoterwise.pm
ok 713 - POD test for Bio/Tools/PrositeScan.pm
ok 714 - POD test for Bio/Tools/Protparam.pm
ok 715 - POD test for Bio/Tools/Pseudowise.pm
ok 716 - POD test for Bio/Tools/pSW.pm
ok 717 - POD test for Bio/Tools/QRNA.pm
ok 718 - POD test for Bio/Tools/RandomDistFunctions.pm
ok 719 - POD test for Bio/Tools/RepeatMasker.pm
ok 720 - POD test for Bio/Tools/RNAMotif.pm
ok 721 - POD test for Bio/Tools/Seg.pm
ok 722 - POD test for Bio/Tools/SeqPattern.pm
ok 723 - POD test for Bio/Tools/SeqStats.pm
ok 724 - POD test for Bio/Tools/SeqWords.pm
ok 725 - POD test for Bio/Tools/Sigcleave.pm
ok 726 - POD test for Bio/Tools/Signalp.pm
ok 727 - POD test for Bio/Tools/SiRNA.pm
ok 728 - POD test for Bio/Tools/TandemRepeatsFinder.pm
ok 729 - POD test for Bio/Tools/TargetP.pm
ok 730 - POD test for Bio/Tools/Tmhmm.pm
ok 731 - POD test for Bio/Tools/tRNAscanSE.pm
ok 732 - POD test for Bio/Tools/Alignment/Consed.pm
ok 733 - POD test for Bio/Tools/Alignment/Trim.pm
ok 734 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 735 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 736 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm
ok 737 - POD test for Bio/Tools/Analysis/Protein/ELM.pm
ok 738 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm
ok 739 - POD test for Bio/Tools/Analysis/Protein/HNN.pm
ok 740 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 741 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm
ok 742 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm
ok 743 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm
ok 744 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 745 - POD test for Bio/Tools/HMMER/Domain.pm
ok 746 - POD test for Bio/Tools/HMMER/Results.pm
ok 747 - POD test for Bio/Tools/HMMER/Set.pm
ok 748 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 749 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 750 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 751 - POD test for Bio/Tools/Phylo/PAML.pm
ok 752 - POD test for Bio/Tools/Phylo/Molphy/Result.pm
ok 753 - POD test for Bio/Tools/Phylo/PAML/Codeml.pm
ok 754 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm
ok 755 - POD test for Bio/Tools/Phylo/PAML/Result.pm
ok 756 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 757 - POD test for Bio/Tools/Prediction/Exon.pm
ok 758 - POD test for Bio/Tools/Prediction/Gene.pm
ok 759 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 760 - POD test for Bio/Tools/Primer/Feature.pm
ok 761 - POD test for Bio/Tools/Primer/Pair.pm
ok 762 - POD test for Bio/Tools/Primer/Assessor/Base.pm
ok 763 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 764 - POD test for Bio/Tools/Run/hmmer3.pm (no pod)
ok 765 - POD test for Bio/Tools/Run/ParametersI.pm
ok 766 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 767 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 768 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 769 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
ok 770 - POD test for Bio/Tools/Run/WrapperBase.pm
ok 771 - POD test for Bio/Tools/Run/WrapperBase/CommandExts.pm
ok 772 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm
ok 773 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 774 - POD test for Bio/Tools/Sim4/Exon.pm
ok 775 - POD test for Bio/Tools/Sim4/Results.pm
ok 776 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 777 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 778 - POD test for Bio/Tools/Spidey/Exon.pm
ok 779 - POD test for Bio/Tools/Spidey/Results.pm
ok 780 - POD test for Bio/Tree/AlleleNode.pm
ok 781 - POD test for Bio/Tree/AnnotatableNode.pm
ok 782 - POD test for Bio/Tree/Compatible.pm
ok 783 - POD test for Bio/Tree/DistanceFactory.pm
ok 784 - POD test for Bio/Tree/Node.pm
ok 785 - POD test for Bio/Tree/NodeI.pm
ok 786 - POD test for Bio/Tree/NodeNHX.pm
ok 787 - POD test for Bio/Tree/RandomFactory.pm
ok 788 - POD test for Bio/Tree/Statistics.pm
ok 789 - POD test for Bio/Tree/Tree.pm
ok 790 - POD test for Bio/Tree/TreeFunctionsI.pm
ok 791 - POD test for Bio/Tree/TreeI.pm
ok 792 - POD test for Bio/Tree/Draw/Cladogram.pm
ok 793 - POD test for Bio/TreeIO/cluster.pm
ok 794 - POD test for Bio/TreeIO/lintree.pm
ok 795 - POD test for Bio/TreeIO/newick.pm
ok 796 - POD test for Bio/TreeIO/NewickParser.pm
ok 797 - POD test for Bio/TreeIO/nexml.pm
ok 798 - POD test for Bio/TreeIO/nexus.pm
ok 799 - POD test for Bio/TreeIO/nhx.pm
ok 800 - POD test for Bio/TreeIO/pag.pm
ok 801 - POD test for Bio/TreeIO/phyloxml.pm
ok 802 - POD test for Bio/TreeIO/svggraph.pm
ok 803 - POD test for Bio/TreeIO/tabtree.pm
ok 804 - POD test for Bio/TreeIO/TreeEventBuilder.pm
ok 805 - POD test for Bio/Variation/AAChange.pm
ok 806 - POD test for Bio/Variation/AAReverseMutate.pm
ok 807 - POD test for Bio/Variation/Allele.pm
ok 808 - POD test for Bio/Variation/DNAMutation.pm
ok 809 - POD test for Bio/Variation/IO.pm
ok 810 - POD test for Bio/Variation/RNAChange.pm
ok 811 - POD test for Bio/Variation/SeqDiff.pm
ok 812 - POD test for Bio/Variation/SNP.pm
ok 813 - POD test for Bio/Variation/VariantI.pm
ok 814 - POD test for Bio/Variation/IO/flat.pm
ok 815 - POD test for Bio/Variation/IO/xml.pm
ok 816 - POD test for scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
ok 817 - POD test for scripts/Bio-DB-GFF/bp_fast_load_gff.pl
ok 818 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff.pl
ok 819 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff3.pl
ok 820 - POD test for scripts/Bio-DB-GFF/bp_generate_histogram.pl
ok 821 - POD test for scripts/Bio-DB-GFF/bp_load_gff.pl
ok 822 - POD test for scripts/Bio-DB-GFF/bp_meta_gff.pl
ok 823 - POD test for scripts/Bio-DB-GFF/bp_process_gadfly.pl
ok 824 - POD test for scripts/Bio-DB-GFF/bp_process_sgd.pl
ok 825 - POD test for scripts/Bio-DB-GFF/bp_process_wormbase.pl
ok 826 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl (no pod)
ok 827 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl (no pod)
ok 828 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
ok 829 - POD test for scripts/das/bp_das_server.pl (no pod)
ok 830 - POD test for scripts/DB/bp_biofetch_genbank_proxy.pl
ok 831 - POD test for scripts/DB/bp_bioflat_index.pl
ok 832 - POD test for scripts/DB/bp_biogetseq.pl
ok 833 - POD test for scripts/DB/bp_flanks.pl
ok 834 - POD test for scripts/DB-HIV/bp_hivq.pl
ok 835 - POD test for scripts/index/bp_fetch.pl
ok 836 - POD test for scripts/index/bp_index.pl
ok 837 - POD test for scripts/index/bp_seqret.pl
ok 838 - POD test for scripts/popgen/bp_composite_LD.pl
ok 839 - POD test for scripts/popgen/bp_heterogeneity_test.pl
ok 840 - POD test for scripts/searchio/bp_fastam9_to_table.pl
ok 841 - POD test for scripts/searchio/bp_filter_search.pl
ok 842 - POD test for scripts/searchio/bp_hmmer_to_table.pl
ok 843 - POD test for scripts/searchio/bp_parse_hmmsearch.pl
ok 844 - POD test for scripts/searchio/bp_search2table.pl
ok 845 - POD test for scripts/seq/bp_extract_feature_seq.pl
ok 846 - POD test for scripts/seq/bp_make_mrna_protein.pl
ok 847 - POD test for scripts/seq/bp_seqconvert.pl
ok 848 - POD test for scripts/seq/bp_seqcut.pl
ok 849 - POD test for scripts/seq/bp_seqpart.pl
ok 850 - POD test for scripts/seq/bp_seqretsplit.pl
ok 851 - POD test for scripts/seq/bp_split_seq.pl
ok 852 - POD test for scripts/seq/bp_translate_seq.pl
ok 853 - POD test for scripts/seq/bp_unflatten_seq.pl
ok 854 - POD test for scripts/seqstats/bp_aacomp.pl
ok 855 - POD test for scripts/seqstats/bp_chaos_plot.pl
ok 856 - POD test for scripts/seqstats/bp_gccalc.pl
ok 857 - POD test for scripts/seqstats/bp_oligo_count.pl
ok 858 - POD test for scripts/taxa/bp_classify_hits_kingdom.pl
ok 859 - POD test for scripts/taxa/bp_local_taxonomydb_query.pl
ok 860 - POD test for scripts/taxa/bp_query_entrez_taxa.pl
ok 861 - POD test for scripts/taxa/bp_taxid4species.pl
ok 862 - POD test for scripts/taxa/bp_taxonomy2tree.pl
ok 863 - POD test for scripts/tree/bp_blast2tree.pl
ok 864 - POD test for scripts/tree/bp_nexus2nh.pl
ok 865 - POD test for scripts/tree/bp_tree2pag.pl
ok 866 - POD test for scripts/utilities/bp_dbsplit.pl
ok 867 - POD test for scripts/utilities/bp_download_query_genbank.pl
ok 868 - POD test for scripts/utilities/bp_mask_by_search.pl
ok 869 - POD test for scripts/utilities/bp_mrtrans.pl
ok 870 - POD test for scripts/utilities/bp_mutate.pl
ok 871 - POD test for scripts/utilities/bp_netinstall.pl
ok 872 - POD test for scripts/utilities/bp_nrdb.pl
ok 873 - POD test for scripts/utilities/bp_pairwise_kaks.pl
ok 874 - POD test for scripts/utilities/bp_remote_blast.pl
ok 875 - POD test for scripts/utilities/bp_revtrans-motif.pl
ok 876 - POD test for scripts/utilities/bp_search2alnblocks.pl
ok 877 - POD test for scripts/utilities/bp_search2BSML.pl
ok 878 - POD test for scripts/utilities/bp_search2gff.pl
ok 879 - POD test for scripts/utilities/bp_search2tribe.pl
ok 880 - POD test for scripts/utilities/bp_seq_length.pl
ok 881 - POD test for scripts/utilities/bp_sreformat.pl
ok 882 - POD test for examples/bioperl.pl (no pod)
ok 883 - POD test for examples/generate_random_seq.pl (no pod)
ok 884 - POD test for examples/longorf.pl
ok 885 - POD test for examples/make_primers.pl (no pod)
ok 886 - POD test for examples/rev_and_trans.pl (no pod)
ok 887 - POD test for examples/revcom_dir.pl (no pod)
ok 888 - POD test for examples/subsequence.cgi (no pod)
ok 889 - POD test for examples/align/align_on_codons.pl (no pod)
ok 890 - POD test for examples/align/aligntutorial.pl (no pod)
ok 891 - POD test for examples/align/clustalw.pl (no pod)
ok 892 - POD test for examples/align/FastAlign.pl
ok 893 - POD test for examples/align/simplealign.pl (no pod)
ok 894 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 895 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 896 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 897 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 898 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 899 - POD test for examples/db/dbfetch
ok 900 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 901 - POD test for examples/db/gb2features.pl (no pod)
ok 902 - POD test for examples/db/get_seqs.pl (no pod)
ok 903 - POD test for examples/db/getGenBank.pl (no pod)
ok 904 - POD test for examples/db/rfetch.pl (no pod)
ok 905 - POD test for examples/db/use_registry.pl (no pod)
ok 906 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 907 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 908 - POD test for examples/quality/svgtrace.pl (no pod)
ok 909 - POD test for examples/root/exceptions1.pl (no pod)
ok 910 - POD test for examples/root/exceptions2.pl (no pod)
ok 911 - POD test for examples/root/exceptions3.pl (no pod)
ok 912 - POD test for examples/root/exceptions4.pl (no pod)
ok 913 - POD test for examples/root/lib/TestInterface.pm
ok 914 - POD test for examples/root/lib/TestObject.pm
ok 915 - POD test for examples/searchio/blast_example.pl (no pod)
ok 916 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 917 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 918 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 919 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 920 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 921 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 922 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 923 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 924 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 925 - POD test for examples/searchio/waba2gff3.pl
ok 926 - POD test for examples/sirna/rnai_finder.cgi
ok 927 - POD test for examples/structure/structure-io.pl (no pod)
ok 928 - POD test for examples/tk/gsequence.pl (no pod)
ok 929 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 930 - POD test for examples/tools/extract_genes.pl
ok 931 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 932 - POD test for examples/tools/gff2ps.pl
ok 933 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 934 - POD test for examples/tools/psw.pl (no pod)
ok 935 - POD test for examples/tools/reverse-translate.pl
ok 936 - POD test for examples/tools/run_genscan.pl (no pod)
ok 937 - POD test for examples/tools/run_primer3.pl
ok 938 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 939 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 940 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 941 - POD test for maintenance/authors.pl
ok 942 - POD test for maintenance/check_NAME.pl
ok 943 - POD test for maintenance/check_URLs.pl
ok 944 - POD test for maintenance/cvs2cl_by_file.pl
ok 945 - POD test for maintenance/dependencies.pl
ok 946 - POD test for maintenance/deprecated.pl
ok 947 - POD test for maintenance/find_mod_deps.pl
ok 948 - POD test for maintenance/module_usage.pl (no pod)
ok 949 - POD test for maintenance/modules.pl
ok 950 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 951 - POD test for maintenance/pod.pl
ok 952 - POD test for maintenance/symlink_script.pl
ok 953 - POD test for maintenance/version.pl
ok
t/PopGen/Coalescent.t .................. 
1..13
ok 1 - use Bio::PopGen::Simulation::Coalescent;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6 - pi
ok 7 - theta
ok 8 - tajimaD
ok 9 - all the mutations should be polymorphic (by definition)
ok 10 - fu and li D
ok 11 - fu and li D*
ok 12 - fu and li F
ok 13 - fu and li F
ok
t/PopGen/HtSNP.t ....................... 
1..8
ok 1 - use Bio::PopGen::HtSNP;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/PopGen/MK.t .......................... 
1..46
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::PopGen::Utilities;
ok 4 - The object isa Bio::PopGen::Statistics
ok 5 - The object isa Bio::SimpleAlign
ok 6 - The object isa Bio::PopGen::Population
ok 7 - Marker Names
ok 8 - Number of Inds
ok 9 - number of ingroup sequences
ok 10 - number of outgroup1 sequences
ok 11 - number of outgroup2 sequences
ok 12 - NSpoly
ok 13 - NSfixed
ok 14 - Spoly
ok 15 - Sfixed
ok 16 - McDonald Kreitman
ok 17 - NSpoly
ok 18 - NSfixed
ok 19 - Spoly
ok 20 - Sfixed
ok 21 - McDonald Kreitman
ok 22 - NSpoly
ok 23 - NSfixed
ok 24 - Spoly
ok 25 - Sfixed
ok 26 - The object isa Bio::SimpleAlign
ok 27 - The object isa Bio::PopGen::Population
ok 28 - Marker Names
ok 29 - Number of Inds
ok 30 - number of ingroup sequences
ok 31 - number of outgroup1 sequences
ok 32 - number of outgroup2 sequences
ok 33 - NSpoly
ok 34 - NSfixed
ok 35 - Spoly
ok 36 - Sfixed
ok 37 - McDonald Kreitman
ok 38 - NSpoly
ok 39 - NSfixed
ok 40 - Spoly
ok 41 - Sfixed
ok 42 - McDonald Kreitman
ok 43 - NSpoly
ok 44 - NSfixed
ok 45 - Spoly
ok 46 - Sfixed
ok
t/PopGen/PopGen.t ...................... 
1..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: Network tests have not been requested
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... 
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV->can(...)
ok 7 - Bio::DB::HIV->can(...)
ok 8 - Bio::DB::HIV->can(...)
ok 9 - lanl_base set in default object
ok 10 - map_db set in default object
ok 11 - make_search_if set in default object
ok 12 - search_ set in default object
ok 13 - url_base_address set in default object
ok 14 - default sequence request format (fasta)
ok 15 - sorry till implemented
ok 16 - sorry till implemented
ok 17 - HIVQuery type exception check
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... 
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
t/RemoteDB/HIV/HIVQuery.t .............. 
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - The object isa Bio::DB::Query::HIVQuery
ok 8 - The object isa Bio::Root::Root
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 - use HTML::Parser;
ok 24 - help html to file
ok 25 - help html parsed
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - The object isa HIVSchema
ok 3 - The object isa QRY
ok 4 - The object isa R
ok 5 - The object isa Q
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} 
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} 
ok 40 - above query is null
ok
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... 
1..16
ok 1 - use Bio::DB::RefSeq;
ok 2 - use Bio::DB::GenBank;
ok 3 - use Bio::DB::EMBL;
ok 4
ok 5
ok 6
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/RemoteDB/SeqHound.t .................. skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ 
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

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Cannot tie to file '/tmp/names2id': Permission denied
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::DB::Taxonomy::flatfile::_build_index Bio/DB/Taxonomy/flatfile.pm:405
STACK: Bio::DB::Taxonomy::flatfile::new Bio/DB/Taxonomy/flatfile.pm:138
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:119
STACK: t/RemoteDB/Taxonomy.t:28
-----------------------------------------------------------
# Looks like you planned 191 tests but ran 5.
# Looks like your test exited with 13 just after 5.
t/RemoteDB/Taxonomy.t .................. 
1..191
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::entrez
ok 5 - The object isa Bio::DB::Taxonomy
Dubious, test returned 13 (wstat 3328, 0xd00)
Failed 186/191 subtests 
t/Restriction/Analysis-refac.t ......... 
1..91
ok 1 - use Bio::Restriction::IO;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Restriction::EnzymeCollection;
ok 4 - use Bio::Restriction::Enzyme;
ok 5 - read withrefm file
ok 6 - parse withrefm file
ok 7 - HindIII: nonambiguous intrasite cutter
ok 8 - AarI: nonambiguous extrasite cutter
ok 9 - AasI: ambiguous intrasite cutter
ok 10 - BceSI: ambiguous extrasite cutter
ok 11 - AjuI: cutter with central recog site
ok 12 - TaqII: multi-extrasite cutter
ok 13
ok 14 - HindIII plus
ok 15 - HindIII minus
ok 16 - AasI plus
ok 17 - AasI  minus
ok 18 - AarI plus
ok 19 - AarI  minus
ok 20 - BceSI plus
ok 21 - BceSI  minus
ok 22 - AjuI plus
ok 23 - AjuI minus
ok 24 - TaqII plus
ok 25 - TaqII minus
ok 26 - build real B:R::Analysis object
ok 27 - 13 fragments
ok 28 - circularize
ok 29 - recut
ok 30 - circ: AasI
# site at origin
ok 31 - circ: still 13 fragments (cut site at origin)
ok 32 - use Bio::Restriction::IO;
ok 33 - use Bio::Restriction::Analysis;
ok 34 - read withrefm file
ok 35 - parse withrefm file
ok 36 - Collection initiated
ok 37 - AbeI: found ok into collection
ok 38 - AccBSI: found ok into collection
ok 39 - AciI: found ok into collection
ok 40 - Asp26HI: found ok into collection
ok 41 - BmgBI: found ok into collection
ok 42 - AbeI plus
ok 43 - AbeI minus
ok 44 - AbeI fragment
ok 45 - AbeI positions
ok 46 - AbeI Overhang
ok 47 - AbeI name
ok 48 - AbeI site
ok 49 - AbeI revcom_site
ok 50 - AbeI cut
ok 51 - AbeI complementary_cut
ok 52 - AccBSI plus
ok 53 - AccBSI minus
ok 54 - AccBSI fragment
ok 55 - AccBSI positions
ok 56 - AccBSI Overhang
ok 57 - AccBSI name
ok 58 - AccBSI site
ok 59 - AccBSI revcom_site
ok 60 - AccBSI cut
ok 61 - AccBSI complementary_cut
ok 62 - AciI plus
ok 63 - AciI minus
ok 64 - AciI fragment
ok 65 - AciI positions
ok 66 - AciI Overhang
ok 67 - AciI name
ok 68 - AciI site
ok 69 - AciI revcom_site
ok 70 - AciI cut
ok 71 - AciI complementary_cut
ok 72 - Asp26HI plus
ok 73 - Asp26HI minus
ok 74 - Asp26HI fragment
ok 75 - Asp26HI positions
ok 76 - Asp26HI Overhang
ok 77 - Asp26HI name
ok 78 - Asp26HI site
ok 79 - Asp26HI revcom_site
ok 80 - Asp26HI cut
ok 81 - Asp26HI complementary_cut
ok 82 - BmgBI plus
ok 83 - BmgBI minus
ok 84 - BmgBI fragment
ok 85 - BmgBI positions
ok 86 - BmgBI Overhang
ok 87 - BmgBI name
ok 88 - BmgBI site
ok 89 - BmgBI revcom_site
ok 90 - BmgBI cut
ok 91 - BmgBI complementary_cut
ok
t/Restriction/Analysis.t ............... 
1..182
ok 1 - use Bio::Restriction::Enzyme;
ok 2 - use Bio::Restriction::Enzyme::MultiCut;
ok 3 - use Bio::Restriction::Enzyme::MultiSite;
ok 4 - use Bio::Restriction::EnzymeCollection;
ok 5 - use Bio::Restriction::Analysis;
ok 6 - use Bio::SeqIO;
ok 7
ok 8 - The object isa Bio::Restriction::EnzymeI
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::PrimarySeqI
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - bug 2179
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76 - The object isa Bio::Restriction::EnzymeI
ok 77 - The object isa Bio::Restriction::EnzymeI
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87 - The object isa Bio::Restriction::EnzymeI
ok 88 - The object isa Bio::Restriction::EnzymeI
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - The object isa Bio::Restriction::Enzyme
ok 100
ok 101
ok 102 - The object isa Bio::Restriction::Enzyme
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118 - number of unique cutters
ok 119 - number of RsaI fragments
ok 120 - number of maximum cutters
ok 121 - number of zero cutters
ok 122 - number of cutters
ok 123 - number of 3x cutters
ok 124 - 4 MseI fragments
ok 125 - 3 MseI cut sites
ok 126 - expected 2 PspEI fragments
ok 127
ok 128
ok 129 - expected 2 sizes for PspEI
ok 130
ok 131 - expected 2 sizes for PspEI
ok 132
ok 133 - not circular expected 1 fragments for MwoI as it doesnt cut
ok 134
ok 135
ok 136 - number of RsaI fragments
ok 137 - 3 circular MseI fragments
ok 138 - 3 circular MseI cut sites
ok 139 - number for AciI a non-palindromic enzyme
ok 140 - 1 fragment for MwoI as it cuts across the circ point
ok 141
ok 142
ok 143
ok 144
ok 145 - 7 fragments in the multiple digest
ok 146 - 7 positions in the multiple digest
ok 147 - 7 sizes in the multiple digest
ok 148
ok 149 -  expected 9 cuts for HindI
ok 150 - expect 9 fragment maps for HindI
ok 151 - sequence for GT
ok 152 - start at 40
ok 153 - end at 41
ok 154 - sequence for GGATTAAAAAAAGAGT
ok 155 - start at 42
ok 156 - end at 57
ok 157 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT
ok 158 - start at 58
ok 159 - end at 92
ok 160 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA
ok 161 - start at 93
ok 162 - end at 123
ok 163 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA
ok 164 - start at 124
ok 165 - end at 155
ok 166 - sequence for CAGACAGATAAAAATTACAGAGTACA
ok 167 - start at 156
ok 168 - end at 181
ok 169 - sequence for CAACATCCATGAAACGCATTAGCA
ok 170 - start at 182
ok 171 - end at 205
ok 172 - sequence for CCA
ok 173 - start at 206
ok 174 - end at 208
ok 175 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT
ok 176 - start at 209
ok 177 - end at 39
ok 178
ok 179 - bug 2139
ok 180 - number of HindIII fragments
ok 181 - number of EcoRI fragments
ok 182 - number of RsaI fragments
ok
t/Restriction/Gel.t .................... 
1..9
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Tools::Gel;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
t/Restriction/IO.t ..................... 
1..18
ok 1 - use Bio::Restriction::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT!
#   Failed (TODO) test at t/Restriction/IO.t line 31.
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok
t/Root/Exception.t ..................... 
1..8
ok 1 - use TestObject;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/RootI.t ......................... 
1..63
ok 1 - use Bio::Root::Root;
ok 2 - use Bio::Seq;
ok 3
ok 4 - The object isa Bio::Root::RootI
ok 5 - threw Regexp ((?^:Testing throw))
ok 6 - threw Regexp ((?^:EXCEPTION: Bio::Root::NotImplemented))
ok 7 - threw Regexp ((?^:EXCEPTION ))
ok 8 - threw Regexp ((?^:Testing throw))
ok 9
ok 10 - threw Regexp ((?^:Testing throw))
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - simple
ok 17 - simple
ok 18 - warns for versions below current version 1.006921
ok 19 - warns for versions below current version 1.006921
ok 20 - throws for versions above 1.006921
ok 21 - throws for versions above 1.006921
ok 22 - throws for versions equal to 1.006921
ok 23 - simple
ok 24 - simple
ok 25 - warns for versions below current version 1.006921
ok 26 - warns for versions below current version 1.006921
ok 27 - throws for versions above 1.006921
ok 28 - throws for versions above 1.006921
ok 29 - arg callable since method was created
ok 30 - mal-formed arg callable since method was created with good name
ok 31 - Bio::Foo2->can('t3')
ok 32 - Methods don't pollute original Bio::Root::Root namespace
ok 33 - Bio::Foo2->can('test_4')
ok 34 - Methods don't pollute original Bio::Root::Root namespace
ok 35 - Bio::Foo3->can('t5')
ok 36 - arg not in method list not created
ok 37 - Bio::Foo3->can('t5')
ok 38 - Methods don't pollute original Bio::Root::Root namespace
ok 39 - verbose was set correctly
ok 40 - synonym was set correctly
ok 41 - real method of synonym was set correctly
ok 42 - mal-formed arg correctly resolved to created method
ok 43 - synonym of set method was set correctly
ok 44 - Bio::Foo4->can('t7')
ok 45 - Methods don't pollute original Bio::Root::Root namespace
ok 46 - Bio::Foo4->can('test7')
ok 47 - Methods don't pollute original Bio::Root::Root namespace
ok 48 - Bio::Foo4->can('test_8')
ok 49 - Methods don't pollute original Bio::Root::Root namespace
ok 50 - Bio::Foo4->can('t8')
ok 51 - Methods don't pollute original Bio::Root::Root namespace
ok 52 - clone
ok 53 - clone
ok 54 - clone
ok 55 - clone changed, original didn't
ok 56 - parameters passed to clone() modify object
ok 57 - original is not modified
ok 58 - must use proper versioning scheme
ok 59 - warns for versions >= 1.006921
ok 60 - warns for versions >= 1.006921
ok 61 - throws for versions >= 1.006921
ok 62 - throws for versions >= 1.006921
ok 63 - No warnings/exceptions below 1.006921
ok
t/Root/RootIO.t ........................ 
1..77
ok 1 - use Bio::Root::IO;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Assembly::IO;
ok 4
ok 5 - throw()
ok 6 - throw() verbose(-1)
ok 7 - warn()
ok 8 - throw() verbose(1)
ok 9 - stack_trace()
ok 10 - set verbosity to 1
ok 11
ok 12
ok 13 - executable file
ok 14 - non-executable file
ok 15 - executable dir
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - filename, read
ok 22
ok 23
ok 24 - filename, write
ok 25
ok 26
ok 27
ok 28
ok 29 - handle, read
ok 30
ok 31
ok 32 - handle, write
ok 33 - The object isa Bio::Root::IO
ok 34 - is a write handle
ok 35 - no warnings in ->close call
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - _print
ok 45
ok 46 - _insert at middle of file
ok 47
ok 48
ok 49
ok 50
ok 51 - _insert in empty file
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63 - Bio::Root::IO->new can handle a Path::Class object
ok 64 - The object isa Bio::Root::IO
ok 65 # skip Network tests have not been requested
ok 66 # skip Network tests have not been requested
ok 67 - default -string method
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
t/Root/Storable.t ...................... 
1..35
ok 1 - use Bio::Root::Storable;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok
t/Root/Tempfile.t ...................... 
1..18
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - The object isa Bio::Root::IO
ok 4
ok 5
ok 6 - auto UNLINK => 1
ok 7
ok 8
ok 9 - tempfile deleted
ok 10
ok 11 - UNLINK => 0
ok 12
ok 13
ok 14
ok 15 - tempfile suffix
ok 16
ok 17 - tempfile() in scalar context
ok 18
ok
t/Root/Utilities.t ..................... 
1..56
ok 1 - use Bio::Root::Utilities;
ok 2 - The object isa Bio::Root::Utilities
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - file_date()
ok 38 - unix (\n or 012 or ^J)
ok 39 - date format
ok 40 - date format
ok 41 - date format
ok 42 - date format
ok 43 - date format
ok 44
ok 45
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.blastxml
ok 3 - fasta for f.fy
ok 4 - exonerate for f.exonerate
ok 5 - blast for f.tblx
ok 6 - fasta for f.fx
ok 7 - fasta for f.osearch
ok 8 - blast for filename.bls
ok 9 - exonerate for f.exon
ok 10 - fasta for f.SSEARCH.m9
ok 11 - blast for filename.blast
ok 12 - fasta for f.m9
ok 13 - blast for f.blx
ok 14 - blastxml for f.xml
ok 15 - fasta for f.fasta
ok 16 - fasta for f.fa
ok 17 - blast for fast.bls
ok 18 - fasta for f.ssearch
ok 19 - fasta for f.psearch
ok
t/SearchIO/SimilarityPair.t ............ 
1..12
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 - The object isa Bio::SeqI
ok 5
ok 6 - The object isa Bio::SearchIO
ok 7
ok 8 - The object isa Bio::Search::Hit::HitI
ok 9
ok 10 - The object isa Bio::SeqFeatureI
ok 11
ok 12
ok
t/SearchIO/Tiling.t .................... 
1..1141
ok 1 - use Bio::Search::Tiling::MapTiling;
ok 2 - use Bio::Search::Tiling::MapTileUtils;
ok 3 - use Bio::SearchIO;
ok 4 - use Bio::Search::Hit::BlastHit;
ok 5 - use File::Spec;
ok 6 - parse data file
ok 7 - got test hit
ok 8 - create tiling
ok 9 - The object isa Bio::Search::Tiling::TilingI
ok 10 - implements 'next_tiling'
ok 11 - implements 'rewind_tilings'
ok 12 - implements 'identities'
ok 13 - implements 'conserved'
ok 14 - implements 'length'
ok 15 - identities regression test
ok 16 - conserved regression test
ok 17 - tiling iterator regression test(1)
ok 18 - tiling iterator regression test(2)
ok 19 - tiling iterator regression test(3, rewind)
ok 20 - ecolitst.wublastp
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - dnaEbsub_ecoli.wublastx
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36 - tricky.wublast
ok 37 - tricky.wublast(1)
ok 38 - tricky.wublast(2)
ok 39 - tricky.wublast(3)
ok 40 - tricky.wublast(4)
ok 41 - ecolitst.bls
ok 42 - tile ecolitst.bls hit 1 \#hsps 1
ok 43 - q id: est (0.98293) = fast (0.98293)
ok 44 - q cn: est (0.98293) = fast (0.98293)
ok 45 - h id: est (0.98293) = fast (0.98293)
ok 46 - h cn: est (0.98293) = fast (0.98293)
ok 47 - tile ecolitst.bls hit 2 \#hsps 1
ok 48 - q id: est (0.30074) = fast (0.30074)
ok 49 - q cn: est (0.49876) = fast (0.49876)
ok 50 - h id: est (0.30759) = fast (0.30759)
ok 51 - h cn: est (0.51013) = fast (0.51013)
ok 52 - tile ecolitst.bls hit 3 \#hsps 1
ok 53 - q id: est (0.31004) = fast (0.31004)
ok 54 - q cn: est (0.49782) = fast (0.49782)
ok 55 - h id: est (0.32054) = fast (0.32054)
ok 56 - h cn: est (0.51467) = fast (0.51467)
ok 57 - tile ecolitst.bls hit 4 \#hsps 1
ok 58 - q id: est (0.30435) = fast (0.30435)
ok 59 - q cn: est (0.47826) = fast (0.47826)
ok 60 - h id: est (0.29787) = fast (0.29787)
ok 61 - h cn: est (0.46809) = fast (0.46809)
ok 62 - tricky.wublast
ok 63 - tile tricky.wublast hit 1 \#hsps 7
ok 64 - q id: exact (0.22153) ~ est (0.22153)
ok 65 - q id: exact (0.22153) <= max (0.22153)
ok 66 - q cn: exact (0.42760) ~ est (0.42760)
ok 67 - q cn: exact (0.42760) <= max (0.42760)
ok 68 - h id: exact (0.22704) ~ est (0.22704)
ok 69 - h id: exact (0.22704) <= max (0.22704)
ok 70 - h cn: exact (0.43335) ~ est (0.43335)
ok 71 - h cn: exact (0.43335) <= max (0.43335)
ok 72 - a_thaliana.blastn
ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1
ok 74 - q id: est (0.96667) = fast (0.96667)
ok 75 - q cn: est (0.96667) = fast (0.96667)
ok 76 - h id: est (0.98305) = fast (0.98305)
ok 77 - h cn: est (0.98305) = fast (0.98305)
ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1
ok 79 - q id: est (0.96667) = fast (0.96667)
ok 80 - q cn: est (0.96667) = fast (0.96667)
ok 81 - h id: est (0.98305) = fast (0.98305)
ok 82 - h cn: est (0.98305) = fast (0.98305)
ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1
ok 84 - q id: est (1.00000) = fast (1.00000)
ok 85 - q cn: est (1.00000) = fast (1.00000)
ok 86 - h id: est (1.00000) = fast (1.00000)
ok 87 - h cn: est (1.00000) = fast (1.00000)
ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1
ok 89 - q id: est (1.00000) = fast (1.00000)
ok 90 - q cn: est (1.00000) = fast (1.00000)
ok 91 - h id: est (1.00000) = fast (1.00000)
ok 92 - h cn: est (1.00000) = fast (1.00000)
ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1
ok 94 - q id: est (0.92308) = fast (0.92308)
ok 95 - q cn: est (0.92308) = fast (0.92308)
ok 96 - h id: est (0.92308) = fast (0.92308)
ok 97 - h cn: est (0.92308) = fast (0.92308)
ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1
ok 99 - q id: est (1.00000) = fast (1.00000)
ok 100 - q cn: est (1.00000) = fast (1.00000)
ok 101 - h id: est (1.00000) = fast (1.00000)
ok 102 - h cn: est (1.00000) = fast (1.00000)
ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1
ok 104 - q id: est (1.00000) = fast (1.00000)
ok 105 - q cn: est (1.00000) = fast (1.00000)
ok 106 - h id: est (1.00000) = fast (1.00000)
ok 107 - h cn: est (1.00000) = fast (1.00000)
ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1
ok 109 - q id: est (1.00000) = fast (1.00000)
ok 110 - q cn: est (1.00000) = fast (1.00000)
ok 111 - h id: est (1.00000) = fast (1.00000)
ok 112 - h cn: est (1.00000) = fast (1.00000)
ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1
ok 114 - q id: est (1.00000) = fast (1.00000)
ok 115 - q cn: est (1.00000) = fast (1.00000)
ok 116 - h id: est (1.00000) = fast (1.00000)
ok 117 - h cn: est (1.00000) = fast (1.00000)
ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1
ok 119 - q id: est (1.00000) = fast (1.00000)
ok 120 - q cn: est (1.00000) = fast (1.00000)
ok 121 - h id: est (1.00000) = fast (1.00000)
ok 122 - h cn: est (1.00000) = fast (1.00000)
ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1
ok 124 - q id: est (1.00000) = fast (1.00000)
ok 125 - q cn: est (1.00000) = fast (1.00000)
ok 126 - h id: est (1.00000) = fast (1.00000)
ok 127 - h cn: est (1.00000) = fast (1.00000)
ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1
ok 129 - q id: est (1.00000) = fast (1.00000)
ok 130 - q cn: est (1.00000) = fast (1.00000)
ok 131 - h id: est (1.00000) = fast (1.00000)
ok 132 - h cn: est (1.00000) = fast (1.00000)
ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1
ok 134 - q id: est (1.00000) = fast (1.00000)
ok 135 - q cn: est (1.00000) = fast (1.00000)
ok 136 - h id: est (1.00000) = fast (1.00000)
ok 137 - h cn: est (1.00000) = fast (1.00000)
ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1
ok 139 - q id: est (1.00000) = fast (1.00000)
ok 140 - q cn: est (1.00000) = fast (1.00000)
ok 141 - h id: est (1.00000) = fast (1.00000)
ok 142 - h cn: est (1.00000) = fast (1.00000)
ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1
ok 144 - q id: est (1.00000) = fast (1.00000)
ok 145 - q cn: est (1.00000) = fast (1.00000)
ok 146 - h id: est (1.00000) = fast (1.00000)
ok 147 - h cn: est (1.00000) = fast (1.00000)
ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1
ok 149 - q id: est (1.00000) = fast (1.00000)
ok 150 - q cn: est (1.00000) = fast (1.00000)
ok 151 - h id: est (1.00000) = fast (1.00000)
ok 152 - h cn: est (1.00000) = fast (1.00000)
ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1
ok 154 - q id: est (1.00000) = fast (1.00000)
ok 155 - q cn: est (1.00000) = fast (1.00000)
ok 156 - h id: est (1.00000) = fast (1.00000)
ok 157 - h cn: est (1.00000) = fast (1.00000)
ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1
ok 159 - q id: est (1.00000) = fast (1.00000)
ok 160 - q cn: est (1.00000) = fast (1.00000)
ok 161 - h id: est (1.00000) = fast (1.00000)
ok 162 - h cn: est (1.00000) = fast (1.00000)
ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1
ok 164 - q id: est (1.00000) = fast (1.00000)
ok 165 - q cn: est (1.00000) = fast (1.00000)
ok 166 - h id: est (1.00000) = fast (1.00000)
ok 167 - h cn: est (1.00000) = fast (1.00000)
ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1
ok 169 - q id: est (0.95238) = fast (0.95238)
ok 170 - q cn: est (0.95238) = fast (0.95238)
ok 171 - h id: est (0.95238) = fast (0.95238)
ok 172 - h cn: est (0.95238) = fast (0.95238)
ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1
ok 174 - q id: est (1.00000) = fast (1.00000)
ok 175 - q cn: est (1.00000) = fast (1.00000)
ok 176 - h id: est (1.00000) = fast (1.00000)
ok 177 - h cn: est (1.00000) = fast (1.00000)
ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1
ok 179 - q id: est (0.95238) = fast (0.95238)
ok 180 - q cn: est (0.95238) = fast (0.95238)
ok 181 - h id: est (0.95238) = fast (0.95238)
ok 182 - h cn: est (0.95238) = fast (0.95238)
ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1
ok 184 - q id: est (1.00000) = fast (1.00000)
ok 185 - q cn: est (1.00000) = fast (1.00000)
ok 186 - h id: est (1.00000) = fast (1.00000)
ok 187 - h cn: est (1.00000) = fast (1.00000)
ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1
ok 189 - q id: est (0.95238) = fast (0.95238)
ok 190 - q cn: est (0.95238) = fast (0.95238)
ok 191 - h id: est (0.95238) = fast (0.95238)
ok 192 - h cn: est (0.95238) = fast (0.95238)
ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1
ok 194 - q id: est (1.00000) = fast (1.00000)
ok 195 - q cn: est (1.00000) = fast (1.00000)
ok 196 - h id: est (1.00000) = fast (1.00000)
ok 197 - h cn: est (1.00000) = fast (1.00000)
ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1
ok 199 - q id: est (1.00000) = fast (1.00000)
ok 200 - q cn: est (1.00000) = fast (1.00000)
ok 201 - h id: est (1.00000) = fast (1.00000)
ok 202 - h cn: est (1.00000) = fast (1.00000)
ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1
ok 204 - q id: est (1.00000) = fast (1.00000)
ok 205 - q cn: est (1.00000) = fast (1.00000)
ok 206 - h id: est (1.00000) = fast (1.00000)
ok 207 - h cn: est (1.00000) = fast (1.00000)
ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1
ok 209 - q id: est (1.00000) = fast (1.00000)
ok 210 - q cn: est (1.00000) = fast (1.00000)
ok 211 - h id: est (1.00000) = fast (1.00000)
ok 212 - h cn: est (1.00000) = fast (1.00000)
ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1
ok 214 - q id: est (1.00000) = fast (1.00000)
ok 215 - q cn: est (1.00000) = fast (1.00000)
ok 216 - h id: est (1.00000) = fast (1.00000)
ok 217 - h cn: est (1.00000) = fast (1.00000)
ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1
ok 219 - q id: est (1.00000) = fast (1.00000)
ok 220 - q cn: est (1.00000) = fast (1.00000)
ok 221 - h id: est (1.00000) = fast (1.00000)
ok 222 - h cn: est (1.00000) = fast (1.00000)
ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1
ok 224 - q id: est (1.00000) = fast (1.00000)
ok 225 - q cn: est (1.00000) = fast (1.00000)
ok 226 - h id: est (1.00000) = fast (1.00000)
ok 227 - h cn: est (1.00000) = fast (1.00000)
ok 228 - brassica_ATH.WUBLASTN
ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3
ok 230 - q id: exact (0.82465) ~ est (0.82343)
ok 231 - q id: exact (0.82465) <= max (0.83333)
ok 232 - q cn: exact (0.85590) ~ est (0.85312)
ok 233 - q cn: exact (0.85590) <= max (0.86458)
ok 234 - h id: exact (0.83920) ~ est (0.83920)
ok 235 - h id: exact (0.83920) <= max (0.83920)
ok 236 - h cn: exact (0.86935) ~ est (0.86935)
ok 237 - h cn: exact (0.86935) <= max (0.86935)
ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2
ok 239 - q id: exact (0.82486) ~ est (0.82486)
ok 240 - q id: exact (0.82486) <= max (0.82486)
ok 241 - q cn: exact (0.85122) ~ est (0.85122)
ok 242 - q cn: exact (0.85122) <= max (0.85122)
ok 243 - h id: exact (0.82955) ~ est (0.82955)
ok 244 - h id: exact (0.82955) <= max (0.82955)
ok 245 - h cn: exact (0.85606) ~ est (0.85606)
ok 246 - h cn: exact (0.85606) <= max (0.85606)
ok 247 - no_hsps.blastp
ok 248 - tile no_hsps.blastp hit 1 \#hsps 0
ok 249 - tile no_hsps.blastp hit 2 \#hsps 0
ok 250 - tile no_hsps.blastp hit 3 \#hsps 0
ok 251 - tile no_hsps.blastp hit 4 \#hsps 0
ok 252 - tile no_hsps.blastp hit 5 \#hsps 0
ok 253 - tile no_hsps.blastp hit 6 \#hsps 0
ok 254 - tile no_hsps.blastp hit 7 \#hsps 0
ok 255 - tile no_hsps.blastp hit 8 \#hsps 0
ok 256 - tile no_hsps.blastp hit 9 \#hsps 0
ok 257 - tile no_hsps.blastp hit 10 \#hsps 0
ok 258 - tile no_hsps.blastp hit 11 \#hsps 0
ok 259 - tile no_hsps.blastp hit 12 \#hsps 0
ok 260 - tile no_hsps.blastp hit 13 \#hsps 0
ok 261 - tile no_hsps.blastp hit 14 \#hsps 0
ok 262 - tile no_hsps.blastp hit 15 \#hsps 0
ok 263 - tile no_hsps.blastp hit 16 \#hsps 0
ok 264 - tile no_hsps.blastp hit 17 \#hsps 0
ok 265 - tile no_hsps.blastp hit 18 \#hsps 0
ok 266 - tile no_hsps.blastp hit 19 \#hsps 0
ok 267 - tile no_hsps.blastp hit 20 \#hsps 0
ok 268 - tile no_hsps.blastp hit 21 \#hsps 0
ok 269 - tile no_hsps.blastp hit 22 \#hsps 0
ok 270 - tile no_hsps.blastp hit 23 \#hsps 0
ok 271 - tile no_hsps.blastp hit 24 \#hsps 0
ok 272 - tile no_hsps.blastp hit 25 \#hsps 0
ok 273 - tile no_hsps.blastp hit 26 \#hsps 0
ok 274 - tile no_hsps.blastp hit 27 \#hsps 0
ok 275 - tile no_hsps.blastp hit 28 \#hsps 0
ok 276 - tile no_hsps.blastp hit 29 \#hsps 0
ok 277 - tile no_hsps.blastp hit 30 \#hsps 0
ok 278 - tile no_hsps.blastp hit 31 \#hsps 0
ok 279 - tile no_hsps.blastp hit 32 \#hsps 0
ok 280 - tile no_hsps.blastp hit 33 \#hsps 0
ok 281 - tile no_hsps.blastp hit 34 \#hsps 0
ok 282 - tile no_hsps.blastp hit 35 \#hsps 0
ok 283 - tile no_hsps.blastp hit 36 \#hsps 0
ok 284 - tile no_hsps.blastp hit 37 \#hsps 0
ok 285 - tile no_hsps.blastp hit 38 \#hsps 0
ok 286 - tile no_hsps.blastp hit 39 \#hsps 0
ok 287 - tile no_hsps.blastp hit 40 \#hsps 0
ok 288 - tile no_hsps.blastp hit 41 \#hsps 0
ok 289 - tile no_hsps.blastp hit 42 \#hsps 0
ok 290 - tile no_hsps.blastp hit 43 \#hsps 0
ok 291 - tile no_hsps.blastp hit 44 \#hsps 0
ok 292 - tile no_hsps.blastp hit 45 \#hsps 0
ok 293 - tile no_hsps.blastp hit 46 \#hsps 0
ok 294 - tile no_hsps.blastp hit 47 \#hsps 0
ok 295 - tile no_hsps.blastp hit 48 \#hsps 0
ok 296 - tile no_hsps.blastp hit 49 \#hsps 0
ok 297 - tile no_hsps.blastp hit 50 \#hsps 0
ok 298 - tile no_hsps.blastp hit 51 \#hsps 0
ok 299 - tile no_hsps.blastp hit 52 \#hsps 0
ok 300 - tile no_hsps.blastp hit 53 \#hsps 0
ok 301 - tile no_hsps.blastp hit 54 \#hsps 0
ok 302 - tile no_hsps.blastp hit 55 \#hsps 0
ok 303 - tile no_hsps.blastp hit 56 \#hsps 0
ok 304 - tile no_hsps.blastp hit 57 \#hsps 0
ok 305 - tile no_hsps.blastp hit 58 \#hsps 0
ok 306 - tile no_hsps.blastp hit 59 \#hsps 0
ok 307 - tile no_hsps.blastp hit 60 \#hsps 0
ok 308 - tile no_hsps.blastp hit 61 \#hsps 0
ok 309 - tile no_hsps.blastp hit 62 \#hsps 0
ok 310 - tile no_hsps.blastp hit 63 \#hsps 0
ok 311 - tile no_hsps.blastp hit 64 \#hsps 0
ok 312 - tile no_hsps.blastp hit 65 \#hsps 0
ok 313 - tile no_hsps.blastp hit 66 \#hsps 0
ok 314 - tile no_hsps.blastp hit 67 \#hsps 0
ok 315 - tile no_hsps.blastp hit 68 \#hsps 0
ok 316 - tile no_hsps.blastp hit 69 \#hsps 0
ok 317 - tile no_hsps.blastp hit 70 \#hsps 0
ok 318 - tile no_hsps.blastp hit 71 \#hsps 0
ok 319 - tile no_hsps.blastp hit 72 \#hsps 0
ok 320 - tile no_hsps.blastp hit 73 \#hsps 0
ok 321 - tile no_hsps.blastp hit 74 \#hsps 0
ok 322 - tile no_hsps.blastp hit 75 \#hsps 0
ok 323 - tile no_hsps.blastp hit 76 \#hsps 0
ok 324 - tile no_hsps.blastp hit 77 \#hsps 0
ok 325 - tile no_hsps.blastp hit 78 \#hsps 0
ok 326 - tile no_hsps.blastp hit 79 \#hsps 0
ok 327 - tile no_hsps.blastp hit 80 \#hsps 0
ok 328 - tile no_hsps.blastp hit 81 \#hsps 0
ok 329 - tile no_hsps.blastp hit 82 \#hsps 0
ok 330 - tile no_hsps.blastp hit 83 \#hsps 0
ok 331 - tile no_hsps.blastp hit 84 \#hsps 0
ok 332 - tile no_hsps.blastp hit 85 \#hsps 0
ok 333 - tile no_hsps.blastp hit 86 \#hsps 0
ok 334 - tile no_hsps.blastp hit 87 \#hsps 0
ok 335 - tile no_hsps.blastp hit 88 \#hsps 0
ok 336 - tile no_hsps.blastp hit 89 \#hsps 0
ok 337 - tile no_hsps.blastp hit 90 \#hsps 0
ok 338 - tile no_hsps.blastp hit 91 \#hsps 0
ok 339 - tile no_hsps.blastp hit 92 \#hsps 0
ok 340 - tile no_hsps.blastp hit 93 \#hsps 0
ok 341 - tile no_hsps.blastp hit 94 \#hsps 0
ok 342 - tile no_hsps.blastp hit 95 \#hsps 0
ok 343 - tile no_hsps.blastp hit 96 \#hsps 0
ok 344 - tile no_hsps.blastp hit 97 \#hsps 0
ok 345 - tile no_hsps.blastp hit 98 \#hsps 0
ok 346 - tile no_hsps.blastp hit 99 \#hsps 0
ok 347 - tile no_hsps.blastp hit 100 \#hsps 0
ok 348 - tile no_hsps.blastp hit 101 \#hsps 0
ok 349 - tile no_hsps.blastp hit 102 \#hsps 0
ok 350 - tile no_hsps.blastp hit 103 \#hsps 0
ok 351 - tile no_hsps.blastp hit 104 \#hsps 0
ok 352 - tile no_hsps.blastp hit 105 \#hsps 0
ok 353 - tile no_hsps.blastp hit 106 \#hsps 0
ok 354 - tile no_hsps.blastp hit 107 \#hsps 0
ok 355 - tile no_hsps.blastp hit 108 \#hsps 0
ok 356 - tile no_hsps.blastp hit 109 \#hsps 0
ok 357 - tile no_hsps.blastp hit 110 \#hsps 0
ok 358 - tile no_hsps.blastp hit 111 \#hsps 0
ok 359 - tile no_hsps.blastp hit 112 \#hsps 0
ok 360 - tile no_hsps.blastp hit 113 \#hsps 0
ok 361 - tile no_hsps.blastp hit 114 \#hsps 0
ok 362 - tile no_hsps.blastp hit 115 \#hsps 0
ok 363 - tile no_hsps.blastp hit 116 \#hsps 0
ok 364 - tile no_hsps.blastp hit 117 \#hsps 0
ok 365 - tile no_hsps.blastp hit 118 \#hsps 0
ok 366 - tile no_hsps.blastp hit 119 \#hsps 0
ok 367 - tile no_hsps.blastp hit 120 \#hsps 0
ok 368 - tile no_hsps.blastp hit 121 \#hsps 0
ok 369 - tile no_hsps.blastp hit 122 \#hsps 0
ok 370 - tile no_hsps.blastp hit 123 \#hsps 0
ok 371 - tile no_hsps.blastp hit 124 \#hsps 0
ok 372 - tile no_hsps.blastp hit 125 \#hsps 0
ok 373 - tile no_hsps.blastp hit 126 \#hsps 0
ok 374 - tile no_hsps.blastp hit 127 \#hsps 0
ok 375 - tile no_hsps.blastp hit 128 \#hsps 0
ok 376 - tile no_hsps.blastp hit 129 \#hsps 0
ok 377 - tile no_hsps.blastp hit 130 \#hsps 0
ok 378 - tile no_hsps.blastp hit 131 \#hsps 0
ok 379 - tile no_hsps.blastp hit 132 \#hsps 0
ok 380 - tile no_hsps.blastp hit 133 \#hsps 0
ok 381 - tile no_hsps.blastp hit 134 \#hsps 0
ok 382 - tile no_hsps.blastp hit 135 \#hsps 0
ok 383 - tile no_hsps.blastp hit 136 \#hsps 0
ok 384 - tile no_hsps.blastp hit 137 \#hsps 0
ok 385 - tile no_hsps.blastp hit 138 \#hsps 0
ok 386 - tile no_hsps.blastp hit 139 \#hsps 0
ok 387 - tile no_hsps.blastp hit 140 \#hsps 0
ok 388 - tile no_hsps.blastp hit 141 \#hsps 0
ok 389 - tile no_hsps.blastp hit 142 \#hsps 0
ok 390 - tile no_hsps.blastp hit 143 \#hsps 0
ok 391 - tile no_hsps.blastp hit 144 \#hsps 0
ok 392 - tile no_hsps.blastp hit 145 \#hsps 0
ok 393 - tile no_hsps.blastp hit 146 \#hsps 0
ok 394 - tile no_hsps.blastp hit 147 \#hsps 0
ok 395 - tile no_hsps.blastp hit 148 \#hsps 0
ok 396 - tile no_hsps.blastp hit 149 \#hsps 0
ok 397 - tile no_hsps.blastp hit 150 \#hsps 0
ok 398 - tile no_hsps.blastp hit 151 \#hsps 0
ok 399 - tile no_hsps.blastp hit 152 \#hsps 0
ok 400 - tile no_hsps.blastp hit 153 \#hsps 0
ok 401 - tile no_hsps.blastp hit 154 \#hsps 0
ok 402 - tile no_hsps.blastp hit 155 \#hsps 0
ok 403 - tile no_hsps.blastp hit 156 \#hsps 0
ok 404 - tile no_hsps.blastp hit 157 \#hsps 0
ok 405 - tile no_hsps.blastp hit 158 \#hsps 0
ok 406 - tile no_hsps.blastp hit 159 \#hsps 0
ok 407 - tile no_hsps.blastp hit 160 \#hsps 0
ok 408 - tile no_hsps.blastp hit 161 \#hsps 0
ok 409 - tile no_hsps.blastp hit 162 \#hsps 0
ok 410 - tile no_hsps.blastp hit 163 \#hsps 0
ok 411 - tile no_hsps.blastp hit 164 \#hsps 0
ok 412 - tile no_hsps.blastp hit 165 \#hsps 0
ok 413 - tile no_hsps.blastp hit 166 \#hsps 0
ok 414 - tile no_hsps.blastp hit 167 \#hsps 0
ok 415 - tile no_hsps.blastp hit 168 \#hsps 0
ok 416 - tile no_hsps.blastp hit 169 \#hsps 0
ok 417 - tile no_hsps.blastp hit 170 \#hsps 0
ok 418 - tile no_hsps.blastp hit 171 \#hsps 0
ok 419 - tile no_hsps.blastp hit 172 \#hsps 0
ok 420 - tile no_hsps.blastp hit 173 \#hsps 0
ok 421 - tile no_hsps.blastp hit 174 \#hsps 0
ok 422 - tile no_hsps.blastp hit 175 \#hsps 0
ok 423 - tile no_hsps.blastp hit 176 \#hsps 0
ok 424 - tile no_hsps.blastp hit 177 \#hsps 0
ok 425 - tile no_hsps.blastp hit 178 \#hsps 0
ok 426 - tile no_hsps.blastp hit 179 \#hsps 0
ok 427 - tile no_hsps.blastp hit 180 \#hsps 0
ok 428 - tile no_hsps.blastp hit 181 \#hsps 0
ok 429 - tile no_hsps.blastp hit 182 \#hsps 0
ok 430 - tile no_hsps.blastp hit 183 \#hsps 0
ok 431 - tile no_hsps.blastp hit 184 \#hsps 0
ok 432 - tile no_hsps.blastp hit 185 \#hsps 0
ok 433 - tile no_hsps.blastp hit 186 \#hsps 0
ok 434 - tile no_hsps.blastp hit 187 \#hsps 0
ok 435 - tile no_hsps.blastp hit 188 \#hsps 0
ok 436 - tile no_hsps.blastp hit 189 \#hsps 0
ok 437 - tile no_hsps.blastp hit 190 \#hsps 0
ok 438 - tile no_hsps.blastp hit 191 \#hsps 0
ok 439 - tile no_hsps.blastp hit 192 \#hsps 0
ok 440 - tile no_hsps.blastp hit 193 \#hsps 0
ok 441 - tile no_hsps.blastp hit 194 \#hsps 0
ok 442 - tile no_hsps.blastp hit 195 \#hsps 0
ok 443 - tile no_hsps.blastp hit 196 \#hsps 0
ok 444 - tile no_hsps.blastp hit 197 \#hsps 0
ok 445 - tile no_hsps.blastp hit 198 \#hsps 0
ok 446 - tile no_hsps.blastp hit 199 \#hsps 0
ok 447 - tile no_hsps.blastp hit 200 \#hsps 0
ok 448 - tile no_hsps.blastp hit 201 \#hsps 0
ok 449 - tile no_hsps.blastp hit 202 \#hsps 0
ok 450 - tile no_hsps.blastp hit 203 \#hsps 0
ok 451 - tile no_hsps.blastp hit 204 \#hsps 0
ok 452 - tile no_hsps.blastp hit 205 \#hsps 0
ok 453 - tile no_hsps.blastp hit 206 \#hsps 0
ok 454 - tile no_hsps.blastp hit 207 \#hsps 0
ok 455 - tile no_hsps.blastp hit 208 \#hsps 0
ok 456 - tile no_hsps.blastp hit 209 \#hsps 0
ok 457 - tile no_hsps.blastp hit 210 \#hsps 0
ok 458 - tile no_hsps.blastp hit 211 \#hsps 0
ok 459 - tile no_hsps.blastp hit 212 \#hsps 0
ok 460 - tile no_hsps.blastp hit 213 \#hsps 0
ok 461 - tile no_hsps.blastp hit 214 \#hsps 0
ok 462 - tile no_hsps.blastp hit 215 \#hsps 0
ok 463 - tile no_hsps.blastp hit 216 \#hsps 0
ok 464 - tile no_hsps.blastp hit 217 \#hsps 0
ok 465 - tile no_hsps.blastp hit 218 \#hsps 0
ok 466 - tile no_hsps.blastp hit 219 \#hsps 0
ok 467 - tile no_hsps.blastp hit 220 \#hsps 0
ok 468 - tile no_hsps.blastp hit 221 \#hsps 0
ok 469 - tile no_hsps.blastp hit 222 \#hsps 0
ok 470 - tile no_hsps.blastp hit 223 \#hsps 0
ok 471 - tile no_hsps.blastp hit 224 \#hsps 0
ok 472 - tile no_hsps.blastp hit 225 \#hsps 0
ok 473 - tile no_hsps.blastp hit 226 \#hsps 0
ok 474 - tile no_hsps.blastp hit 227 \#hsps 0
ok 475 - tile no_hsps.blastp hit 228 \#hsps 0
ok 476 - tile no_hsps.blastp hit 229 \#hsps 0
ok 477 - tile no_hsps.blastp hit 230 \#hsps 0
ok 478 - tile no_hsps.blastp hit 231 \#hsps 0
ok 479 - tile no_hsps.blastp hit 232 \#hsps 0
ok 480 - tile no_hsps.blastp hit 233 \#hsps 0
ok 481 - tile no_hsps.blastp hit 234 \#hsps 0
ok 482 - tile no_hsps.blastp hit 235 \#hsps 0
ok 483 - tile no_hsps.blastp hit 236 \#hsps 0
ok 484 - tile no_hsps.blastp hit 237 \#hsps 0
ok 485 - tile no_hsps.blastp hit 238 \#hsps 0
ok 486 - tile no_hsps.blastp hit 239 \#hsps 0
ok 487 - tile no_hsps.blastp hit 240 \#hsps 0
ok 488 - tile no_hsps.blastp hit 241 \#hsps 0
ok 489 - tile no_hsps.blastp hit 242 \#hsps 0
ok 490 - tile no_hsps.blastp hit 243 \#hsps 0
ok 491 - tile no_hsps.blastp hit 244 \#hsps 0
ok 492 - tile no_hsps.blastp hit 245 \#hsps 0
ok 493 - tile no_hsps.blastp hit 246 \#hsps 0
ok 494 - tile no_hsps.blastp hit 247 \#hsps 0
ok 495 - tile no_hsps.blastp hit 248 \#hsps 0
ok 496 - tile no_hsps.blastp hit 249 \#hsps 0
ok 497 - tile no_hsps.blastp hit 250 \#hsps 0
ok 498 - tile no_hsps.blastp hit 251 \#hsps 0
ok 499 - tile no_hsps.blastp hit 252 \#hsps 0
ok 500 - tile no_hsps.blastp hit 253 \#hsps 0
ok 501 - tile no_hsps.blastp hit 254 \#hsps 0
ok 502 - tile no_hsps.blastp hit 255 \#hsps 0
ok 503 - tile no_hsps.blastp hit 256 \#hsps 0
ok 504 - tile no_hsps.blastp hit 257 \#hsps 0
ok 505 - tile no_hsps.blastp hit 258 \#hsps 0
ok 506 - tile no_hsps.blastp hit 259 \#hsps 0
ok 507 - tile no_hsps.blastp hit 260 \#hsps 0
ok 508 - tile no_hsps.blastp hit 261 \#hsps 0
ok 509 - tile no_hsps.blastp hit 262 \#hsps 0
ok 510 - tile no_hsps.blastp hit 263 \#hsps 0
ok 511 - tile no_hsps.blastp hit 264 \#hsps 0
ok 512 - tile no_hsps.blastp hit 265 \#hsps 0
ok 513 - tile no_hsps.blastp hit 266 \#hsps 0
ok 514 - tile no_hsps.blastp hit 267 \#hsps 0
ok 515 - tile no_hsps.blastp hit 268 \#hsps 0
ok 516 - tile no_hsps.blastp hit 269 \#hsps 0
ok 517 - tile no_hsps.blastp hit 270 \#hsps 0
ok 518 - tile no_hsps.blastp hit 271 \#hsps 0
ok 519 - tile no_hsps.blastp hit 272 \#hsps 0
ok 520 - tile no_hsps.blastp hit 273 \#hsps 0
ok 521 - tile no_hsps.blastp hit 274 \#hsps 0
ok 522 - tile no_hsps.blastp hit 275 \#hsps 0
ok 523 - tile no_hsps.blastp hit 276 \#hsps 0
ok 524 - tile no_hsps.blastp hit 277 \#hsps 0
ok 525 - tile no_hsps.blastp hit 278 \#hsps 0
ok 526 - tile no_hsps.blastp hit 279 \#hsps 0
ok 527 - tile no_hsps.blastp hit 280 \#hsps 0
ok 528 - tile no_hsps.blastp hit 281 \#hsps 0
ok 529 - tile no_hsps.blastp hit 282 \#hsps 0
ok 530 - tile no_hsps.blastp hit 283 \#hsps 0
ok 531 - tile no_hsps.blastp hit 284 \#hsps 0
ok 532 - tile no_hsps.blastp hit 285 \#hsps 0
ok 533 - tile no_hsps.blastp hit 286 \#hsps 0
ok 534 - tile no_hsps.blastp hit 287 \#hsps 0
ok 535 - tile no_hsps.blastp hit 288 \#hsps 0
ok 536 - tile no_hsps.blastp hit 289 \#hsps 0
ok 537 - tile no_hsps.blastp hit 290 \#hsps 0
ok 538 - tile no_hsps.blastp hit 291 \#hsps 0
ok 539 - tile no_hsps.blastp hit 292 \#hsps 0
ok 540 - tile no_hsps.blastp hit 293 \#hsps 0
ok 541 - tile no_hsps.blastp hit 294 \#hsps 0
ok 542 - tile no_hsps.blastp hit 295 \#hsps 0
ok 543 - tile no_hsps.blastp hit 296 \#hsps 0
ok 544 - tile no_hsps.blastp hit 297 \#hsps 0
ok 545 - tile no_hsps.blastp hit 298 \#hsps 0
ok 546 - tile no_hsps.blastp hit 299 \#hsps 0
ok 547 - tile no_hsps.blastp hit 300 \#hsps 0
ok 548 - tile no_hsps.blastp hit 301 \#hsps 0
ok 549 - tile no_hsps.blastp hit 302 \#hsps 0
ok 550 - tile no_hsps.blastp hit 303 \#hsps 0
ok 551 - tile no_hsps.blastp hit 304 \#hsps 0
ok 552 - tile no_hsps.blastp hit 305 \#hsps 0
ok 553 - tile no_hsps.blastp hit 306 \#hsps 0
ok 554 - tile no_hsps.blastp hit 307 \#hsps 0
ok 555 - tile no_hsps.blastp hit 308 \#hsps 0
ok 556 - tile no_hsps.blastp hit 309 \#hsps 0
ok 557 - tile no_hsps.blastp hit 310 \#hsps 0
ok 558 - tile no_hsps.blastp hit 311 \#hsps 0
ok 559 - tile no_hsps.blastp hit 312 \#hsps 0
ok 560 - tile no_hsps.blastp hit 313 \#hsps 0
ok 561 - tile no_hsps.blastp hit 314 \#hsps 0
ok 562 - tile no_hsps.blastp hit 315 \#hsps 0
ok 563 - tile no_hsps.blastp hit 316 \#hsps 0
ok 564 - tile no_hsps.blastp hit 317 \#hsps 0
ok 565 - tile no_hsps.blastp hit 318 \#hsps 0
ok 566 - tile no_hsps.blastp hit 319 \#hsps 0
ok 567 - tile no_hsps.blastp hit 320 \#hsps 0
ok 568 - tile no_hsps.blastp hit 321 \#hsps 0
ok 569 - tile no_hsps.blastp hit 322 \#hsps 0
ok 570 - tile no_hsps.blastp hit 323 \#hsps 0
ok 571 - tile no_hsps.blastp hit 324 \#hsps 0
ok 572 - tile no_hsps.blastp hit 325 \#hsps 0
ok 573 - tile no_hsps.blastp hit 326 \#hsps 0
ok 574 - tile no_hsps.blastp hit 327 \#hsps 0
ok 575 - tile no_hsps.blastp hit 328 \#hsps 0
ok 576 - tile no_hsps.blastp hit 329 \#hsps 0
ok 577 - tile no_hsps.blastp hit 330 \#hsps 0
ok 578 - tile no_hsps.blastp hit 331 \#hsps 0
ok 579 - tile no_hsps.blastp hit 332 \#hsps 0
ok 580 - tile no_hsps.blastp hit 333 \#hsps 0
ok 581 - tile no_hsps.blastp hit 334 \#hsps 0
ok 582 - tile no_hsps.blastp hit 335 \#hsps 0
ok 583 - tile no_hsps.blastp hit 336 \#hsps 0
ok 584 - tile no_hsps.blastp hit 337 \#hsps 0
ok 585 - tile no_hsps.blastp hit 338 \#hsps 0
ok 586 - tile no_hsps.blastp hit 339 \#hsps 0
ok 587 - tile no_hsps.blastp hit 340 \#hsps 0
ok 588 - tile no_hsps.blastp hit 341 \#hsps 0
ok 589 - tile no_hsps.blastp hit 342 \#hsps 0
ok 590 - tile no_hsps.blastp hit 343 \#hsps 0
ok 591 - tile no_hsps.blastp hit 344 \#hsps 0
ok 592 - tile no_hsps.blastp hit 345 \#hsps 0
ok 593 - tile no_hsps.blastp hit 346 \#hsps 0
ok 594 - tile no_hsps.blastp hit 347 \#hsps 0
ok 595 - tile no_hsps.blastp hit 348 \#hsps 0
ok 596 - tile no_hsps.blastp hit 349 \#hsps 0
ok 597 - tile no_hsps.blastp hit 350 \#hsps 0
ok 598 - tile no_hsps.blastp hit 351 \#hsps 0
ok 599 - tile no_hsps.blastp hit 352 \#hsps 0
ok 600 - tile no_hsps.blastp hit 353 \#hsps 0
ok 601 - tile no_hsps.blastp hit 354 \#hsps 0
ok 602 - tile no_hsps.blastp hit 355 \#hsps 0
ok 603 - tile no_hsps.blastp hit 356 \#hsps 0
ok 604 - tile no_hsps.blastp hit 357 \#hsps 0
ok 605 - tile no_hsps.blastp hit 358 \#hsps 0
ok 606 - tile no_hsps.blastp hit 359 \#hsps 0
ok 607 - tile no_hsps.blastp hit 360 \#hsps 0
ok 608 - tile no_hsps.blastp hit 361 \#hsps 0
ok 609 - tile no_hsps.blastp hit 362 \#hsps 0
ok 610 - tile no_hsps.blastp hit 363 \#hsps 0
ok 611 - tile no_hsps.blastp hit 364 \#hsps 0
ok 612 - tile no_hsps.blastp hit 365 \#hsps 0
ok 613 - tile no_hsps.blastp hit 366 \#hsps 0
ok 614 - tile no_hsps.blastp hit 367 \#hsps 0
ok 615 - tile no_hsps.blastp hit 368 \#hsps 0
ok 616 - tile no_hsps.blastp hit 369 \#hsps 0
ok 617 - tile no_hsps.blastp hit 370 \#hsps 0
ok 618 - tile no_hsps.blastp hit 371 \#hsps 0
ok 619 - tile no_hsps.blastp hit 372 \#hsps 0
ok 620 - tile no_hsps.blastp hit 373 \#hsps 0
ok 621 - tile no_hsps.blastp hit 374 \#hsps 0
ok 622 - tile no_hsps.blastp hit 375 \#hsps 0
ok 623 - tile no_hsps.blastp hit 376 \#hsps 0
ok 624 - tile no_hsps.blastp hit 377 \#hsps 0
ok 625 - tile no_hsps.blastp hit 378 \#hsps 0
ok 626 - tile no_hsps.blastp hit 379 \#hsps 0
ok 627 - tile no_hsps.blastp hit 380 \#hsps 0
ok 628 - tile no_hsps.blastp hit 381 \#hsps 0
ok 629 - tile no_hsps.blastp hit 382 \#hsps 0
ok 630 - tile no_hsps.blastp hit 383 \#hsps 0
ok 631 - tile no_hsps.blastp hit 384 \#hsps 0
ok 632 - tile no_hsps.blastp hit 385 \#hsps 0
ok 633 - tile no_hsps.blastp hit 386 \#hsps 0
ok 634 - tile no_hsps.blastp hit 387 \#hsps 0
ok 635 - tile no_hsps.blastp hit 388 \#hsps 0
ok 636 - tile no_hsps.blastp hit 389 \#hsps 0
ok 637 - tile no_hsps.blastp hit 390 \#hsps 0
ok 638 - tile no_hsps.blastp hit 391 \#hsps 0
ok 639 - tile no_hsps.blastp hit 392 \#hsps 0
ok 640 - tile no_hsps.blastp hit 393 \#hsps 0
ok 641 - tile no_hsps.blastp hit 394 \#hsps 0
ok 642 - tile no_hsps.blastp hit 395 \#hsps 0
ok 643 - tile no_hsps.blastp hit 396 \#hsps 0
ok 644 - tile no_hsps.blastp hit 397 \#hsps 0
ok 645 - tile no_hsps.blastp hit 398 \#hsps 0
ok 646 - tile no_hsps.blastp hit 399 \#hsps 0
ok 647 - tile no_hsps.blastp hit 400 \#hsps 0
ok 648 - tile no_hsps.blastp hit 401 \#hsps 0
ok 649 - tile no_hsps.blastp hit 402 \#hsps 0
ok 650 - tile no_hsps.blastp hit 403 \#hsps 0
ok 651 - tile no_hsps.blastp hit 404 \#hsps 0
ok 652 - tile no_hsps.blastp hit 405 \#hsps 0
ok 653 - tile no_hsps.blastp hit 406 \#hsps 0
ok 654 - tile no_hsps.blastp hit 407 \#hsps 0
ok 655 - tile no_hsps.blastp hit 408 \#hsps 0
ok 656 - tile no_hsps.blastp hit 409 \#hsps 0
ok 657 - tile no_hsps.blastp hit 410 \#hsps 0
ok 658 - tile no_hsps.blastp hit 411 \#hsps 0
ok 659 - tile no_hsps.blastp hit 412 \#hsps 0
ok 660 - tile no_hsps.blastp hit 413 \#hsps 0
ok 661 - tile no_hsps.blastp hit 414 \#hsps 0
ok 662 - tile no_hsps.blastp hit 415 \#hsps 0
ok 663 - catalase-webblast.BLASTP
ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1
ok 665 - q id: est (1.00000) = fast (1.00000)
ok 666 - q cn: est (1.00000) = fast (1.00000)
ok 667 - h id: est (1.00000) = fast (1.00000)
ok 668 - h cn: est (1.00000) = fast (1.00000)
ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1
ok 670 - q id: est (0.80973) = fast (0.80973)
ok 671 - q cn: est (0.89006) = fast (0.89006)
ok 672 - h id: est (0.82543) = fast (0.82543)
ok 673 - h cn: est (0.90733) = fast (0.90733)
ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1
ok 675 - q id: est (0.71670) = fast (0.71670)
ok 676 - q cn: est (0.84144) = fast (0.84144)
ok 677 - h id: est (0.72747) = fast (0.72747)
ok 678 - h cn: est (0.85408) = fast (0.85408)
ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1
ok 680 - q id: est (0.58910) = fast (0.58910)
ok 681 - q cn: est (0.70860) = fast (0.70860)
ok 682 - h id: est (0.65654) = fast (0.65654)
ok 683 - h cn: est (0.78972) = fast (0.78972)
ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1
ok 685 - q id: est (0.49245) = fast (0.49245)
ok 686 - q cn: est (0.65257) = fast (0.65257)
ok 687 - h id: est (0.49544) = fast (0.49544)
ok 688 - h cn: est (0.65653) = fast (0.65653)
ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1
ok 690 - q id: est (0.44366) = fast (0.44366)
ok 691 - q cn: est (0.58920) = fast (0.58920)
ok 692 - h id: est (0.44787) = fast (0.44787)
ok 693 - h cn: est (0.59479) = fast (0.59479)
ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1
ok 695 - q id: est (0.42564) = fast (0.42564)
ok 696 - q cn: est (0.61282) = fast (0.61282)
ok 697 - h id: est (0.43229) = fast (0.43229)
ok 698 - h cn: est (0.62240) = fast (0.62240)
ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1
ok 700 - q id: est (0.48358) = fast (0.48358)
ok 701 - q cn: est (0.63881) = fast (0.63881)
ok 702 - h id: est (0.48943) = fast (0.48943)
ok 703 - h cn: est (0.64653) = fast (0.64653)
ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1
ok 705 - q id: est (0.42308) = fast (0.42308)
ok 706 - q cn: est (0.61282) = fast (0.61282)
ok 707 - h id: est (0.42969) = fast (0.42969)
ok 708 - h cn: est (0.62240) = fast (0.62240)
ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1
ok 710 - q id: est (0.39675) = fast (0.39675)
ok 711 - q cn: est (0.58933) = fast (0.58933)
ok 712 - h id: est (0.39767) = fast (0.39767)
ok 713 - h cn: est (0.59070) = fast (0.59070)
ok 714 - dcr1_sp.WUBLASTP
ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1
ok 716 - q id: est (1.00000) = fast (1.00000)
ok 717 - q cn: est (1.00000) = fast (1.00000)
ok 718 - h id: est (1.00000) = fast (1.00000)
ok 719 - h cn: est (1.00000) = fast (1.00000)
ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4
ok 721 - q id: exact (0.36876) ~ est (0.36973)
ok 722 - q id: exact (0.36876) <= max (0.37070)
ok 723 - q cn: exact (0.55022) ~ est (0.55041)
ok 724 - q cn: exact (0.55022) <= max (0.55105)
ok 725 - h id: exact (0.35111) ~ est (0.35111)
ok 726 - h id: exact (0.35111) <= max (0.35111)
ok 727 - h cn: exact (0.52305) ~ est (0.52305)
ok 728 - h cn: exact (0.52305) <= max (0.52305)
ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1
ok 730 - q id: est (0.38685) = fast (0.38685)
ok 731 - q cn: est (0.55397) = fast (0.55397)
ok 732 - h id: est (0.37613) = fast (0.37613)
ok 733 - h cn: est (0.53863) = fast (0.53863)
ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1
ok 735 - q id: est (0.38247) = fast (0.38247)
ok 736 - q cn: est (0.55068) = fast (0.55068)
ok 737 - h id: est (0.37306) = fast (0.37306)
ok 738 - h cn: est (0.53715) = fast (0.53715)
ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5
ok 740 - q id: exact (0.35010) ~ est (0.35010)
ok 741 - q id: exact (0.35010) <= max (0.35010)
ok 742 - q cn: exact (0.53183) ~ est (0.53183)
ok 743 - q cn: exact (0.53183) <= max (0.53183)
ok 744 - h id: exact (0.35082) ~ est (0.35082)
ok 745 - h id: exact (0.35082) <= max (0.35082)
ok 746 - h cn: exact (0.53292) ~ est (0.53292)
ok 747 - h cn: exact (0.53292) <= max (0.53292)
ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8
ok 749 - q id: exact (0.30547) ~ est (0.30659)
ok 750 - q id: exact (0.30547) <= max (0.30623)
ok 751 - q cn: exact (0.50076) ~ est (0.50205)
ok 752 - q cn: exact (0.50076) <= max (0.50076)
ok 753 - h id: exact (0.31390) ~ est (0.31179)
ok 754 - h id: exact (0.31390) <= max (0.31795)
ok 755 - h cn: exact (0.50531) ~ est (0.50557)
ok 756 - h cn: exact (0.50531) <= max (0.51091)
ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7
ok 758 - q id: exact (0.30136) ~ est (0.30184)
ok 759 - q id: exact (0.30136) <= max (0.30498)
ok 760 - q cn: exact (0.48688) ~ est (0.48742)
ok 761 - q cn: exact (0.48688) <= max (0.49140)
ok 762 - h id: exact (0.30944) ~ est (0.31034)
ok 763 - h id: exact (0.30944) <= max (0.30988)
ok 764 - h cn: exact (0.50178) ~ est (0.50277)
ok 765 - h cn: exact (0.50178) <= max (0.50223)
ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10
ok 767 - q id: exact (0.28918) ~ est (0.28961)
ok 768 - q id: exact (0.28918) <= max (0.28955)
ok 769 - q cn: exact (0.46418) ~ est (0.46247)
ok 770 - q cn: exact (0.46418) <= max (0.46866)
ok 771 - h id: exact (0.30166) ~ est (0.30299)
ok 772 - h id: exact (0.30166) <= max (0.30800)
ok 773 - h cn: exact (0.48179) ~ est (0.48439)
ok 774 - h cn: exact (0.48179) <= max (0.48535)
ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8
ok 776 - q id: exact (0.30289) ~ est (0.30238)
ok 777 - q id: exact (0.30289) <= max (0.30651)
ok 778 - q cn: exact (0.49955) ~ est (0.49787)
ok 779 - q cn: exact (0.49955) <= max (0.50362)
ok 780 - h id: exact (0.31395) ~ est (0.31347)
ok 781 - h id: exact (0.31395) <= max (0.31721)
ok 782 - h cn: exact (0.51535) ~ est (0.51578)
ok 783 - h cn: exact (0.51535) <= max (0.51814)
ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5
ok 785 - q id: exact (0.29334) ~ est (0.29534)
ok 786 - q id: exact (0.29334) <= max (0.29810)
ok 787 - q cn: exact (0.46617) ~ est (0.46719)
ok 788 - q cn: exact (0.46617) <= max (0.47040)
ok 789 - h id: exact (0.31176) ~ est (0.31176)
ok 790 - h id: exact (0.31176) <= max (0.31176)
ok 791 - h cn: exact (0.49299) ~ est (0.49299)
ok 792 - h cn: exact (0.49299) <= max (0.49299)
ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7
ok 794 - q id: exact (0.30456) ~ est (0.30514)
ok 795 - q id: exact (0.30456) <= max (0.30650)
ok 796 - q cn: exact (0.48739) ~ est (0.48879)
ok 797 - q cn: exact (0.48739) <= max (0.49370)
ok 798 - h id: exact (0.32062) ~ est (0.31987)
ok 799 - h id: exact (0.32062) <= max (0.32932)
ok 800 - h cn: exact (0.51071) ~ est (0.51306)
ok 801 - h cn: exact (0.51071) <= max (0.52410)
ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8
ok 803 - q id: exact (0.29615) ~ est (0.29879)
ok 804 - q id: exact (0.29615) <= max (0.30009)
ok 805 - q cn: exact (0.47419) ~ est (0.47394)
ok 806 - q cn: exact (0.47419) <= max (0.48119)
ok 807 - h id: exact (0.31611) ~ est (0.31482)
ok 808 - h id: exact (0.31611) <= max (0.32227)
ok 809 - h cn: exact (0.49779) ~ est (0.49788)
ok 810 - h cn: exact (0.49779) <= max (0.50616)
ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8
ok 812 - q id: exact (0.30390) ~ est (0.30440)
ok 813 - q id: exact (0.30390) <= max (0.30701)
ok 814 - q cn: exact (0.45874) ~ est (0.45993)
ok 815 - q cn: exact (0.45874) <= max (0.45963)
ok 816 - h id: exact (0.32282) ~ est (0.32324)
ok 817 - h id: exact (0.32282) <= max (0.32560)
ok 818 - h cn: exact (0.48052) ~ est (0.48136)
ok 819 - h cn: exact (0.48052) <= max (0.48330)
ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6
ok 821 - q id: exact (0.29769) ~ est (0.29851)
ok 822 - q id: exact (0.29769) <= max (0.29769)
ok 823 - q cn: exact (0.48480) ~ est (0.48628)
ok 824 - q cn: exact (0.48480) <= max (0.48637)
ok 825 - h id: exact (0.30704) ~ est (0.30810)
ok 826 - h id: exact (0.30704) <= max (0.30917)
ok 827 - h cn: exact (0.50107) ~ est (0.50292)
ok 828 - h cn: exact (0.50107) <= max (0.50320)
ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6
ok 830 - q id: exact (0.27854) ~ est (0.27854)
ok 831 - q id: exact (0.27854) <= max (0.27854)
ok 832 - q cn: exact (0.48174) ~ est (0.48174)
ok 833 - q cn: exact (0.48174) <= max (0.48174)
ok 834 - h id: exact (0.28514) ~ est (0.28623)
ok 835 - h id: exact (0.28514) <= max (0.28594)
ok 836 - h cn: exact (0.49197) ~ est (0.49154)
ok 837 - h cn: exact (0.49197) <= max (0.49237)
ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8
ok 839 - q id: exact (0.30362) ~ est (0.30824)
ok 840 - q id: exact (0.30362) <= max (0.30852)
ok 841 - q cn: exact (0.47111) ~ est (0.47587)
ok 842 - q cn: exact (0.47111) <= max (0.47405)
ok 843 - h id: exact (0.32347) ~ est (0.32392)
ok 844 - h id: exact (0.32347) <= max (0.32643)
ok 845 - h cn: exact (0.49310) ~ est (0.49360)
ok 846 - h cn: exact (0.49310) <= max (0.49606)
ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4
ok 848 - q id: exact (0.29174) ~ est (0.29174)
ok 849 - q id: exact (0.29174) <= max (0.29174)
ok 850 - q cn: exact (0.46230) ~ est (0.46230)
ok 851 - q cn: exact (0.46230) <= max (0.46230)
ok 852 - h id: exact (0.30204) ~ est (0.30204)
ok 853 - h id: exact (0.30204) <= max (0.30204)
ok 854 - h cn: exact (0.47862) ~ est (0.47862)
ok 855 - h cn: exact (0.47862) <= max (0.47862)
ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6
ok 857 - q id: exact (0.29064) ~ est (0.29089)
ok 858 - q id: exact (0.29064) <= max (0.29115)
ok 859 - q cn: exact (0.48765) ~ est (0.48670)
ok 860 - q cn: exact (0.48765) <= max (0.48868)
ok 861 - h id: exact (0.29848) ~ est (0.29887)
ok 862 - h id: exact (0.29848) <= max (0.29902)
ok 863 - h cn: exact (0.50108) ~ est (0.50116)
ok 864 - h cn: exact (0.50108) <= max (0.50163)
ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5
ok 866 - q id: exact (0.29510) ~ est (0.29505)
ok 867 - q id: exact (0.29510) <= max (0.29510)
ok 868 - q cn: exact (0.48982) ~ est (0.49039)
ok 869 - q cn: exact (0.48982) <= max (0.49029)
ok 870 - h id: exact (0.30019) ~ est (0.30019)
ok 871 - h id: exact (0.30019) <= max (0.30019)
ok 872 - h cn: exact (0.49906) ~ est (0.49906)
ok 873 - h cn: exact (0.49906) <= max (0.49906)
ok 874 - 503384.MEGABLAST.2
ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5
ok 876 - q id: exact (0.91435) ~ est (0.91435)
ok 877 - q id: exact (0.91435) <= max (0.91435)
ok 878 - q cn: exact (0.91435) ~ est (0.91435)
ok 879 - q cn: exact (0.91435) <= max (0.91435)
ok 880 - h id: exact (0.91157) ~ est (0.91157)
ok 881 - h id: exact (0.91157) <= max (0.91157)
ok 882 - h cn: exact (0.91157) ~ est (0.91157)
ok 883 - h cn: exact (0.91157) <= max (0.91157)
ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9
ok 885 - q id: exact (0.92895) ~ est (0.92895)
ok 886 - q id: exact (0.92895) <= max (0.92895)
ok 887 - q cn: exact (0.92895) ~ est (0.92895)
ok 888 - q cn: exact (0.92895) <= max (0.92895)
ok 889 - h id: exact (0.92854) ~ est (0.92854)
ok 890 - h id: exact (0.92854) <= max (0.92854)
ok 891 - h cn: exact (0.92854) ~ est (0.92854)
ok 892 - h cn: exact (0.92854) <= max (0.92854)
ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3
ok 894 - q id: exact (0.93516) ~ est (0.93516)
ok 895 - q id: exact (0.93516) <= max (0.93516)
ok 896 - q cn: exact (0.93516) ~ est (0.93516)
ok 897 - q cn: exact (0.93516) <= max (0.93516)
ok 898 - h id: exact (0.93651) ~ est (0.93651)
ok 899 - h id: exact (0.93651) <= max (0.93651)
ok 900 - h cn: exact (0.93651) ~ est (0.93651)
ok 901 - h cn: exact (0.93651) <= max (0.93651)
ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3
ok 903 - q id: exact (0.93064) ~ est (0.93064)
ok 904 - q id: exact (0.93064) <= max (0.93064)
ok 905 - q cn: exact (0.93064) ~ est (0.93064)
ok 906 - q cn: exact (0.93064) <= max (0.93064)
ok 907 - h id: exact (0.92885) ~ est (0.92885)
ok 908 - h id: exact (0.92885) <= max (0.92885)
ok 909 - h cn: exact (0.92885) ~ est (0.92885)
ok 910 - h cn: exact (0.92885) <= max (0.92885)
ok 911 - bl2seq.blastx.out
ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6
ok 913 - q id: est (0.71429) = fast (0.71429)
ok 914 - q cn: est (1.00000) = fast (1.00000)
ok 915 - q id: exact (0.70536) ~ est (0.70495)
ok 916 - q id: exact (0.70536) <= max (0.94286)
ok 917 - q cn: exact (0.78810) ~ est (0.78803)
ok 918 - q cn: exact (0.78810) <= max (0.96429)
ok 919 - q id: est (0.35714) = fast (0.35714)
ok 920 - q cn: est (0.57143) = fast (0.57143)
ok 921 - h id: exact (0.61923) ~ est (0.61955)
ok 922 - h id: exact (0.61923) <= max (0.64231)
ok 923 - h cn: exact (0.73077) ~ est (0.73077)
ok 924 - h cn: exact (0.73077) <= max (0.75000)
ok 925 - dnaEbsub_ecoli.wublastx
ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1
ok 927 - q id: est (0.36386) = fast (0.36386)
ok 928 - q cn: est (0.53735) = fast (0.53735)
ok 929 - h id: est (0.36562) = fast (0.36562)
ok 930 - h cn: est (0.53995) = fast (0.53995)
ok 931 - tblastn.out
ok 932 - tile tblastn.out hit 1 \#hsps 2
ok 933 - q id: exact (0.31250) ~ est (0.33325)
ok 934 - q id: exact (0.31250) <= max (0.33333)
ok 935 - q cn: exact (0.44792) ~ est (0.47055)
ok 936 - q cn: exact (0.44792) <= max (0.45833)
ok 937 - h id: exact (0.33333) ~ est (0.33333)
ok 938 - h id: exact (0.33333) <= max (0.33333)
ok 939 - h cn: exact (0.47059) ~ est (0.47059)
ok 940 - h cn: exact (0.47059) <= max (0.47059)
ok 941 - tile tblastn.out hit 2 \#hsps 2
ok 942 - q id: exact (0.68750) ~ est (0.68750)
ok 943 - q id: exact (0.68750) <= max (0.68750)
ok 944 - q cn: exact (0.81250) ~ est (0.81250)
ok 945 - q cn: exact (0.81250) <= max (0.81250)
ok 946 - h id: est (0.66667) = fast (0.66667)
ok 947 - h cn: est (0.77778) = fast (0.77778)
ok 948 - h id: est (0.71429) = fast (0.71429)
ok 949 - h cn: est (0.85714) = fast (0.85714)
ok 950 - dnaEbsub_ecoli.wutblastn
ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1
ok 952 - q id: est (0.36386) = fast (0.36386)
ok 953 - q cn: est (0.53735) = fast (0.53735)
ok 954 - h id: est (0.36562) = fast (0.36562)
ok 955 - h cn: est (0.53995) = fast (0.53995)
ok 956 - HUMBETGLOA.tblastx
ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1
ok 958 - q id: est (0.42308) = fast (0.42308)
ok 959 - q cn: est (0.61538) = fast (0.61538)
ok 960 - h id: est (0.42308) = fast (0.42308)
ok 961 - h cn: est (0.61538) = fast (0.61538)
ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1
ok 963 - q id: est (0.47059) = fast (0.47059)
ok 964 - q cn: est (0.76471) = fast (0.76471)
ok 965 - h id: est (0.47059) = fast (0.47059)
ok 966 - h cn: est (0.76471) = fast (0.76471)
ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1
ok 968 - q id: est (0.36000) = fast (0.36000)
ok 969 - q cn: est (0.56000) = fast (0.56000)
ok 970 - h id: est (0.36000) = fast (0.36000)
ok 971 - h cn: est (0.56000) = fast (0.56000)
ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1
ok 973 - q id: est (0.29268) = fast (0.29268)
ok 974 - q cn: est (0.58537) = fast (0.58537)
ok 975 - h id: est (0.29268) = fast (0.29268)
ok 976 - h cn: est (0.58537) = fast (0.58537)
ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1
ok 978 - q id: est (0.38889) = fast (0.38889)
ok 979 - q cn: est (0.55556) = fast (0.55556)
ok 980 - h id: est (0.38889) = fast (0.38889)
ok 981 - h cn: est (0.55556) = fast (0.55556)
ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1
ok 983 - q id: est (0.43590) = fast (0.43590)
ok 984 - q cn: est (0.51282) = fast (0.51282)
ok 985 - h id: est (0.43590) = fast (0.43590)
ok 986 - h cn: est (0.51282) = fast (0.51282)
ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1
ok 988 - q id: est (0.35714) = fast (0.35714)
ok 989 - q cn: est (0.42857) = fast (0.42857)
ok 990 - h id: est (0.35714) = fast (0.35714)
ok 991 - h cn: est (0.42857) = fast (0.42857)
ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1
ok 993 - q id: est (0.33333) = fast (0.33333)
ok 994 - q cn: est (0.66667) = fast (0.66667)
ok 995 - h id: est (0.33333) = fast (0.33333)
ok 996 - h cn: est (0.66667) = fast (0.66667)
ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2
ok 998 - q id: exact (0.40541) ~ est (0.40541)
ok 999 - q id: exact (0.40541) <= max (0.40541)
ok 1000 - q cn: exact (0.56757) ~ est (0.56757)
ok 1001 - q cn: exact (0.56757) <= max (0.56757)
ok 1002 - h id: est (0.36364) = fast (0.36364)
ok 1003 - h cn: est (0.63636) = fast (0.63636)
ok 1004 - h id: est (0.42308) = fast (0.42308)
ok 1005 - h cn: est (0.53846) = fast (0.53846)
ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1
ok 1007 - q id: est (0.29167) = fast (0.29167)
ok 1008 - q cn: est (0.39583) = fast (0.39583)
ok 1009 - h id: est (0.29167) = fast (0.29167)
ok 1010 - h cn: est (0.39583) = fast (0.39583)
ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1
ok 1012 - q id: est (0.60000) = fast (0.60000)
ok 1013 - q cn: est (0.65000) = fast (0.65000)
ok 1014 - h id: est (0.60000) = fast (0.60000)
ok 1015 - h cn: est (0.65000) = fast (0.65000)
ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1
ok 1017 - q id: est (0.50000) = fast (0.50000)
ok 1018 - q cn: est (0.68182) = fast (0.68182)
ok 1019 - h id: est (0.50000) = fast (0.50000)
ok 1020 - h cn: est (0.68182) = fast (0.68182)
ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1
ok 1022 - q id: est (0.29630) = fast (0.29630)
ok 1023 - q cn: est (0.48148) = fast (0.48148)
ok 1024 - h id: est (0.29630) = fast (0.29630)
ok 1025 - h cn: est (0.48148) = fast (0.48148)
ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1
ok 1027 - q id: est (0.47826) = fast (0.47826)
ok 1028 - q cn: est (0.52174) = fast (0.52174)
ok 1029 - h id: est (0.47826) = fast (0.47826)
ok 1030 - h cn: est (0.52174) = fast (0.52174)
ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1
ok 1032 - q id: est (0.47368) = fast (0.47368)
ok 1033 - q cn: est (0.63158) = fast (0.63158)
ok 1034 - h id: est (0.47368) = fast (0.47368)
ok 1035 - h cn: est (0.63158) = fast (0.63158)
ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1
ok 1037 - q id: est (0.44444) = fast (0.44444)
ok 1038 - q cn: est (0.55556) = fast (0.55556)
ok 1039 - h id: est (0.44444) = fast (0.44444)
ok 1040 - h cn: est (0.55556) = fast (0.55556)
ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1
ok 1042 - q id: est (0.47059) = fast (0.47059)
ok 1043 - q cn: est (0.70588) = fast (0.70588)
ok 1044 - h id: est (0.47059) = fast (0.47059)
ok 1045 - h cn: est (0.70588) = fast (0.70588)
ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1
ok 1047 - q id: est (0.38889) = fast (0.38889)
ok 1048 - q cn: est (0.66667) = fast (0.66667)
ok 1049 - h id: est (0.38889) = fast (0.38889)
ok 1050 - h cn: est (0.66667) = fast (0.66667)
ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1
ok 1052 - q id: est (0.27660) = fast (0.27660)
ok 1053 - q cn: est (0.48936) = fast (0.48936)
ok 1054 - h id: est (0.27660) = fast (0.27660)
ok 1055 - h cn: est (0.48936) = fast (0.48936)
ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1
ok 1057 - q id: est (0.40000) = fast (0.40000)
ok 1058 - q cn: est (0.60000) = fast (0.60000)
ok 1059 - h id: est (0.40000) = fast (0.40000)
ok 1060 - h cn: est (0.60000) = fast (0.60000)
ok 1061 - dnaEbsub_ecoli.wutblastx
ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12
ok 1063 - q id: exact (0.40224) ~ est (0.40912)
ok 1064 - q id: exact (0.40224) <= max (0.42628)
ok 1065 - q cn: exact (0.58494) ~ est (0.58968)
ok 1066 - q cn: exact (0.58494) <= max (0.62179)
ok 1067 - q id: est (0.25352) = fast (0.25352)
ok 1068 - q cn: est (0.47887) = fast (0.47887)
ok 1069 - q id: est (0.37500) = fast (0.37500)
ok 1070 - q cn: est (0.62500) = fast (0.62500)
ok 1071 - q id: exact (0.44118) ~ est (0.44118)
ok 1072 - q id: exact (0.44118) <= max (0.44118)
ok 1073 - q cn: exact (0.54412) ~ est (0.54412)
ok 1074 - q cn: exact (0.54412) <= max (0.54412)
ok 1075 - h id: est (0.25352) = fast (0.25352)
ok 1076 - h cn: est (0.47887) = fast (0.47887)
ok 1077 - h id: exact (0.39848) ~ est (0.40304)
ok 1078 - h id: exact (0.39848) <= max (0.40355)
ok 1079 - h cn: exact (0.58376) ~ est (0.58889)
ok 1080 - h cn: exact (0.58376) <= max (0.58883)
ok 1081 - h id: exact (0.44118) ~ est (0.44118)
ok 1082 - h id: exact (0.44118) <= max (0.44118)
ok 1083 - h cn: exact (0.54412) ~ est (0.54412)
ok 1084 - h cn: exact (0.54412) <= max (0.54412)
ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2
ok 1086 - q id: exact (0.41818) ~ est (0.41818)
ok 1087 - q id: exact (0.41818) <= max (0.41818)
ok 1088 - q cn: exact (0.52727) ~ est (0.52727)
ok 1089 - q cn: exact (0.52727) <= max (0.52727)
ok 1090 - h id: est (0.53333) = fast (0.53333)
ok 1091 - h cn: est (0.66667) = fast (0.66667)
ok 1092 - h id: est (0.37500) = fast (0.37500)
ok 1093 - h cn: est (0.47500) = fast (0.47500)
ok 1094 - bug2942: query m0: range correct
ok 1095 - bug2942: query m1: range correct
ok 1096 - bug2942: query m2: range correct
ok 1097 - bug2942: subject all : range correct
ok 1098 - get_tiled_alns
ok 1099 - got all alns
ok 1100
ok 1101 - aln and qfeat lengths correspond
ok 1102 - q length correct
ok 1103
ok 1104 - features on q and s correspond
ok 1105 - aln and hfeat lengths correspond
ok 1106 - s length correct
ok 1107
ok 1108 - aln and qfeat lengths correspond
ok 1109 - q length correct
ok 1110
ok 1111 - features on q and s correspond
ok 1112 - aln and hfeat lengths correspond
ok 1113 - s length correct
ok 1114
ok 1115 - aln and qfeat lengths correspond
ok 1116 - q length correct
ok 1117
ok 1118 - features on q and s correspond
ok 1119 - aln and hfeat lengths correspond
ok 1120 - s length correct
ok 1121
ok 1122 - aln and qfeat lengths correspond
ok 1123 - q length correct
ok 1124
ok 1125 - features on q and s correspond
ok 1126 - aln and hfeat lengths correspond
ok 1127 - s length correct
ok 1128
ok 1129 - aln and qfeat lengths correspond
ok 1130 - q length correct
ok 1131
ok 1132 - features on q and s correspond
ok 1133 - aln and hfeat lengths correspond
ok 1134 - s length correct
ok 1135
ok 1136 - aln and qfeat lengths correspond
ok 1137 - q length correct
ok 1138
ok 1139 - features on q and s correspond
ok 1140 - aln and hfeat lengths correspond
ok 1141 - s length correct
ok
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 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object 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 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object 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 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object 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 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object 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..1360
ok 1 - use Bio::SearchIO;
ok 2 - Bio::SearchIO->new can handle a Path::Class object
ok 3 - The object isa Bio::Root::IO
ok 4 - Bio::SearchIO->new can handle a Path::Class object
ok 5 - The object 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
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ok 17
ok 18
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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
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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
ok 605
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ok 878
ok 879
ok 880
ok 881
ok 882
ok 883
ok 884
ok 885 - The object isa Bio::Search::Result::ResultI
ok 886
ok 887
ok 888
ok 889
ok 890
ok 891
ok 892
ok 893
ok 894
ok 895
ok 896
ok 897
ok 898
ok 899
ok 900
ok 901
ok 902
ok 903
ok 904
ok 905 - The object isa Bio::Search::Result::ResultI
ok 906
ok 907
ok 908
ok 909
ok 910
ok 911
ok 912
ok 913
ok 914
ok 915
ok 916
ok 917
ok 918
ok 919
ok 920
ok 921
ok 922
ok 923
ok 924
ok 925
ok 926
ok 927
ok 928
ok 929 - The object isa Bio::Search::Result::ResultI
ok 930
ok 931
ok 932
ok 933
ok 934
ok 935
ok 936
ok 937
ok 938
ok 939
ok 940
ok 941
ok 942
ok 943
ok 944
ok 945
ok 946
ok 947
ok 948
ok 949
ok 950
ok 951
ok 952
ok 953 - The object isa Bio::Search::Result::ResultI
ok 954
ok 955
ok 956
ok 957
ok 958
ok 959
ok 960
ok 961
ok 962
ok 963
ok 964
ok 965
ok 966
ok 967
ok 968
ok 969
ok 970
ok 971
ok 972
ok 973
ok 974
ok 975
ok 976
ok 977
ok 978 - The object isa Bio::Search::Result::ResultI
ok 979
ok 980
ok 981
ok 982
ok 983
ok 984
ok 985
ok 986
ok 987
ok 988
ok 989
ok 990
ok 991
ok 992
ok 993
ok 994
ok 995
ok 996
ok 997
ok 998
ok 999
ok 1000
ok 1001
ok 1002
ok 1003
ok 1004
ok 1005
ok 1006 - The object isa Bio::Search::Result::ResultI
ok 1007
ok 1008
ok 1009
ok 1010
ok 1011
ok 1012
ok 1013
ok 1014
ok 1015
ok 1016
ok 1017
ok 1018
ok 1019
ok 1020
ok 1021
ok 1022
ok 1023
ok 1024
ok 1025
ok 1026
ok 1027
ok 1028
ok 1029
ok 1030
ok 1031
ok 1032
ok 1033
ok 1034
ok 1035 - The object isa Bio::Search::Result::ResultI
ok 1036
ok 1037
ok 1038
ok 1039
ok 1040
ok 1041
ok 1042
ok 1043
ok 1044
ok 1045
ok 1046
ok 1047
ok 1048
ok 1049
ok 1050
ok 1051
ok 1052
ok 1053
ok 1054 - blastxml for f.blastxml
ok 1055 - fasta for f.fy
ok 1056 - exonerate for f.exonerate
ok 1057 - blast for f.tblx
ok 1058 - fasta for f.fx
ok 1059 - fasta for f.osearch
ok 1060 - blast for filename.bls
ok 1061 - exonerate for f.exon
ok 1062 - fasta for f.SSEARCH.m9
ok 1063 - blast for filename.blast
ok 1064 - fasta for f.m9
ok 1065 - blast for f.blx
ok 1066 - blastxml for f.xml
ok 1067 - fasta for f.fasta
ok 1068 - fasta for f.fa
ok 1069 - blast for fast.bls
ok 1070 - fasta for f.ssearch
ok 1071 - fasta for f.psearch
ok 1072
ok 1073
ok 1074
ok 1075
ok 1076
ok 1077
ok 1078
ok 1079
ok 1080
ok 1081
ok 1082
ok 1083
ok 1084
ok 1085
ok 1086
ok 1087 - full hit name
ok 1088 - hit accession
ok 1089
ok 1090
ok 1091 - query start
ok 1092 - query start
ok 1093
ok 1094
ok 1095
ok 1096
ok 1097
ok 1098
ok 1099
ok 1100
ok 1101
ok 1102
ok 1103
ok 1104
ok 1105
ok 1106
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ok 1108
ok 1109
ok 1110
ok 1111
ok 1112
ok 1113
ok 1114
ok 1115
ok 1116
ok 1117
ok 1118
ok 1119
ok 1120
ok 1121
ok 1122
ok 1123
ok 1124
ok 1125
ok 1126
ok 1127
ok 1128
ok 1129
ok 1130
ok 1131
ok 1132
ok 1133
ok 1134
ok 1135
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ok 1137
ok 1138
ok 1139
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ok 1150
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ok 1160
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ok 1180
ok 1181
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ok 1349
ok 1350
ok 1351
ok 1352
ok 1353
ok 1354
ok 1355 - testing Bug 3298
ok 1356 - testing Bug 3298
ok 1357 - testing Bug 3298
ok 1358 - testing Bug 3251
ok 1359 - testing Bug 3251
ok 1360 - testing Bug 3251
ok
t/SearchIO/blast_pull.t ................ 
1..289
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
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ok 55
ok 56
ok 57
ok 58
ok 59 - database_name()
ok 60
ok 61
ok 62
ok 63
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ok 189
ok 190
not ok 191 # TODO frac_identical failing!
#   Failed (TODO) test at t/SearchIO/blast_pull.t line 260.
#          got: '0.946'
#     expected: '0.943'
ok 192
ok 193
ok 194
ok 195
ok 196 - Multiblast query test
ok 197 - Multiblast query test
ok 198 - Multiblast query test
ok 199 - Multiblast query test
ok 200
ok 201
ok 202
ok 203 - full hit name
ok 204 - hit accession
ok 205
ok 206 - query start
ok 207 - query start
ok 208
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ok 289
ok

--------------------- WARNING ---------------------
MSG: Did not define the number of conserved matches in the HSP; assuming conserved == identical (247)
---------------------------------------------------
t/SearchIO/blasttable.t ................ 
1..166
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::Search::SearchUtils;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6 - hit1_bits
ok 7 - hit1_name
ok 8 - hsp1_bits
ok 9 - hsp1_gaps
ok 10 - hsp1_he
ok 11 - hsp1_hs
ok 12 - hsp1_hstr
ok 13 - hsp1_qe
ok 14 - hsp1_qs
ok 15 - hsp1_qstr
ok 16 - hsp2_bits
ok 17 - hsp2_gaps
ok 18 - hsp2_he
ok 19 - hsp2_hs
ok 20 - hsp2_hstr
ok 21 - hsp2_qe
ok 22 - hsp2_qs
ok 23 - hsp2_qstr
ok 24 - hsp3_bits
ok 25 - hsp3_gaps
ok 26 - hsp3_he
ok 27 - hsp3_hs
ok 28 - hsp3_hstr
ok 29 - hsp3_qe
ok 30 - hsp3_qs
ok 31 - hsp3_qstr
ok 32 - hsp4_bits
ok 33 - hsp4_gaps
ok 34 - hsp4_he
ok 35 - hsp4_hs
ok 36 - hsp4_hstr
ok 37 - hsp4_qe
ok 38 - hsp4_qs
ok 39 - hsp4_qstr
ok 40 - hsp5_bits
ok 41 - hsp5_gaps
ok 42 - hsp5_he
ok 43 - hsp5_hs
ok 44 - hsp5_hstr
ok 45 - hsp5_qe
ok 46 - hsp5_qs
ok 47 - hsp5_qstr
ok 48 - hsp6_bits
ok 49 - hsp6_gaps
ok 50 - hsp6_he
ok 51 - hsp6_hs
ok 52 - hsp6_hstr
ok 53 - hsp6_qe
ok 54 - hsp6_qs
ok 55 - hsp6_qstr
ok 56 - hsp7_bits
ok 57 - hsp7_gaps
ok 58 - hsp7_he
ok 59 - hsp7_hs
ok 60 - hsp7_hstr
ok 61 - hsp7_qe
ok 62 - hsp7_qs
ok 63 - hsp7_qstr
ok 64 - hsp8_bits
ok 65 - hsp8_gaps
ok 66 - hsp8_he
ok 67 - hsp8_hs
ok 68 - hsp8_hstr
ok 69 - hsp8_qe
ok 70 - hsp8_qs
ok 71 - hsp8_qstr
ok 72 - query_name
ok 73 - The object isa Bio::Search::Result::ResultI
ok 74
ok 75
ok 76 - hit1_bits
ok 77 - hit1_name
ok 78 - hsp1_bits
ok 79 - hsp1_gaps
ok 80 - hsp1_he
ok 81 - hsp1_hs
ok 82 - hsp1_hstr
ok 83 - hsp1_qe
ok 84 - hsp1_qs
ok 85 - hsp1_qstr
ok 86 - hsp2_bits
ok 87 - hsp2_gaps
ok 88 - hsp2_he
ok 89 - hsp2_hs
ok 90 - hsp2_hstr
ok 91 - hsp2_qe
ok 92 - hsp2_qs
ok 93 - hsp2_qstr
ok 94 - hsp3_bits
ok 95 - hsp3_gaps
ok 96 - hsp3_he
ok 97 - hsp3_hs
ok 98 - hsp3_hstr
ok 99 - hsp3_qe
ok 100 - hsp3_qs
ok 101 - hsp3_qstr
ok 102 - hsp4_bits
ok 103 - hsp4_gaps
ok 104 - hsp4_he
ok 105 - hsp4_hs
ok 106 - hsp4_hstr
ok 107 - hsp4_qe
ok 108 - hsp4_qs
ok 109 - hsp4_qstr
ok 110 - hsp5_bits
ok 111 - hsp5_gaps
ok 112 - hsp5_he
ok 113 - hsp5_hs
ok 114 - hsp5_hstr
ok 115 - hsp5_qe
ok 116 - hsp5_qs
ok 117 - hsp5_qstr
ok 118 - hsp6_bits
ok 119 - hsp6_gaps
ok 120 - hsp6_he
ok 121 - hsp6_hs
ok 122 - hsp6_hstr
ok 123 - hsp6_qe
ok 124 - hsp6_qs
ok 125 - hsp6_qstr
ok 126 - hsp7_bits
ok 127 - hsp7_gaps
ok 128 - hsp7_he
ok 129 - hsp7_hs
ok 130 - hsp7_hstr
ok 131 - hsp7_qe
ok 132 - hsp7_qs
ok 133 - hsp7_qstr
ok 134 - hsp8_bits
ok 135 - hsp8_gaps
ok 136 - hsp8_he
ok 137 - hsp8_hs
ok 138 - hsp8_hstr
ok 139 - hsp8_qe
ok 140 - hsp8_qs
ok 141 - hsp8_qstr
ok 142 - query_name
ok 143
ok 144
ok 145
ok 146
ok 147 - hit score
ok 148 - hit raw_score
ok 149 - The object isa Bio::SeqFeatureI
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157 - fixed bug 3343 (percent identity)
ok 158 - side effect of fixing bug 3343 (number of gaps)
ok 159 - The object isa Bio::SeqFeatureI
ok 160
ok 161
ok 162
ok 163 - The object isa Bio::SeqFeatureI
ok 164
ok 165
ok 166
ok
t/SearchIO/blastxml.t .................. 
1..391
ok 1 - use Bio::SearchIO;
ok 2
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4 - database_name()
ok 5 - query_name()
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - database_name()
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60 - query name on HSP
ok 61 - query desc on HSP
ok 62 - hitname
ok 63 - hitdesc
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
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ok 75
ok 76
ok 77
ok 78
ok 79
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ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90 - The object isa Bio::Search::Hit::HitI
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
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ok 153
ok 154
ok 155
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ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168 - query name on HSP
ok 169 - query desc on HSP
ok 170 - hitname
ok 171 - hitdesc
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
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ok 200
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ok 210
ok 211
ok 212
ok 213
ok 214 - query name on HSP
ok 215 - query desc on HSP
ok 216 - hitname
ok 217 - hitdesc
ok 218
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ok 243
ok 244
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ok 246
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ok 249
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ok 255
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ok 257
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ok 391
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 - The object isa Bio::Search::Result::ResultI
ok 3 - Result ERPIN
ok 4 - Result ERPIN reference
ok 5 - Result ERPIN version
ok 6 - Result parameters
ok 7 - Result statistics
ok 8 - Result entries
ok 9 - Result letters
ok 10 - Result database_name
ok 11 - Result num_hits
ok 12 - Result program_reference
ok 13 - Result query_accession
ok 14 - Result query_description
ok 15 - Result query_name
ok 16 - The object isa Bio::Search::Hit::HitI
ok 17 - Hit accession
ok 18 - Hit GI
ok 19 - Hit algorithm
ok 20 - Hit bits
ok 21 - Hit description
ok 22 - Hit length
ok 23 - Hit locus
ok 24 - Hit n
ok 25 - Hit name
ok 26 - Hit num_hsps
ok 27 - Hit overlap
ok 28 - Hit query_length
ok 29 - Hit rank
ok 30 - Hit raw_score
ok 31 - Hit score
ok 32
ok 33 - The object isa Bio::Search::HSP::HSPI
ok 34 - HSP algorithm
ok 35
ok 36 - The object isa Bio::SeqFeature::Similarity
ok 37 - The object isa Bio::SeqFeature::Similarity
ok 38 - HSP frame
ok 39 - HSP gaps
ok 40 - HSP hit isa Bio::SeqFeature::Similarity
ok 41 - HSP hit_string
ok 42 - HSP homology_string
ok 43 - HSP hsp_group
ok 44 - HSP hsp_length
ok 45 - HSP length
ok 46 - HSP links
ok 47 - HSP query isa Bio::SeqFeature::Similarity
ok 48 - HSP query_string
ok 49 - HSP range
ok 50 - HSP rank
ok 51
ok 52 - HSP expect
ok 53 - The object isa Bio::LocatableSeq
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58
ok 59
ok 60 - HSP strand
ok 61
ok 62
ok 63 - ERPIN get_aln warning
ok 64 - The object isa Bio::Search::HSP::HSPI
ok 65 - HSP algorithm
ok 66
ok 67 - The object isa Bio::SeqFeature::Similarity
ok 68 - The object isa Bio::SeqFeature::Similarity
ok 69 - HSP frame
ok 70 - HSP gaps
ok 71 - HSP hit isa Bio::SeqFeature::Similarity
ok 72 - HSP hit_string
ok 73 - HSP homology_string
ok 74 - HSP query_string
ok 75 - HSP hsp_group
ok 76 - HSP hsp_length
ok 77 - HSP length
ok 78 - HSP links
ok 79 - The object isa Bio::SeqFeature::Similarity
ok 80 - HSP range
ok 81 - HSP rank
ok 82
ok 83 - HSP end
ok 84 - HSP expect
ok 85 - The object isa Bio::LocatableSeq
ok 86 - HSP seq_str
ok 87 - HSP start
ok 88 - HSP custom_score
ok 89
ok 90
ok 91 - HSP strand
ok
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
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 # skip no query length available in default output
ok 26
ok 27 # skip no hit length available in default output
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - query_name
ok 47
ok 48 - query_name
ok 49
ok 50 - query_name
ok 51
ok 52
ok
t/SearchIO/fasta.t ..................... 
1..299
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
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ok 51
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ok 206
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ok 215
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ok 217
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ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
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ok 231
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ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
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ok 243
ok 244
ok 245
ok 246
ok 247
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ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267 - TFASTXY
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274
ok 275
ok 276
ok 277
ok 278
ok 279
ok 280
ok 281
ok 282
ok 283
ok 284
ok 285
ok 286 - 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 - The object isa Bio::Search::Hit::HitI
ok 8 - Check the name
ok 9 - Check the hit length
ok 10 - Check the number of hsps
ok 11 - Check the query length
ok 12 - The object isa Bio::Search::HSP::HSPI
ok 13 - Check the algorithm
ok 14 - Count gaps in the query
ok 15 - Count gaps in the hit
ok 16 - Length of the query
ok 17 - Length of the hit
ok 18 - Query sequence
ok 19 - Hit sequence
ok 20 - Check query start
ok 21 - Check query end
ok 22 - Check query end
ok 23 - Check the homology string
ok 24 - Check seq_inds
ok 25 - Check hit start
ok 26 - Check hit end
ok 27 - Check hit end
ok 28 - Did we get a Result? isa Bio::Search::Result::GenericResult
ok 29 - Did we get the expected number of hits?
ok 30 - Did we get the expected algorithm?
ok 31 - Did we get the expected query_name?
ok 32 - The object isa Bio::Search::Hit::HitI
ok 33 - Check the name
ok 34 - Check the hit length
ok 35 - Check the number of hsps
ok 36 - Check the query length
ok 37 - The object isa Bio::Search::HSP::HSPI
ok 38 - Check the algorithm
ok 39 - Count gaps in the query
ok 40 - Count gaps in the hit
ok 41 - Length of the query
ok 42 - Length of the hit
ok 43 - Query sequence
ok 44 - Hit sequence
ok 45 - Check query start
ok 46 - Check query end
ok 47 - Check query end
ok 48 - Check the homology string
ok 49 - Check seq_inds
ok 50 - Check hit start
ok 51 - Check hit end
ok 52 - Check hit end
ok 53 - Can we loop over multiple results properly (expecting 58)?
ok 54 - simple query_name now caught, bug 3021
ok
t/SearchIO/hmmer.t ..................... 
1..327
ok 1 - use Bio::SearchIO;
ok 2 - Check for the correct result reference type
ok 3 - Check algorithm
ok 4 - Check algorithm version
ok 5 - Check hmm_name
ok 6 - Check sequence_file
ok 7 - Check query_name
ok 8 - Check query_description
ok 9 - Check num_hits
ok 10 - Check hit name
ok 11 - Check hit raw_score
ok 12 - Check hit significance
ok 13 - Check for the correct hit reference type
ok 14 - Check num_hsps
ok 15 - Check for hit hmmfrom value
ok 16 - Check for hit hmm to value
ok 17 - Check for query alifrom value
ok 18 - Check for query ali to value
ok 19 - Check for hsp score
ok 20 - Check for hsp c-Evalue
ok 21 - Check for query string
ok 22 - Check for number of gaps in query
ok 23 - Check for hit string
ok 24 - Check for homology string
ok 25 - Check if homology string and hit string have an equal lenght
ok 26 - Check if query string and homology string have an equal lenght
ok 27 - Check for hit hmmfrom value
ok 28 - Check for hit hmm to value
ok 29 - Check for query alifrom value
ok 30 - Check for query ali to value
ok 31 - Check for hsp score
ok 32 - Check for hsp c-Evalue
ok 33 - Check for query string
ok 34 - Check for number of gaps in query
ok 35 - Check for hit string
ok 36 - Check for homology string
ok 37 - Check if homology string and hit string have an equal lenght
ok 38 - Check if query string and homology string have an equal lenght
ok 39 - Check for the correct result reference type
ok 40 - Check algorithm
ok 41 - Check algorithm version
ok 42 - Check hmm_name
ok 43 - Check sequence_file
ok 44 - Check database_name
ok 45 - Check query_name
ok 46 - Check query_description
ok 47 - Check num_hits
ok 48 - Check hit name
ok 49 - Check for hit description
ok 50 - Check hit significance
ok 51 - Check hit raw_score
ok 52 - Check for hsp score
ok 53 - Check for hsp c-Evalue
ok 54 - Check for query alifrom value
ok 55 - Check for query ali to value
ok 56 - Check for hit hmmfrom value
ok 57 - Check for hit hmm to value
ok 58 - Check for query seq_id
ok 59 - Check for hit seq_id
ok 60 - Check for the correct result reference type
ok 61 - Check algorithm
ok 62 - Check algorithm version
ok 63 - Check hmm_name
ok 64 - Check sequence_file
ok 65 - Check query_name
ok 66 - Check query_description
ok 67 - Check num_hits
ok 68 - Check hit name
ok 69 - Check for hit description
ok 70 - Check hit significance
ok 71 - Check hit raw_score
ok 72 - Check for hsp score
ok 73 - Check for hsp evalue
ok 74 - Check for query alifrom value
ok 75 - Check for query ali to value
ok 76 - Check for hit hmmfrom value
ok 77 - Check for hit hmm to value
ok 78 - Check for query seq_id
ok 79 - Check for hit seq_id
ok 80 - Check for hiy string
ok 81 - Check for query string
ok 82 - Check for homology string
ok 83 - Check for nomatch indices in query
ok 84 - Check for nomatch indices in hit
ok 85 - Check for gap indices in query
ok 86 - Check for gap indices in hit
ok 87 - Check for the correct result reference type
ok 88 - Check algorithm
ok 89 - Check algorithm version
ok 90 - Check hmm_name
ok 91 - Check database_name
ok 92 - Check sequence_file
ok 93 - Check query_name
ok 94 - Check query_accession
ok 95 - Check query_description
ok 96 - Check num_hits
ok 97 - Check hit name
ok 98 - Check for hit description
ok 99 - Check hit significance
ok 100 - Check hit raw_score
ok 101 - Check for hsp score
ok 102 - Check for hsp evalue
ok 103 - Check for query alifrom value
ok 104 - Check for query ali to value
ok 105 - Check for hit hmmfrom value
ok 106 - Check for hit hmm to value
ok 107 - Check for query seq_id
ok 108 - Check for hit seq_id
ok 109 - Check for hiy string
ok 110 - Check for homology string
ok 111 - Check for query string
ok 112 - Check hit name
ok 113 - Check for hit description
ok 114 - Check hit significance
ok 115 - Check hit raw_score
ok 116 - Check for hsp seq_str
ok 117 - Check if correct searchio object is returned
ok 118 - Check for the correct result reference type
ok 119 - Check algorithm
ok 120 - Check algorithm version
ok 121 - Check hmm_name
ok 122 - Check sequence_file
ok 123 - Check query_name
ok 124 - Check query_length
ok 125 - Check query_description
ok 126 - Check num_hits
ok 127 - Check for the correct hit reference type
ok 128 - Check hit name
ok 129 - Check for hit description
ok 130 - Check hit raw_score
ok 131 - Check hit significance
ok 132 - Check num_hsps
ok 133 - Check for correct hsp reference type
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 c-Evalue
ok 140 - Check for query string
ok 141 - Check for hit string
ok 142 - Check for homology string
ok 143 - Check for the correct result reference type
ok 144 - Check algorithm
ok 145 - Check algorithm version
ok 146 - Check hmm_name
ok 147 - Check sequence_file
ok 148 - Check query_name
ok 149 - Check query_length
ok 150 - Check query_description
ok 151 - Check num_hits
ok 152 - Check for the correct result reference type
ok 153 - Check algorithm
ok 154 - Check algorithm version
ok 155 - Check hmm_name
ok 156 - Check sequence_file
ok 157 - Check query_name
ok 158 - Check query_length
ok 159 - Check query_description
ok 160 - Check num_hits
ok 161 - Check for the correct hit reference type
ok 162 - Check hit name
ok 163 - Check for hit description
ok 164 - Check hit raw_score
ok 165 - Check hit significance
ok 166 - Check num_hsps
ok 167 - Check for correct hsp reference type
ok 168 - Check for hit envfrom value
ok 169 - Check for hit env to value
ok 170 - Check for query hmmfrom value
ok 171 - Check for query hmm to value
ok 172 - Check for hsp score
ok 173 - Check for hsp c-Evalue
ok 174 - Check for correct hsp reference type
ok 175 - Check for hit envfrom value
ok 176 - Check for hit env to value
ok 177 - Check for query hmmfrom value
ok 178 - Check for query hmm to value
ok 179 - Check for hsp score
ok 180 - Check for hsp c-Evalue
ok 181 - Check for correct hsp reference type
ok 182 - Check for hit envfrom value
ok 183 - Check for hit env to value
ok 184 - Check for query hmmfrom value
ok 185 - Check for query hmm to value
ok 186 - Check for hsp score
ok 187 - Check for hsp c-Evalue
ok 188 - Check for correct hsp reference type
ok 189 - Check for hit envfrom value
ok 190 - Check for hit env to value
ok 191 - Check for query hmmfrom value
ok 192 - Check for query hmm to value
ok 193 - Check for hsp score
ok 194 - Check for hsp c-Evalue
ok 195 - Check for correct hsp reference type
ok 196 - Check for hit envfrom value
ok 197 - Check for hit env to value
ok 198 - Check for query hmmfrom value
ok 199 - Check for query hmm to value
ok 200 - Check for hsp score
ok 201 - Check for hsp c-Evalue
ok 202 - Check for correct hsp reference type
ok 203 - Check for hit envfrom value
ok 204 - Check for hit env to value
ok 205 - Check for query hmmfrom value
ok 206 - Check for query hmm to value
ok 207 - Check for hsp score
ok 208 - Check for hsp c-Evalue
ok 209 - Check for the correct hit reference type
ok 210 - Check hit name
ok 211 - Check for hit description
ok 212 - Check hit raw_score
ok 213 - Check hit significance
ok 214 - Check num_hsps
ok 215 - Check for correct hsp reference type
ok 216 - Check for hit envfrom value
ok 217 - Check for hit env to value
ok 218 - Check for query hmmfrom value
ok 219 - Check for query hmm to value
ok 220 - Check for hsp score
ok 221 - Check for hsp c-Evalue
ok 222 - Check for correct hsp reference type
ok 223 - Check for hit envfrom value
ok 224 - Check for hit env to value
ok 225 - Check for query hmmfrom value
ok 226 - Check for query hmm to value
ok 227 - Check for hsp score
ok 228 - Check for hsp c-Evalue
ok 229 - Check for correct hsp reference type
ok 230 - Check for hit envfrom value
ok 231 - Check for hit env to value
ok 232 - Check for query hmmfrom value
ok 233 - Check for query hmm to value
ok 234 - Check for hsp score
ok 235 - Check for hsp c-Evalue
ok 236 - Check for the correct result reference type
ok 237 - Check algorithm
ok 238 - Check algorithm version
ok 239 - Check hmm_name
ok 240 - Check sequence_file
ok 241 - Check query_name
ok 242 - Check query_length
ok 243 - Check query_description
ok 244 - Check num_hits
ok 245 - Check for the correct hit reference type
ok 246 - Check hit name
ok 247 - Check for hit description
ok 248 - Check hit raw_score
ok 249 - Check hit significance
ok 250 - Check num_hsps
ok 251 - Check for correct hsp reference type
ok 252 - Check hit sequence
ok 253 - Check query sequence
ok 254 - Check for correct hsp reference type
ok 255 - Check hit sequence
ok 256 - Check query sequence
ok 257 - Check for the correct hit reference type
ok 258 - Check hit name
ok 259 - Check for hit description
ok 260 - Check hit raw_score
ok 261 - Check hit significance
ok 262 - Check num_hsps
ok 263 - Check for correct hsp reference type
ok 264 - Check hit sequence
ok 265 - Check query sequence
ok 266 - Check for correct hsp reference type
ok 267 - Check hit sequence
ok 268 - Check query sequence
ok 269 - Check for the correct hit reference type
ok 270 - Check hit name
ok 271 - Check for hit description
ok 272 - Check hit raw_score
ok 273 - Check hit significance
ok 274 - Check num_hsps
ok 275 - Check for correct hsp reference type
ok 276 - Check hit sequence
ok 277 - Check query sequence
ok 278 - Check for correct hsp reference type
ok 279 - Check hit sequence
ok 280 - Check query sequence
ok 281 - Check if loading hmmpfam output via the hmm2 parser directly works
ok 282 - Check for the correct result reference type
ok 283 - Check if loading hmmsearch2 output via the hmm2 parser directly works
ok 284 - Check for the correct result reference type
ok 285 - Check if loading hmmscan output via the hmm3 parser directly works
ok 286 - Check for the correct result reference type
ok 287 - Check if loading hmmsearch3 output via the hmm3 parser directly works
ok 288 - Check for the correct result reference type
ok 289 - Check if selecting the correct hmmpfam parser using -version works
ok 290 - Check for the correct result reference type
ok 291 - Check if selecting the correct hmmsearch2 parser using -version works
ok 292 - Check for the correct result reference type
ok 293 - Check if selecting the correct hmmscan parser using -version works
ok 294 - Check for the correct result reference type
ok 295 - Check if selecting the correct hmmsearch3 parser using -version works
ok 296 - Check for the correct result reference type
ok 297 - Check if reading from a pipe works
ok 298 - Check for the correct result reference type
ok 299 - Check num_hits
ok 300 - bug3376
ok 301 - bug3421 - Check if can correctly parse an HSP with line full of dashes
ok 302 - bug3302 - Check if can parse multiresult hmmer
ok 303 - Check nhmmer algorithm version
ok 304 - Check nhmmer hit name
ok 305 - Check nhmmer hit description
ok 306 - Check nhmmer hit significance
ok 307 - Check nhmmer hit score
ok 308 - Check nhmmer hsp score
ok 309 - Check nhmmer hsp score
ok 310 - Check nhmmer hsp hit start
ok 311 - Check nhmmer hsp hit end
ok 312 - Check nhmmer hsp query start
ok 313 - Check nhmmer hsp query end
ok 314 - Check nhmmer hsp hit strand
ok 315 - Check nhmmer hsp query strand
ok 316 - Check nhmmer hit name
ok 317 - Check nhmmer hit description
ok 318 - Check nhmmer hit significance
ok 319 - Check nhmmer hit score
ok 320 - Check nhmmer hsp score
ok 321 - Check nhmmer hsp score
ok 322 - Check nhmmer hsp query start
ok 323 - Check nhmmer hsp query end
ok 324 - Check nhmmer hsp hit start
ok 325 - Check nhmmer hsp hit end
ok 326 - Check nhmmer hsp hit strand
ok 327 - Check nhmmer hsp query strand
ok
t/SearchIO/hmmer_pull.t ................ 
1..290
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
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t/SearchIO/infernal.t .................. 
1..412
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::Search::Result::ResultI
ok 3 - Result
ok 4 - Result reference
ok 5 - Result version
ok 6 - Result parameters
ok 7 - Result statistics
ok 8 - Result entries
ok 9 - Result letters
ok 10 - Result database_name
ok 11 - Result num_hits
ok 12 - Result program_reference
ok 13 - Result query_accession
ok 14 - Result query_description
ok 15 - Result query_length
ok 16 - Result query_name
ok 17 - The object isa Bio::Search::Hit::HitI
ok 18 - Hit GI
ok 19 - Hit accession
ok 20 - Hit algorithm
ok 21 - Hit bits
ok 22 - Hit description
ok 23 - Hit locus
ok 24 - Hit n
ok 25 - Hit name
ok 26 - Hit num_hsps
ok 27 - Hit length_aln() not implemented
ok 28 - Hit num_unaligned_hit() not implemented
ok 29 - Hit num_unaligned_query() not implemented
ok 30 - Hit num_unaligned_sbjct() not implemented
ok 31 - Hit start not implemented
ok 32 - Hit end not implemented
ok 33 - Hit strand not implemented
ok 34 - Hit logical_length not implemented
ok 35 - Hit frac_aligned_hit not implemented
ok 36 - Hit frac_aligned_query not implemented
ok 37 - Hit frac_conserved not implemented
ok 38 - Hit frac_identical not implemented
ok 39 - Hit matches not implemented
ok 40 - Hit gaps not implemented
ok 41 - Hit frame not implemented
ok 42 - Hit range not implemented
ok 43 - Hit seq_inds not implemented
ok 44 - Hit length
ok 45 - Hit overlap
ok 46 - Hit query_length
ok 47 - Hit rank
ok 48 - Hit raw_score
ok 49 - Hit score
ok 50 - Hit p
ok 51
ok 52 - The object isa Bio::Search::HSP::HSPI
ok 53 - HSP algorithm
ok 54
ok 55 - The object isa Bio::SeqFeature::Similarity
ok 56 - The object isa Bio::SeqFeature::Similarity
ok 57
ok 58
ok 59 - HSP frame
ok 60 - HSP gaps
ok 61 - Hit length
ok 62 - The object isa Bio::Align::AlignI
ok 63 - HSP hit isa Bio::SeqFeature::Similarity
ok 64 - HSP hit_string
ok 65 - HSP homology_string
ok 66 - HSP hsp_group
ok 67 - HSP hsp_length
ok 68 - HSP length
ok 69 - HSP links
ok 70 - HSP n
ok 71 - HSP pvalue
ok 72 - HSP query isa Bio::SeqFeature::Similarity
ok 73 - HSP query_string
ok 74 - HSP range
ok 75 - HSP rank
ok 76
ok 77 - HSP end
ok 78 - HSP expect
ok 79 - HSP seq_inds not implemented
ok 80 - HSP matches not implemented
ok 81 - HSP frac_conserved not implemented
ok 82 - HSP frac_identical not implemented
ok 83 - HSP num_conserved not implemented
ok 84 - HSP num_identical not implemented
ok 85 - HSP percent_identity not implemented
ok 86 - HSP cigar_string not implemented
ok 87 - HSP cigar_string not implemented
ok 88 - The object isa Bio::LocatableSeq
ok 89 - HSP seq_str
ok 90 - HSP start
ok 91 - HSP custom_score
ok 92 - HSP meta
ok 93 - HSP strand
ok 94 - The object isa Bio::Search::HSP::HSPI
ok 95 - HSP algorithm
ok 96
ok 97 - The object isa Bio::SeqFeature::Similarity
ok 98 - The object isa Bio::SeqFeature::Similarity
ok 99 - HSP frame
ok 100 - HSP gaps
ok 101 - The object isa Bio::Align::AlignI
ok 102 - HSP hit isa Bio::SeqFeature::Similarity
ok 103 - HSP hit_string
ok 104 - HSP homology_string
ok 105 - HSP hsp_group
ok 106 - HSP hsp_length
ok 107 - HSP length
ok 108 - HSP links
ok 109 - HSP n
ok 110 - HSP pvalue
ok 111 - HSP query isa Bio::SeqFeature::Similarity
ok 112 - HSP query_string
ok 113 - HSP range
ok 114 - HSP rank
ok 115
ok 116 - HSP end
ok 117 - HSP expect
ok 118 - The object isa Bio::LocatableSeq
ok 119 - HSP seq_str
ok 120 - HSP start
ok 121 - HSP custom_score
ok 122 - HSP meta
ok 123 - HSP strand
ok 124 - The object isa Bio::Search::Result::ResultI
ok 125 - Result CMSEARCH
ok 126 - Result CMSEARCH reference
ok 127 - Result CMSEARCH version
ok 128 - Result parameters
ok 129 - Result statistics
ok 130 - Result entries
ok 131 - Result letters
ok 132 - Result database_name
ok 133 - Result num_hits
ok 134 - Result program_reference
ok 135 - Result query_accession
ok 136 - Result query_description
ok 137 - Result query_length
ok 138 - Result query_name
ok 139 - The object isa Bio::Search::Hit::HitI
ok 140 - Hit GI
ok 141 - Hit accession
ok 142 - Hit algorithm
ok 143 - Hit bits
ok 144 - Hit description
ok 145 - Hit locus
ok 146 - Hit n
ok 147 - Hit name
ok 148 - Hit num_hsps
ok 149 - No p values
ok 150 - Hit length
ok 151 - Hit overlap
ok 152 - Hit query_length
ok 153 - Hit rank
ok 154 - Hit raw_score
ok 155 - Hit score
ok 156
ok 157 - The object isa Bio::Search::HSP::HSPI
ok 158 - HSP algorithm
ok 159
ok 160 - The object isa Bio::SeqFeature::Similarity
ok 161 - The object isa Bio::SeqFeature::Similarity
ok 162
ok 163
ok 164 - HSP frame
ok 165 - HSP gaps
ok 166 - Hit length
ok 167 - The object isa Bio::Align::AlignI
ok 168 - HSP hit isa Bio::SeqFeature::Similarity
ok 169 - HSP hit_string
ok 170 - HSP homology_string
ok 171 - HSP hsp_group
ok 172 - HSP hsp_length
ok 173 - HSP length
ok 174 - HSP links
ok 175 - HSP n
ok 176 - HSP pvalue
ok 177 - HSP query isa Bio::SeqFeature::Similarity
ok 178 - HSP query_string
ok 179 - HSP range
ok 180 - HSP rank
ok 181
ok 182 - HSP end
ok 183 - HSP expect
ok 184 - The object isa Bio::LocatableSeq
ok 185 - HSP seq_str
ok 186 - HSP start
ok 187 - HSP custom_score
ok 188 - HSP meta
ok 189 - HSP strand
ok 190 - The object isa Bio::Search::HSP::HSPI
ok 191 - HSP algorithm
ok 192
ok 193 - The object isa Bio::SeqFeature::Similarity
ok 194 - The object isa Bio::SeqFeature::Similarity
ok 195 - HSP frame
ok 196 - HSP gaps
ok 197 - The object isa Bio::Align::AlignI
ok 198 - HSP hit isa Bio::SeqFeature::Similarity
ok 199 - HSP hit_string
ok 200 - HSP homology_string
ok 201 - HSP hsp_group
ok 202 - HSP hsp_length
ok 203 - HSP length
ok 204 - HSP links
ok 205 - HSP n
ok 206 - HSP pvalue
ok 207 - HSP query isa Bio::SeqFeature::Similarity
ok 208 - HSP query_string
ok 209 - HSP range
ok 210 - HSP rank
ok 211
ok 212 - HSP end
ok 213 - HSP expect
ok 214 - The object isa Bio::LocatableSeq
ok 215 - HSP seq_str
ok 216 - HSP start
ok 217 - HSP custom_score
ok 218 - HSP meta
ok 219 - HSP strand
ok 220 - The object isa Bio::Search::Hit::HitI
ok 221 - Hit accession
ok 222 - Hit GI
ok 223 - Hit algorithm
ok 224 - Hit bits
ok 225 - Hit description
ok 226 - Hit length
ok 227 - Hit locus
ok 228 - Hit n
ok 229 - Hit name
ok 230 - Hit num_hsps
ok 231 - Hit overlap
ok 232 - Hit query_length
ok 233 - Hit rank
ok 234 - Hit raw_score
ok 235 - Hit score
ok 236
ok 237 - The object isa Bio::Search::HSP::HSPI
ok 238 - HSP algorithm
ok 239
ok 240 - The object isa Bio::SeqFeature::Similarity
ok 241 - The object isa Bio::SeqFeature::Similarity
ok 242 - HSP frame
ok 243 - HSP gaps
ok 244 - The object isa Bio::Align::AlignI
ok 245 - HSP hit isa Bio::SeqFeature::Similarity
ok 246 - HSP hit_string
ok 247 - HSP homology_string
ok 248 - HSP hsp_group
ok 249 - HSP hsp_length
ok 250 - HSP length
ok 251 - HSP links
ok 252 - HSP n
ok 253 - HSP query isa Bio::SeqFeature::Similarity
ok 254 - HSP query_string
ok 255 - HSP range
ok 256 - HSP rank
ok 257
ok 258 - HSP end
ok 259 - HSP expect
ok 260 - The object isa Bio::LocatableSeq
ok 261 - HSP seq_str
ok 262 - HSP start
ok 263 - HSP custom_score
ok 264 - HSP meta
ok 265 - HSP strand
ok 266 - HSP meta gap bug
ok 267 - HSP meta
ok 268 - HSP meta
ok 269
ok 270
ok 271 - The object isa Bio::Search::Result::ResultI
ok 272 - Result CMSEARCH
ok 273 - Result CMSEARCH reference
ok 274 - Result CMSEARCH version
ok 275 - Result parameters
ok 276 - Result statistics
ok 277 - Result entries
ok 278 - Result letters
ok 279 - Result database_name
ok 280 - Result num_hits
ok 281 - Result program_reference
ok 282 - Result query_accession
ok 283 - Result query_description
ok 284 - Result query_length
ok 285 - Result query_name
ok 286 - The object isa Bio::Search::Hit::HitI
ok 287 - Hit GI
ok 288 - Hit accession
ok 289 - Hit algorithm
ok 290 - Hit bits
ok 291 - Hit description
ok 292 - Hit locus
ok 293 - Hit n
ok 294 - Hit name
ok 295 - Hit num_hsps
ok 296 - No p values
ok 297 - Hit length
ok 298 - Hit overlap
ok 299 - Hit query_length
ok 300 - Hit rank
ok 301 - Hit raw_score
ok 302 - Hit score
ok 303
ok 304 - The object isa Bio::Search::HSP::HSPI
ok 305 - HSP algorithm
ok 306
ok 307 - The object isa Bio::SeqFeature::Similarity
ok 308 - The object isa Bio::SeqFeature::Similarity
ok 309
ok 310
ok 311 - HSP frame
ok 312 - HSP gaps
ok 313 - Hit length
ok 314 - The object isa Bio::Align::AlignI
ok 315 - HSP hit isa Bio::SeqFeature::Similarity
ok 316 - HSP hit_string
ok 317 - HSP homology_string
ok 318 - HSP hsp_group
ok 319 - HSP hsp_length
ok 320 - HSP length
ok 321 - HSP links
ok 322 - HSP n
ok 323 - HSP pvalue
ok 324 - HSP query isa Bio::SeqFeature::Similarity
ok 325 - HSP query_string
ok 326 - HSP range
ok 327 - HSP rank
ok 328
ok 329 - HSP end
ok 330 - HSP expect
ok 331 - The object isa Bio::LocatableSeq
ok 332 - HSP seq_str
ok 333 - HSP start
ok 334 - HSP custom_score
ok 335 - HSP meta
ok 336 - HSP strand
ok 337 - The object isa Bio::Search::HSP::HSPI
ok 338 - HSP algorithm
ok 339
ok 340 - The object isa Bio::SeqFeature::Similarity
ok 341 - The object isa Bio::SeqFeature::Similarity
ok 342 - HSP frame
ok 343 - HSP gaps
ok 344 - The object isa Bio::Align::AlignI
ok 345 - HSP hit isa Bio::SeqFeature::Similarity
ok 346 - HSP hit_string
ok 347 - HSP homology_string
ok 348 - HSP hsp_group
ok 349 - HSP hsp_length
ok 350 - HSP length
ok 351 - HSP links
ok 352 - HSP n
ok 353 - HSP pvalue
ok 354 - HSP query isa Bio::SeqFeature::Similarity
ok 355 - HSP query_string
ok 356 - HSP range
ok 357 - HSP rank
ok 358
ok 359 - HSP end
ok 360 - HSP expect
ok 361 - The object isa Bio::LocatableSeq
ok 362 - HSP seq_str
ok 363 - HSP start
ok 364 - HSP custom_score
ok 365 - HSP meta
ok 366 - HSP strand
ok 367 - The object isa Bio::Search::Hit::HitI
ok 368 - Hit accession
ok 369 - Hit GI
ok 370 - Hit algorithm
ok 371 - Hit bits
ok 372 - Hit description
ok 373 - Hit length
ok 374 - Hit locus
ok 375 - Hit n
ok 376 - Hit name
ok 377 - Hit num_hsps
ok 378 - Hit overlap
ok 379 - Hit query_length
ok 380 - Hit rank
ok 381 - Hit raw_score
ok 382 - Hit score
ok 383
ok 384 - The object isa Bio::Search::HSP::HSPI
ok 385 - HSP algorithm
ok 386
ok 387 - The object isa Bio::SeqFeature::Similarity
ok 388 - The object isa Bio::SeqFeature::Similarity
ok 389 - HSP frame
ok 390 - HSP gaps
ok 391 - The object isa Bio::Align::AlignI
ok 392 - HSP hit isa Bio::SeqFeature::Similarity
ok 393 - HSP hit_string
ok 394 - HSP homology_string
ok 395 - HSP hsp_group
ok 396 - HSP hsp_length
ok 397 - HSP length
ok 398 - HSP links
ok 399 - HSP n
ok 400 - HSP query isa Bio::SeqFeature::Similarity
ok 401 - HSP query_string
ok 402 - HSP range
ok 403 - HSP rank
ok 404
ok 405 - HSP end
ok 406 - HSP expect
ok 407 - The object isa Bio::LocatableSeq
ok 408 - HSP seq_str
ok 409 - HSP start
ok 410 - HSP custom_score
ok 411 - HSP meta
ok 412 - HSP strand
ok
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 - The object isa Bio::Search::Result::ResultI
ok 3 - Result RNAMOTIF
ok 4 - Result RNAMOTIF reference
ok 5 - Result RNAMOTIF version
ok 6 - Result entries
ok 7 - Result letters
ok 8 - Result database_name
ok 9 - Result num_hits
ok 10 - Result program_reference
ok 11 - Result query_accession
ok 12 - Result query_description
ok 13 - Result query_length
ok 14 - Result query_name
ok 15 - The object isa Bio::Search::Hit::HitI
ok 16 - Hit accession
ok 17 - Hit GI
ok 18 - Hit algorithm
ok 19 - Hit description
ok 20 - Hit length
ok 21 - Hit locus
ok 22 - Hit n
ok 23 - Hit name
ok 24 - Hit num_hsps
ok 25 - Hit overlap
ok 26 - Hit rank
ok 27 - Hit raw_score
ok 28 - Hit score
ok 29
ok 30 - The object isa Bio::Search::HSP::HSPI
ok 31 - HSP algorithm
ok 32
ok 33 - The object isa Bio::SeqFeature::Similarity
ok 34 - The object isa Bio::SeqFeature::Similarity
ok 35 - HSP frame
ok 36 - HSP gaps
ok 37 - RNAMotif get_aln warning
ok 38 - HSP hit isa Bio::SeqFeature::Similarity
ok 39 - HSP hit_string
ok 40 - HSP homology_string
ok 41 - HSP hsp_group
ok 42 - HSP hsp_length
ok 43 - HSP length
ok 44 - HSP links
ok 45 - HSP n
ok 46 - HSP query isa Bio::SeqFeature::Similarity
ok 47 - HSP query_string
ok 48 - HSP range
ok 49 - HSP rank
ok 50
ok 51 - HSP end
ok 52 - HSP expect
ok 53 - The object isa Bio::LocatableSeq
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58 - HSP strand
ok 59
ok 60
ok
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 - The object isa Bio::SearchIO
ok 3 - query_name
ok 4 - query database
ok 5 - database name
ok 6 - name
ok 7 - hsps
ok 8 - total length
ok 9 - start
ok 10 - end
ok 11 - strand
ok 12 - start
ok 13 - end
ok 14 - strand
ok 15 - query string
ok 16 - hit_string
ok 17 - hmmstate string
ok 18
ok 19
ok 20
ok 21 - total length
ok 22 - start
ok 23 - end
ok 24 - strand
ok 25 - start
ok 26 - end
ok 27 - strand
ok 28 - query string
ok 29 - hit_string
ok 30 - hmmstate string
ok 31
ok 32
ok 33
ok 34 - total length
ok 35 - start
ok 36 - end
ok 37 - strand
ok 38 - start
ok 39 - end
ok 40 - strand
ok 41 - query string
ok 42 - hit_string
ok 43 - hmmstate string
ok 44
ok 45
ok 46
ok 47 - query_name
ok 48 - query database
ok 49 - database name
ok 50 - name
ok 51 - hsps
ok 52 - total length
ok 53 - start
ok 54 - end
ok 55 - strand
ok 56 - start
ok 57 - end
ok 58 - strand
ok 59 - query string
ok 60 - hit_string
ok 61 - hmmstate string
ok 62
ok 63
ok 64
ok
t/SearchIO/wise.t ...................... 
1..20
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok
t/Seq/DBLink.t ......................... 
1..131
ok 1 - use Bio::SeqIO;
ok 2 - "swissprot:K1C9_HUMAN"
ok 3 - no double colon
ok 4 - no trailing colon
ok 5 - no double space
ok 6 - dblink value is splittable
ok 7 - "GenBank:Z29074.1"
ok 8 - no double colon
ok 9 - no trailing colon
ok 10 - no double space
ok 11 - dblink value is splittable
ok 12 - "GenPept:CAA82315.1"
ok 13 - no double colon
ok 14 - no trailing colon
ok 15 - no double space
ok 16 - dblink value is splittable
ok 17 - "GenBank:S69510.1"
ok 18 - no double colon
ok 19 - no trailing colon
ok 20 - no double space
ok 21 - dblink value is splittable
ok 22 - "GenPept:AAC60619.1"
ok 23 - no double colon
ok 24 - no trailing colon
ok 25 - no double space
ok 26 - dblink value is splittable
ok 27 - "GenBank:X75015.1"
ok 28 - no double colon
ok 29 - no trailing colon
ok 30 - no double space
ok 31 - dblink value is splittable
ok 32 - "GenPept:CAA52924.1"
ok 33 - no double colon
ok 34 - no trailing colon
ok 35 - no double space
ok 36 - dblink value is splittable
ok 37 - "GenBank:AB001594.1"
ok 38 - no double colon
ok 39 - no trailing colon
ok 40 - no double space
ok 41 - dblink value is splittable
ok 42 - "GenPept:BAA19418.1"
ok 43 - no double colon
ok 44 - no trailing colon
ok 45 - no double space
ok 46 - dblink value is splittable
ok 47 - "GenBank:I37984"
ok 48 - no double colon
ok 49 - no trailing colon
ok 50 - no double space
ok 51 - dblink value is splittable
ok 52 - "HSSP:P08670"
ok 53 - no double colon
ok 54 - no trailing colon
ok 55 - no double space
ok 56 - dblink value is splittable
ok 57 - "IntAct:P35527"
ok 58 - no double colon
ok 59 - no trailing colon
ok 60 - no double space
ok 61 - dblink value is splittable
ok 62 - "Ensembl:ENSG00000171403"
ok 63 - no double colon
ok 64 - no trailing colon
ok 65 - no double space
ok 66 - dblink value is splittable
ok 67 - "KEGG:hsa:3857"
ok 68 - no double colon
ok 69 - no trailing colon
ok 70 - no double space
ok 71 - dblink value is splittable
ok 72 - "HGNC:6447"
ok 73 - no double colon
ok 74 - no trailing colon
ok 75 - no double space
ok 76 - dblink value is splittable
ok 77 - "MIM:144200"
ok 78 - no double colon
ok 79 - no trailing colon
ok 80 - no double space
ok 81 - dblink value is splittable
ok 82 - "MIM:607606"
ok 83 - no double colon
ok 84 - no trailing colon
ok 85 - no double space
ok 86 - dblink value is splittable
ok 87 - "ArrayExpress:P35527"
ok 88 - no double colon
ok 89 - no trailing colon
ok 90 - no double space
ok 91 - dblink value is splittable
ok 92 - "GO:0005200"
ok 93 - no double colon
ok 94 - no trailing colon
ok 95 - no double space
ok 96 - dblink value is splittable
ok 97 - "GO:0008544"
ok 98 - no double colon
ok 99 - no trailing colon
ok 100 - no double space
ok 101 - dblink value is splittable
ok 102 - "InterPro:IPR011000"
ok 103 - no double colon
ok 104 - no trailing colon
ok 105 - no double space
ok 106 - dblink value is splittable
ok 107 - "InterPro:IPR001664"
ok 108 - no double colon
ok 109 - no trailing colon
ok 110 - no double space
ok 111 - dblink value is splittable
ok 112 - "InterPro:IPR002957"
ok 113 - no double colon
ok 114 - no trailing colon
ok 115 - no double space
ok 116 - dblink value is splittable
ok 117 - "Pfam:PF00038"
ok 118 - no double colon
ok 119 - no trailing colon
ok 120 - no double space
ok 121 - dblink value is splittable
ok 122 - "PRINTS:PR01248"
ok 123 - no double colon
ok 124 - no trailing colon
ok 125 - no double space
ok 126 - dblink value is splittable
ok 127 - "PROSITE:PS00226"
ok 128 - no double colon
ok 129 - no trailing colon
ok 130 - no double space
ok 131 - dblink value is splittable
ok
t/Seq/EncodedSeq.t ..................... 
1..37
ok 1 - use Bio::Seq::EncodedSeq;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Location::Simple
ok 12
ok 13
ok 14 - The object isa Bio::Location::Simple
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/Seq/LargeLocatableSeq.t .............. 
1..8
ok 1 - use Bio::Seq::LargeLocatableSeq;
ok 2
ok 3 - The object isa Bio::Seq::LargeSeqI
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Seq/LargePSeq.t ...................... 
1..30
ok 1 - use Bio::Seq::LargePrimarySeq;
ok 2 - use Bio::Seq::LargeSeq;
ok 3 - use Bio::Location::Simple;
ok 4 - use Bio::Location::Fuzzy;
ok 5 - use Bio::Location::Split;
ok 6 - use Bio::SeqIO;
ok 7
ok 8
ok 9 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 10 - Subseq is GGGGT
ok 11
ok 12
ok 13
ok 14 - trunc seq was GGGGTGAA
ok 15
ok 16
ok 17
ok 18 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 19
ok 20 - output via Bio::SeqIO::fasta
ok 21 - Subseq is GGGGT
ok 22 - trunc seq was GGGGTGAA
ok 23
ok 24
ok 25
ok 26 - Sequence is ATGGGGTGGGGT
ok 27 - Subseq is GGGGT
ok 28 - trunc seq was GGGGT
ok 29
ok 30
ok
t/Seq/LocatableSeq.t ................... 
1..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 - The object isa Bio::Location::Simple
ok 13
ok 14
ok 15 - The object isa Bio::Location::Simple
ok 16
ok 17
ok 18
ok 19
not ok 20 # TODO Need to fix columns before start of seq w/ start > 1
#   Failed (TODO) test at t/Seq/LocatableSeq.t line 47.
#          got: 'Bio::Location::Simple=HASH(0x10081fa28)'
#     expected: undef
ok 21
ok 22 - The object 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 - The object isa Bio::Location::Simple
ok 51
ok 52
ok 53 - The object 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 - The reference 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..181
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 - The object 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 - The object isa Bio::IdentifiableI
ok 26 - The object 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 - The object isa Bio::PrimarySeqI
ok 55
ok 56 - The object isa Bio::PrimarySeqI
ok 57
ok 58 - The object isa Bio::PrimarySeqI
ok 59
ok 60 - The object isa Bio::PrimarySeqI
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
not ok 67 - is_circular copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcom()

#   Failed (TODO) test 'is_circular copied through revcom'
#   at t/Seq/PrimarySeq.t line 164.
#          got: undef
#     expected: '0'
not ok 68 - version copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcom()

#   Failed (TODO) test 'version copied through revcom'
#   at t/Seq/PrimarySeq.t line 165.
#          got: undef
#     expected: '47'
not ok 69 - authority copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcom()

#   Failed (TODO) test 'authority copied through revcom'
#   at t/Seq/PrimarySeq.t line 166.
#          got: undef
#     expected: 'bioperl.org'
not ok 70 - namespace copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcom()

#   Failed (TODO) test 'namespace copied through revcom'
#   at t/Seq/PrimarySeq.t line 167.
#          got: ''
#     expected: 't'
not ok 71 - namespace_string copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcom()

#   Failed (TODO) test 'namespace_string copied through revcom'
#   at t/Seq/PrimarySeq.t line 168.
#          got: ':X677667'
#     expected: 't:X677667.47'
ok 72 - Translation: LVAST
ok 73 - Translation: MVAST
ok 74 - Translation: MVAST
ok 75 - Translation: MVAST*
ok 76 - Translation: M*
ok 77 - Translation: M
ok 78
ok 79 - Translation: MWP
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91 - Alphabet
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 - Bug 2438
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134 - Bug \#2864
ok 135 - Terminator + inside sequence
ok 136
ok 137 - Length method
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 - threw Regexp ((?^:.+))
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169 - threw Regexp ((?^:.+))
ok 170 - Validation
ok 171
ok 172
ok 173 - threw Regexp ((?^:.+))
ok 174
ok 175
ok 176 - _find_orfs 1
ok 177 - orfs are sorted by descending length
ok 178 - got correct -orf => "longest" seq
ok 179 - _find_orfs 1
ok 180 - orfs are sorted by descending length
ok 181 - got correct -orf => "longest" seq
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 - The object isa Bio::SeqFeature::Primer
ok 13
ok 14
ok 15 - The object 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
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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..73
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 - The object 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 - The object isa Bio::IdentifiableI
ok 20 - The object 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
ok 63
ok 64
ok 65 - Bug \#2864
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
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 - The object isa Bio::Seq::SimulatedRead
ok 8 - The object isa Bio::LocatableSeq
ok 9 - The object 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 - The object isa Bio::Seq::PrimaryQual
ok 20 - The object 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 - The object isa Bio::SeqEvolution::DNAPoint
ok 5
ok 6 - The object isa Bio::SeqEvolution::DNAPoint
ok 7
ok 8 - The object isa Bio::SeqEvolution::DNAPoint
ok 9
ok 10
ok 11 - get rate()
ok 12 - get and set rate()
ok 13 - identity()
ok 14 - identity()
ok 15 - pam()
ok 16 - pam()
ok 17 - mutation_count()
ok 18 - mutation_count()
ok 19 - seq_type()
ok 20 - seq_type()
ok 21 - next_seq()
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27 - each_mutation()
ok 28
ok 29
ok 30 - get_alignment_identity()
ok 31
ok 32
ok 33 - get_mutation_counter()
ok 34 - get_sequence_counter()
ok 35 - reset_sequence_counter()
ok 36 - get_sequence_counter() == 0
ok 37
ok 38
ok 39 - The object isa Bio::SimpleAlign
ok
t/SeqFeature/Amplicon.t ................ 
1..21
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqFeature::Primer;
ok 3 - use Bio::SeqFeature::Amplicon;
ok 4 - The object isa Bio::SeqFeature::Amplicon
ok 5 - The object isa Bio::SeqFeature::SubSeq
ok 6
ok 7
ok 8 - The object isa Bio::PrimarySeq
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::PrimarySeq
ok 16
ok 17
ok 18
ok 19
ok 20 - The object 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 .............. 
1..24
ok 1 - use Bio::SeqFeature::Collection;
ok 2 - use Bio::Location::Simple;
ok 3 - use Bio::Tools::GFF;
ok 4 - use Bio::SeqIO;
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/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..362
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 - The object isa Bio::SeqIO
ok 55
ok 56 - The object 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 - The object isa Bio::SeqIO
ok 65
ok 66 - The object 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 - The object 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 - The object isa Bio::Location::SplitLocationI
ok 340
ok 341 - Feature string
ok 342 - First ten nucleotides
ok 343 - Strand
not ok 344 - Start # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'Start'
#   at t/SeqFeature/Generic.t line 328.
#          got: '1'
#     expected: '3981'
not ok 345 - End # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'End'
#   at t/SeqFeature/Generic.t line 329.
#          got: '5386'
#     expected: '136'
not ok 346 - Expected length # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'Expected length'
#   at t/SeqFeature/Generic.t line 330.
#          got: '5386'
#     expected: '1542'
ok 347 - The object isa Bio::Location::SplitLocationI
ok 348
ok 349 - Feature string
ok 350 - First ten nucleotides
ok 351 - Strand
not ok 352 - Start # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'Start'
#   at t/SeqFeature/Generic.t line 328.
#          got: '1'
#     expected: '4497'
not ok 353 - End # TODO Need to define how to deal with start, end length for circular sequences

#   Failed (TODO) test 'End'
#   at t/SeqFeature/Generic.t line 329.
#          got: '5386'
#     expected: '136'
not ok 354 - Expected length # TODO Need to define how to deal with start, end length for circular sequences

#   Failed (TODO) test 'Expected length'
#   at t/SeqFeature/Generic.t line 330.
#          got: '5386'
#     expected: '1026'
ok 355 - The object isa Bio::Location::SplitLocationI
ok 356
ok 357 - Feature string
ok 358 - First ten nucleotides
ok 359 - Strand
not ok 360 - Start # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'Start'
#   at t/SeqFeature/Generic.t line 328.
#          got: '1'
#     expected: '5075'
not ok 361 - End # TODO Need to define how to deal with start, end length for circular sequences

#   Failed (TODO) test 'End'
#   at t/SeqFeature/Generic.t line 329.
#          got: '5386'
#     expected: '136'
not ok 362 - Expected length # TODO Need to define how to deal with start, end length for circular sequences
#   Failed (TODO) test 'Expected length'
#   at t/SeqFeature/Generic.t line 330.
#          got: '5386'
#     expected: '363'
ok
t/SeqFeature/Location.t ................ 
1..103
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Location::Split;
ok 3 - use Bio::Location::Fuzzy;
ok 4 - use Bio::SeqFeature::Generic;
ok 5 - use Bio::SeqFeature::SimilarityPair;
ok 6 - use Bio::SeqFeature::FeaturePair;
ok 7 - The object isa Bio::LocationI
ok 8 - The object isa Bio::RangeI
ok 9 - Bio::Location::Simple tests
ok 10
ok 11
ok 12
ok 13
ok 14 - Bio::SeqFeature::Generic isa Bio::SeqFeatureI
ok 15 - The object isa Bio::RangeI
ok 16
ok 17
ok 18 - Bio::SeqFeature::FeaturePair tests
ok 19
ok 20
ok 21
ok 22 - Bio::SeqFeature::Generic tests
ok 23
ok 24 - Bio::Location::Fuzzy tests
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38 - Bio::Location::Split tests
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55 - Bugfix 1074
ok 56
ok 57
ok 58
ok 59 - Positive length
ok 60
ok 61 - seq_id() on Bio::Location::Split
ok 62
ok 63
ok 64 - The object isa Bio::LocationI
ok 65 - The object isa Bio::RangeI
ok 66 - Bio::Location::Simple EXACT
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - Bio::Location::Simple IN-BETWEEN
ok 73
ok 74
ok 75
ok 76
ok 77 - Testing error handling
ok 78
ok 79
ok 80
ok 81 - use Bio::Location::WidestCoordPolicy;
ok 82 - use Bio::Location::NarrowestCoordPolicy;
ok 83 - use Bio::Location::AvWithinCoordPolicy;
ok 84 - Default coodinate policy
ok 85
ok 86
ok 87
ok 88 - The object isa Bio::Location::WidestCoordPolicy
ok 89 - Narrowest coodinate policy
ok 90
ok 91
ok 92
ok 93 - The object isa Bio::Location::NarrowestCoordPolicy
ok 94 - Average coodinate policy
ok 95
ok 96
ok 97
ok 98 - The object isa Bio::Location::AvWithinCoordPolicy
ok 99 - Widest coodinate policy
ok 100
ok 101
ok 102
ok 103 - The object isa Bio::Location::WidestCoordPolicy
ok
t/SeqFeature/LocationFactory.t ......... 
1..272
ok 1 - use Bio::Factory::FTLocationFactory;
ok 2 - The object isa Bio::Factory::LocationFactoryI
ok 3 - Bio::Location::Simple
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - Location String: J00194:100..202
ok 13
ok 14 - Bio::Location::Fuzzy
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - Location String: 1..?
ok 24
ok 25 - Bio::Location::Fuzzy
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - Location String: (122.133)..(204.221)
ok 35
ok 36 - Bio::Location::Fuzzy
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45 - Location String: (102.110)
ok 46
ok 47 - Bio::Location::Simple
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - Location String: 340..565
ok 57
ok 58 - Bio::Location::Split
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - Location String: join(12..78,134..202)
ok 68
ok 69 - Bio::Location::Fuzzy
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78 - Location String: ?..?
ok 79
ok 80 - Bio::Location::Fuzzy
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - Location String: <345..500
ok 90
ok 91 - Bio::Location::Fuzzy
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100 - Location String: ?22..?64
ok 101
ok 102 - Bio::Location::Simple
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 - Location String: J00194:100..202
ok 112
ok 113 - Bio::Location::Simple
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122 - Location String: 467
ok 123
ok 124 - Bio::Location::Fuzzy
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133 - Location String: (23.45)..600
ok 134
ok 135 - Bio::Location::Simple
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144 - Location String: 123^124
ok 145
ok 146 - Bio::Location::Fuzzy
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155 - Location String: <1..?
ok 156
ok 157 - Bio::Location::Fuzzy
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166 - Location String: 145^177
ok 167
ok 168 - Bio::Location::Fuzzy
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177 - Location String: 22..?64
ok 178
ok 179 - Bio::Location::Fuzzy
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188 - Location String: complement(34..(122.126))
ok 189
ok 190 - Bio::Location::Split
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199 - Location String: complement(join(4918..5163,2691..4571))
ok 200
ok 201 - Bio::Location::Split
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
ok 211
ok 212 - Bio::Location::Fuzzy
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221 - Location String: ?..>393
ok 222
ok 223 - Bio::Location::Fuzzy
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232 - Location String: ?2465..2774
ok 233
ok 234 - Bio::Location::Fuzzy
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243 - Location String: (122.133)..(204.221)
ok 244
ok 245 - Bio::Location::Fuzzy
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254 - Location String: ?..536
ok 255
ok 256 - Bio::Location::Fuzzy
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265 - Location String: <1..888
ok 266
ok 267 - join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294)))
ok 268 - join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))
ok 269 - join(20464..20694,21548..22763,complement(join(314652..314672,232596..232990,231520..231669)))
ok 270 - join(20464..20694,21548..22763,join(complement(231520..231669),complement(232596..232990),complement(314652..314672)))
ok 271 - join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)
ok 272 - order(S67862.1:72..75,join(S67863.1:1..788,1..19))
ok
t/SeqFeature/Primer.t .................. 
1..47
ok 1 - use Bio::SeqFeature::Primer;
ok 2 - use Bio::PrimarySeq;
ok 3 - Implied primer sequence
ok 4 - The object isa Bio::SeqFeature::Primer
ok 5 - The object isa Bio::SeqFeature::SubSeq
ok 6
ok 7
ok 8 - The object isa Bio::PrimarySeqI
ok 9
ok 10 - PrimarySeq primer
ok 11
ok 12
ok 13 - The object 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 - The object isa Bio::LocationI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41 - The object isa Bio::SeqFeature::Primer
ok 42
ok 43
ok 44 - The object isa Bio::SeqFeature::Primer
ok 45 - The object 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 - The object isa Bio::SeqIO
ok 4 - The object isa Bio::PrimarySeqI
ok 5 - The object isa Bio::SeqAnalysisParserI
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::PrimarySeqI
ok 10 - The object isa Bio::SeqAnalysisParserI
ok 11
ok 12
ok 13 - The object isa Bio::SeqAnalysisParserI
ok 14
ok
t/SeqFeature/SubSeq.t .................. 
1..37
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqFeature::SubSeq;
ok 3 - The object isa Bio::SeqFeature::SubSeq
ok 4 - The object isa Bio::SeqFeature::Generic
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::PrimarySeq
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::PrimarySeq
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::PrimarySeq
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::PrimarySeq
ok 26
ok 27
ok 28
ok 29
ok 30 - The object isa Bio::PrimarySeq
ok 31
ok 32
ok 33
ok 34
ok 35 - The object isa Bio::PrimarySeq
ok 36
ok 37
ok
t/SeqFeature/Unflattener.t ............. 
1..11
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::SeqFeature::Tools::Unflattener;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
t/SeqFeature/Unflattener2.t ............ 
1..12
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::SeqFeature::Tools::Unflattener;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/SeqIO/Handler.t ...................... 
1..561
ok 1 - use Bio::SeqIO;
ok 2 - AI129902
ok 3
ok 4
ok 5
ok 6 - NT_021877
ok 7
ok 8
ok 9
ok 10
ok 11 - BAB68554
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - operator overloading in AnnotationI is deprecated
ok 22 - NC_006346
ok 23
ok 24
ok 25 - U71225
ok 26
ok 27 - AB077698
ok 28
ok 29 - DQ018368
ok 30 - D10483
ok 31
ok 32
ok 33
ok 34 - bug 1487
ok 35
ok 36 - bug 1647
ok 37
ok 38
ok 39 - bug 1673
ok 40
ok 41
ok 42
ok 43 - AF165282
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52 - species parsing incorrect for genbank
ok 53 - genus duplicated in genbank parsing
ok 54
ok 55
ok 56 - species parsing incorrect for genbank
ok 57 - genus duplicated in genbank parsing
ok 58
ok 59
ok 60 - species parsing incorrect for genbank
ok 61 - genus duplicated in genbank parsing
ok 62
ok 63 - streaming
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69 - Total number of sequences in test file
ok 70
ok 71 - Fuzzy in
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83 - Fuzzy out
ok 84 - BK000016
ok 85
ok 86 - BK000016
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101 - BK000016
ok 102 - roundtrip
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120 - revcomp split location
ok 121 - Bug 1925
ok 122
ok 123
ok 124 - wgs
ok 125
ok 126 - wgs_scafld
ok 127
ok 128 - wgs_scafld
ok 129
ok 130
ok 131 - BC000007
ok 132 - BK000016-tpa.gbk
ok 133 - ay116458.gb
ok 134 - ay149291.gb
ok 135 - NC_006346.gb
ok 136 - ay007676.gb
ok 137 - dq519393.gb
ok 138
ok 139 - swissprot:K1C9_HUMAN
ok 140
ok 141 - swissprot
ok 142
ok 143 - GenBank:Z29074.1
ok 144
ok 145 - GenBank
ok 146
ok 147 - GenPept:CAA82315.1
ok 148
ok 149 - GenPept
ok 150
ok 151 - GenBank:S69510.1
ok 152
ok 153 - GenBank
ok 154
ok 155 - GenPept:AAC60619.1
ok 156
ok 157 - GenPept
ok 158
ok 159 - GenBank:X75015.1
ok 160
ok 161 - GenBank
ok 162
ok 163 - GenPept:CAA52924.1
ok 164
ok 165 - GenPept
ok 166
ok 167 - GenBank:AB001594.1
ok 168
ok 169 - GenBank
ok 170
ok 171 - GenPept:BAA19418.1
ok 172
ok 173 - GenPept
ok 174
ok 175 - GenBank:I37984
ok 176
ok 177 - GenBank
ok 178
ok 179 - HSSP:P08670
ok 180
ok 181 - HSSP
ok 182
ok 183 - IntAct:P35527
ok 184
ok 185 - IntAct
ok 186
ok 187 - Ensembl:ENSG00000171403
ok 188
ok 189 - Ensembl
ok 190
ok 191 - KEGG:hsa:3857
ok 192
ok 193 - KEGG
ok 194
ok 195 - HGNC:6447
ok 196
ok 197 - HGNC
ok 198
ok 199 - MIM:144200
ok 200
ok 201 - MIM
ok 202
ok 203 - MIM:607606
ok 204
ok 205 - MIM
ok 206
ok 207 - ArrayExpress:P35527
ok 208
ok 209 - ArrayExpress
ok 210
ok 211 - GO:0005200
ok 212
ok 213 - GO
ok 214
ok 215 - GO:0008544
ok 216
ok 217 - GO
ok 218
ok 219 - InterPro:IPR011000
ok 220
ok 221 - InterPro
ok 222
ok 223 - InterPro:IPR001664
ok 224
ok 225 - InterPro
ok 226
ok 227 - InterPro:IPR002957
ok 228
ok 229 - InterPro
ok 230
ok 231 - Pfam:PF00038
ok 232
ok 233 - Pfam
ok 234
ok 235 - PRINTS:PR01248
ok 236
ok 237 - PRINTS
ok 238
ok 239 - PROSITE:PS00226
ok 240
ok 241 - PROSITE
ok 242
ok 243 - Bug 2195
ok 244 - Bug 2195
ok 245 - The object isa Bio::Annotation::SimpleValue
ok 246
ok 247 - The object isa Bio::Annotation::SimpleValue
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273 - success reading Embl with ^ location and badly split double quotes
ok 274
ok 275
ok 276 - success writing Embl format with ^ < and > locations
ok 277
ok 278
ok 279
ok 280
ok 281
ok 282
ok 283
ok 284
ok 285
ok 286
ok 287
ok 288
ok 289
ok 290
ok 291
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298
ok 299
ok 300
ok 301
ok 302
ok 303
ok 304
ok 305
ok 306
ok 307
ok 308
ok 309 - genus duplication test
ok 310
ok 311
ok 312 - The object isa Bio::SeqIO
ok 313 - The object isa Bio::Species
ok 314
ok 315
ok 316 - operator overloading in AnnotationI is deprecated
ok 317
ok 318 - dates
ok 319 - dates
ok 320 - dates
ok 321
ok 322 - The object isa Bio::Seq::RichSeqI
ok 323
ok 324
ok 325
ok 326 - operator overloading in AnnotationI is deprecated
ok 327
ok 328
ok 329
ok 330
ok 331 - id is ROA1_HUMAN
ok 332
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339 - operator overloading in AnnotationI is deprecated
ok 340
ok 341
ok 342
ok 343 - The object isa Bio::Seq::RichSeqI
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353 - operator overloading in AnnotationI is deprecated
ok 354
ok 355
ok 356
ok 357 - GC1QBP
ok 358 - HABP1
ok 359 - SF2P32
ok 360 - C1QBP
ok 361
ok 362 - The object isa Bio::Seq::RichSeqI
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369 - F54H12.1
ok 370 - The object isa Bio::Seq::RichSeqI
ok 371
ok 372
ok 373
ok 374
ok 375
ok 376
ok 377
ok 378
ok 379
ok 380
ok 381
ok 382 - The object isa Bio::Seq::RichSeqI
ok 383
ok 384
ok 385
ok 386
ok 387 - The object isa Bio::Seq::RichSeqI
ok 388
ok 389
ok 390
ok 391
ok 392
ok 393
ok 394
ok 395
ok 396
ok 397
ok 398
ok 399
ok 400
ok 401 - The object isa Bio::Seq::RichSeqI
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
ok 416
ok 417
ok 418
ok 419
ok 420
ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
ok 437
ok 438
ok 439
ok 440
ok 441
ok 442
ok 443
ok 444
ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok 451
ok 452
ok 453
ok 454
ok 455
ok 456
ok 457
ok 458
ok 459
ok 460
ok 461
ok 462
ok 463
ok 464
ok 465
ok 466
ok 467
ok 468
ok 469
ok 470
ok 471
ok 472
ok 473
ok 474
ok 475
ok 476
ok 477
ok 478
ok 479
ok 480
ok 481
ok 482
ok 483
ok 484
ok 485 - The object isa Bio::Species
ok 486
ok 487
ok 488
ok 489
ok 490
ok 491
ok 492
ok 493
ok 494
ok 495
ok 496
ok 497
ok 498
ok 499
ok 500
ok 501
ok 502
ok 503
ok 504
ok 505
ok 506
ok 507
ok 508
ok 509
ok 510
ok 511
ok 512
ok 513
ok 514
ok 515
ok 516
ok 517 - The object isa Bio::Species
ok 518
ok 519
ok 520 - operator overloading in AnnotationI is deprecated
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528
ok 529
ok 530
ok 531
ok 532
ok 533
ok 534
ok 535
ok 536
ok 537
ok 538
ok 539
ok 540
ok 541
ok 542
ok 543
ok 544
ok 545
ok 546
ok 547
ok 548
ok 549
ok 550
ok 551 - P39765
ok 552
ok 553
ok 554
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561 - operator overloading in AnnotationI is deprecated
ok
t/SeqIO/MultiFile.t .................... 
1..3
ok 1 - use Bio::SeqIO::MultiFile;
ok 2
ok 3
ok
t/SeqIO/Multiple_fasta.t ............... 
1..9
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - all sequences in the file
ok
t/SeqIO/SeqBuilder.t ................... 
1..137
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41 - The object isa Bio::Factory::ObjectBuilderI
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
t/SeqIO/SeqIO.t ........................ 
1..51
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4 - ID for format gcg
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - ID for format fasta
ok 11
ok 12
ok 13
ok 14 - accession.version
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - ID for format pir
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - ID for format tab
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - ID for format ace
ok 38
ok 39
ok 40
ok 41
ok 42 - use Algorithm::Diff;
ok 43 - use IO::ScalarArray;
ok 44 - use IO::String;
ok 45
ok 46
ok 47
not ok 48 - Must pass a file or file handle # TODO file/fh-based tests should be in Bio::Root::IO, see issue #3204
#   Failed (TODO) test 'Must pass a file or file handle'
#   at t/SeqIO/SeqIO.t line 123.
# expecting: Regexp ((?^:No file, fh, or string argument provided))
# found: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: Could not guess format from file/fh
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::SeqIO::new Bio/SeqIO.pm:403
# STACK: Test::Exception::throws_ok t/SeqIO/SeqIO.t:122
# STACK: t/SeqIO/SeqIO.t:123
# -----------------------------------------------------------
# )
ok 49 - Must pass a file or file handle
ok 50 - Must pass a file or file handle
ok 51 - Must pass a real file
ok
t/SeqIO/Splicedseq.t ................... 
1..14
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - get_SeqFeatures()
ok 12 - protein sequence
ok 13 - nucleotide sequence - correct CDS range
ok 14 - nucleotide length
ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t .......................... 
1..7
ok 1 - use Bio::SeqIO;
ok 2 - number of sequence objects
ok 3 - unescaping of characters, Name; 4% strewn with \ various / escaped characters
ok 4 - alphabets detected
ok 5 - alphabets detected
ok 6 - writing sequence
ok 7 - test output
ok
t/SeqIO/agave.t ........................ 
1..8
ok 1 - use Bio::SeqIO::agave;
not ok 2 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for agave format -- no sample file to test against
ok
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t .................... 
1..2
ok 1 - use Bio::SeqIO;
not ok 2 # TODO Output doesn't exists on darwin
#   Failed (TODO) test at t/SeqIO/asciitree.t line 39.
ok
t/SeqIO/bsml.t ......................... 
1..16
ok 1 - use XML::DOM;
ok 2 - use Bio::SeqIO::bsml;
ok 3 - The object isa Bio::Seq::RichSeqI
ok 4 - got correct number of refs
ok 5 - display_id
ok 6 - molecule
ok 7 - is_circular
ok 8 - dates
ok 9 - accession_number
ok 10 - seq_version
ok 11 - got correct number of SeqFeatures
ok 12 - feature start
ok 13 - feature end
ok 14 - get_tag_values db_xref
ok 15 - get_Annotations reference
ok 16 - get_Annotations dblink
ok
t/SeqIO/bsml_sax.t ..................... 
1..15
ok 1 - use Bio::SeqIO;
ok 2 - The object isa Bio::Seq::RichSeqI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/SeqIO/chadoxml.t ..................... 
1..8
ok 1 - use Bio::SeqIO::chadoxml;
not ok 2 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
ok
t/SeqIO/chaos.t ........................ 
1..8
ok 1 - use Bio::SeqIO::chaos;
not ok 2 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for chaos format -- no sample file to test against
ok
t/SeqIO/chaosxml.t ..................... 
1..2
ok 1 - use Bio::SeqIO;
ok 2
ok
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ......................... 
1..96
ok 1 - use Bio::SeqIO::embl;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 - success reading Embl with ^ location and badly split double quotes
ok 25
ok 26 - success writing Embl format with ^ < and > locations
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54 - genus duplication test
ok 55
ok 56
ok 57
ok 58
ok 59 - CDS - accession on PA line
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - CDS - OX tagname
ok 68 - CDS - OX database
ok 69 - CDS - OX primary_id
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85 - Check if product was parsed correctly
ok 86 - Parse long qualifier
ok 87
ok 88 - TaxID set correctly
ok 89 - The read sequence has a species object
ok 90 - NCBI TaxID has roundtripped
ok 91 - Name has roundtripped
ok 92 - TaxID set correctly
ok 93 - The read sequence has a species object
ok 94 - The taxid of the source feature overrides that of the OX line
ok 95 - Name has roundtripped
ok 96 - The ID field was written correctly
ok
t/SeqIO/entrezgene.t ................... 
1..1422
ok 1 - use Bio::SeqIO::entrezgene;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - correct number of loops for T3
ok 10
ok 11 - correct number of loops for T4
ok 12 - correct number of loops for T5
ok 13 - correct number of loops for T6
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - correct number of loops for T7
ok 20 - correct number of loops for T8
ok 21
ok 22
ok 23
ok 24 - correct number of loops for T10
ok 25 - correct number of loops for T11a
ok 26 - correct number of loops for T11a
ok 27 - correct number of loops for T11a
ok 28 - correct number of loops for T11
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - correct number of loops for T12
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 - correct number of loops for T15
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65 - correct number of loops for T3
ok 66
ok 67 - correct number of loops for T4
ok 68 - correct number of loops for T5
ok 69 - correct number of loops for T6
ok 70
ok 71
ok 72
ok 73 - correct number of loops for T7
ok 74 - correct number of loops for T8
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 - correct number of loops for T10
ok 132 - correct number of loops for T11a
ok 133 - correct number of loops for T11a
ok 134 - correct number of loops for T11a
ok 135 - correct number of loops for T11
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 - correct number of loops for T15
ok 168
ok 169
ok 170
ok 171
ok 172 - correct number of loops for T3
ok 173
ok 174 - correct number of loops for T4
ok 175 - correct number of loops for T5
ok 176 - correct number of loops for T6
ok 177 - correct number of loops for T7
ok 178 - correct number of loops for T8
ok 179
ok 180 - correct number of loops for T10
ok 181 - correct number of loops for T11a
ok 182 - correct number of loops for T11
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189 - correct number of loops for T15
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195 - correct number of loops for T3
ok 196
ok 197 - correct number of loops for T4
ok 198 - correct number of loops for T5
ok 199 - correct number of loops for T6
ok 200
ok 201 - correct number of loops for T7
ok 202 - correct number of loops for T8
ok 203
ok 204 - correct number of loops for T10
ok 205 - correct number of loops for T11
ok 206 - correct number of loops for T15
ok 207
ok 208
ok 209
ok 210
ok 211 - correct number of loops for T3
ok 212 - correct number of loops for T4
ok 213 - correct number of loops for T5
ok 214
ok 215 - correct number of loops for T6
ok 216
ok 217 - correct number of loops for T7
ok 218 - correct number of loops for T8
ok 219
ok 220 - correct number of loops for T10
ok 221 - correct number of loops for T11
ok 222 - correct number of loops for T15
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228 - correct number of loops for T3
ok 229 - correct number of loops for T4
ok 230 - correct number of loops for T5
ok 231
ok 232 - correct number of loops for T6
ok 233
ok 234 - correct number of loops for T7
ok 235 - correct number of loops for T8
ok 236
ok 237 - correct number of loops for T10
ok 238 - correct number of loops for T11
ok 239 - correct number of loops for T15
ok 240
ok 241
ok 242
ok 243
ok 244 - correct number of loops for T3
ok 245 - correct number of loops for T4
ok 246 - correct number of loops for T5
ok 247
ok 248 - correct number of loops for T6
ok 249
ok 250 - correct number of loops for T7
ok 251 - correct number of loops for T8
ok 252
ok 253 - correct number of loops for T10
ok 254 - correct number of loops for T11
ok 255 - correct number of loops for T15
ok 256
ok 257
ok 258
ok 259
ok 260 - correct number of loops for T3
ok 261 - correct number of loops for T4
ok 262 - correct number of loops for T5
ok 263 - correct number of loops for T6
ok 264 - correct number of loops for T7
ok 265 - correct number of loops for T8
ok 266
ok 267 - correct number of loops for T10
ok 268
ok 269 - correct number of loops for T11a
ok 270 - correct number of loops for T11a
ok 271 - correct number of loops for T11a
ok 272 - correct number of loops for T11
ok 273 - correct number of loops for T15
ok 274
ok 275
ok 276
ok 277
ok 278 - correct number of loops for T3
ok 279
ok 280 - correct number of loops for T4
ok 281 - correct number of loops for T5
ok 282 - correct number of loops for T6
ok 283
ok 284 - correct number of loops for T7
ok 285 - correct number of loops for T8
ok 286
ok 287
ok 288
ok 289
ok 290
ok 291
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298
ok 299
ok 300
ok 301
ok 302
ok 303
ok 304
ok 305
ok 306
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312
ok 313
ok 314
ok 315
ok 316
ok 317
ok 318
ok 319
ok 320
ok 321
ok 322
ok 323
ok 324
ok 325
ok 326
ok 327 - correct number of loops for T10
ok 328 - correct number of loops for T11a
ok 329
ok 330 - correct number of loops for T11a
ok 331 - correct number of loops for T11a
ok 332 - correct number of loops for T11
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339
ok 340
ok 341
ok 342
ok 343
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353
ok 354
ok 355
ok 356
ok 357
ok 358
ok 359
ok 360
ok 361
ok 362
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369
ok 370
ok 371
ok 372
ok 373
ok 374
ok 375 - correct number of loops for T15
ok 376
ok 377
ok 378
ok 379
ok 380 - correct number of loops for T3
ok 381 - correct number of loops for T4
ok 382
ok 383 - correct number of loops for T5
ok 384 - correct number of loops for T6
ok 385
ok 386 - correct number of loops for T7
ok 387
ok 388 - correct number of loops for T8
ok 389
ok 390
ok 391
ok 392
ok 393
ok 394
ok 395
ok 396
ok 397
ok 398
ok 399
ok 400
ok 401
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
ok 416
ok 417
ok 418
ok 419
ok 420
ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
ok 437
ok 438
ok 439
ok 440
ok 441
ok 442
ok 443
ok 444
ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok 451
ok 452
ok 453
ok 454
ok 455
ok 456
ok 457
ok 458
ok 459
ok 460
ok 461
ok 462
ok 463
ok 464
ok 465
ok 466 - correct number of loops for T10
ok 467 - correct number of loops for T11a
ok 468 - correct number of loops for T11a
ok 469 - correct number of loops for T11a
ok 470 - correct number of loops for T11
ok 471
ok 472
ok 473
ok 474
ok 475
ok 476
ok 477
ok 478
ok 479
ok 480
ok 481
ok 482
ok 483
ok 484
ok 485
ok 486
ok 487
ok 488
ok 489
ok 490
ok 491
ok 492
ok 493
ok 494
ok 495
ok 496
ok 497
ok 498
ok 499
ok 500
ok 501
ok 502
ok 503
ok 504
ok 505
ok 506
ok 507
ok 508
ok 509
ok 510
ok 511
ok 512
ok 513
ok 514
ok 515
ok 516
ok 517
ok 518
ok 519
ok 520
ok 521
ok 522
ok 523 - correct number of loops for T15
ok 524
ok 525
ok 526
ok 527
ok 528 - correct number of loops for T3
ok 529 - correct number of loops for T4
ok 530 - correct number of loops for T5
ok 531 - correct number of loops for T6
ok 532
ok 533 - correct number of loops for T7
ok 534
ok 535 - correct number of loops for T8
ok 536
ok 537 - correct number of loops for T10
ok 538 - correct number of loops for T11a
ok 539 - correct number of loops for T11
ok 540
ok 541 - correct number of loops for T15
ok 542
ok 543
ok 544
ok 545
ok 546 - correct number of loops for T3
ok 547 - correct number of loops for T4
ok 548 - correct number of loops for T5
ok 549 - correct number of loops for T6
ok 550
ok 551
ok 552
ok 553 - correct number of loops for T7
ok 554 - correct number of loops for T8
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561
ok 562
ok 563
ok 564
ok 565
ok 566
ok 567
ok 568
ok 569
ok 570
ok 571
ok 572
ok 573
ok 574
ok 575
ok 576
ok 577
ok 578 - correct number of loops for T10
ok 579 - correct number of loops for T11a
ok 580 - correct number of loops for T11a
ok 581 - correct number of loops for T11a
ok 582 - correct number of loops for T11
ok 583
ok 584
ok 585
ok 586
ok 587
ok 588
ok 589
ok 590
ok 591
ok 592
ok 593
ok 594
ok 595
ok 596
ok 597
ok 598
ok 599
ok 600
ok 601
ok 602
ok 603
ok 604
ok 605
ok 606
ok 607
ok 608
ok 609
ok 610
ok 611
ok 612
ok 613
ok 614
ok 615
ok 616
ok 617 - correct number of loops for T15
ok 618
ok 619
ok 620
ok 621
ok 622 - correct number of loops for T3
ok 623 - correct number of loops for T4
ok 624
ok 625 - correct number of loops for T5
ok 626 - correct number of loops for T6
ok 627
ok 628 - correct number of loops for T7
ok 629
ok 630 - correct number of loops for T8
ok 631
ok 632 - correct number of loops for T10
ok 633 - correct number of loops for T11a
ok 634 - correct number of loops for T11a
ok 635 - correct number of loops for T11a
ok 636 - correct number of loops for T11
ok 637
ok 638
ok 639
ok 640
ok 641
ok 642
ok 643
ok 644
ok 645
ok 646
ok 647
ok 648 - correct number of loops for T15
ok 649
ok 650
ok 651
ok 652
ok 653 - correct number of loops for T3
ok 654 - correct number of loops for T4
ok 655
ok 656 - correct number of loops for T5
ok 657 - correct number of loops for T6
ok 658 - correct number of loops for T7
ok 659 - correct number of loops for T8
ok 660
ok 661 - correct number of loops for T10
ok 662 - correct number of loops for T11a
ok 663 - correct number of loops for T11a
ok 664 - correct number of loops for T11a
ok 665 - correct number of loops for T11
ok 666
ok 667
ok 668
ok 669
ok 670
ok 671
ok 672
ok 673
ok 674
ok 675
ok 676
ok 677
ok 678
ok 679
ok 680
ok 681
ok 682
ok 683
ok 684
ok 685
ok 686
ok 687 - correct number of loops for T15
ok 688
ok 689
ok 690
ok 691
ok 692 - correct number of loops for T3
ok 693 - correct number of loops for T4
ok 694 - correct number of loops for T5
ok 695 - correct number of loops for T6
ok 696
ok 697
ok 698 - correct number of loops for T7
ok 699 - correct number of loops for T8
ok 700
ok 701
ok 702
ok 703
ok 704
ok 705 - correct number of loops for T10
ok 706 - correct number of loops for T11a
ok 707 - correct number of loops for T11a
ok 708 - correct number of loops for T11a
ok 709 - correct number of loops for T11
ok 710
ok 711
ok 712
ok 713
ok 714
ok 715
ok 716
ok 717
ok 718
ok 719
ok 720
ok 721
ok 722
ok 723
ok 724
ok 725
ok 726
ok 727
ok 728
ok 729
ok 730
ok 731
ok 732
ok 733
ok 734 - correct number of loops for T15
ok 735
ok 736
ok 737
ok 738
ok 739 - correct number of loops for T3
ok 740 - correct number of loops for T4
ok 741 - correct number of loops for T5
ok 742 - correct number of loops for T6
ok 743 - correct number of loops for T7
ok 744 - correct number of loops for T8
ok 745
ok 746 - correct number of loops for T10
ok 747 - correct number of loops for T11
ok 748 - correct number of loops for T15
ok 749
ok 750
ok 751
ok 752
ok 753 - correct number of loops for T3
ok 754 - correct number of loops for T4
ok 755 - correct number of loops for T5
ok 756 - correct number of loops for T6
ok 757 - correct number of loops for T7
ok 758 - correct number of loops for T8
ok 759
ok 760 - correct number of loops for T10
ok 761 - correct number of loops for T11
ok 762 - correct number of loops for T15
ok 763
ok 764
ok 765
ok 766
ok 767 - correct number of loops for T3
ok 768 - correct number of loops for T4
ok 769
ok 770 - correct number of loops for T5
ok 771 - correct number of loops for T6
ok 772
ok 773
ok 774
ok 775 - correct number of loops for T7
ok 776 - correct number of loops for T8
ok 777
ok 778 - correct number of loops for T10
ok 779 - correct number of loops for T11a
ok 780 - correct number of loops for T11
ok 781
ok 782
ok 783
ok 784
ok 785
ok 786
ok 787
ok 788
ok 789
ok 790
ok 791
ok 792 - correct number of loops for T15
ok 793
ok 794
ok 795
ok 796
ok 797
ok 798 - correct number of loops for T3
ok 799 - correct number of loops for T4
ok 800 - correct number of loops for T5
ok 801 - correct number of loops for T6
ok 802 - correct number of loops for T7
ok 803 - correct number of loops for T8
ok 804
ok 805 - correct number of loops for T10
ok 806 - correct number of loops for T11
ok 807 - correct number of loops for T15
ok 808
ok 809
ok 810
ok 811
ok 812 - correct number of loops for T3
ok 813 - correct number of loops for T4
ok 814 - correct number of loops for T5
ok 815 - correct number of loops for T6
ok 816 - correct number of loops for T7
ok 817 - correct number of loops for T8
ok 818
ok 819 - correct number of loops for T10
ok 820 - correct number of loops for T11
ok 821 - correct number of loops for T15
ok 822
ok 823
ok 824
ok 825
ok 826
ok 827 - correct number of loops for T3
ok 828 - correct number of loops for T4
ok 829 - correct number of loops for T5
ok 830 - correct number of loops for T6
ok 831 - correct number of loops for T7
ok 832 - correct number of loops for T8
ok 833
ok 834 - correct number of loops for T10
ok 835 - correct number of loops for T11
ok 836 - correct number of loops for T15
ok 837
ok 838
ok 839
ok 840
ok 841 - correct number of loops for T3
ok 842 - correct number of loops for T4
ok 843 - correct number of loops for T5
ok 844 - correct number of loops for T6
ok 845 - correct number of loops for T7
ok 846 - correct number of loops for T8
ok 847
ok 848 - correct number of loops for T10
ok 849 - correct number of loops for T11
ok 850 - correct number of loops for T15
ok 851
ok 852
ok 853
ok 854
ok 855 - correct number of loops for T3
ok 856 - correct number of loops for T4
ok 857 - correct number of loops for T5
ok 858 - correct number of loops for T6
ok 859 - correct number of loops for T7
ok 860 - correct number of loops for T8
ok 861
ok 862 - correct number of loops for T10
ok 863 - correct number of loops for T11
ok 864 - correct number of loops for T15
ok 865
ok 866
ok 867
ok 868
ok 869 - correct number of loops for T3
ok 870 - correct number of loops for T4
ok 871 - correct number of loops for T5
ok 872 - correct number of loops for T6
ok 873 - correct number of loops for T7
ok 874 - correct number of loops for T8
ok 875
ok 876 - correct number of loops for T10
ok 877 - correct number of loops for T11
ok 878 - correct number of loops for T15
ok 879
ok 880
ok 881
ok 882
ok 883 - correct number of loops for T3
ok 884 - correct number of loops for T4
ok 885 - correct number of loops for T5
ok 886 - correct number of loops for T6
ok 887 - correct number of loops for T7
ok 888 - correct number of loops for T8
ok 889
ok 890 - correct number of loops for T10
ok 891 - correct number of loops for T11
ok 892 - correct number of loops for T15
ok 893
ok 894
ok 895
ok 896
ok 897 - correct number of loops for T3
ok 898 - correct number of loops for T4
ok 899
ok 900 - correct number of loops for T5
ok 901 - correct number of loops for T6
ok 902
ok 903
ok 904
ok 905 - correct number of loops for T7
ok 906 - correct number of loops for T8
ok 907
ok 908
ok 909
ok 910 - correct number of loops for T10
ok 911
ok 912 - correct number of loops for T11a
ok 913 - correct number of loops for T11
ok 914
ok 915
ok 916
ok 917
ok 918
ok 919
ok 920
ok 921
ok 922
ok 923
ok 924
ok 925
ok 926
ok 927
ok 928
ok 929
ok 930
ok 931 - correct number of loops for T13/14
ok 932
ok 933
ok 934
ok 935
ok 936
ok 937
ok 938
ok 939
ok 940
ok 941
ok 942
ok 943
ok 944
ok 945
ok 946
ok 947
ok 948
ok 949 - correct number of loops for T15
ok 950
ok 951
ok 952
ok 953
ok 954 - correct number of loops for T3
ok 955 - correct number of loops for T4
ok 956 - correct number of loops for T5
ok 957 - correct number of loops for T6
ok 958 - correct number of loops for T7
ok 959 - correct number of loops for T8
ok 960
ok 961 - correct number of loops for T10
ok 962 - correct number of loops for T11
ok 963 - correct number of loops for T15
ok 964
ok 965
ok 966
ok 967
ok 968 - correct number of loops for T3
ok 969 - correct number of loops for T4
ok 970 - correct number of loops for T5
ok 971 - correct number of loops for T6
ok 972 - correct number of loops for T7
ok 973 - correct number of loops for T8
ok 974
ok 975 - correct number of loops for T10
ok 976 - correct number of loops for T11
ok 977 - correct number of loops for T15
ok 978
ok 979
ok 980
ok 981
ok 982 - correct number of loops for T3
ok 983 - correct number of loops for T4
ok 984 - correct number of loops for T5
ok 985 - correct number of loops for T6
ok 986 - correct number of loops for T7
ok 987 - correct number of loops for T8
ok 988
ok 989 - correct number of loops for T10
ok 990 - correct number of loops for T11
ok 991 - correct number of loops for T15
ok 992
ok 993
ok 994
ok 995
ok 996 - correct number of loops for T3
ok 997 - correct number of loops for T4
ok 998 - correct number of loops for T5
ok 999 - correct number of loops for T6
ok 1000
ok 1001
ok 1002 - correct number of loops for T7
ok 1003 - correct number of loops for T8
ok 1004
ok 1005
ok 1006
ok 1007 - correct number of loops for T10
ok 1008 - correct number of loops for T11a
ok 1009 - correct number of loops for T11
ok 1010
ok 1011
ok 1012
ok 1013
ok 1014
ok 1015
ok 1016
ok 1017
ok 1018
ok 1019
ok 1020
ok 1021
ok 1022
ok 1023
ok 1024
ok 1025
ok 1026
ok 1027
ok 1028
ok 1029 - correct number of loops for T15
ok 1030
ok 1031
ok 1032
ok 1033
ok 1034 - correct number of loops for T3
ok 1035 - correct number of loops for T4
ok 1036 - correct number of loops for T5
ok 1037 - correct number of loops for T6
ok 1038
ok 1039 - correct number of loops for T7
ok 1040
ok 1041 - correct number of loops for T8
ok 1042
ok 1043
ok 1044
ok 1045
ok 1046
ok 1047
ok 1048
ok 1049
ok 1050
ok 1051
ok 1052
ok 1053
ok 1054
ok 1055
ok 1056
ok 1057
ok 1058
ok 1059
ok 1060
ok 1061
ok 1062
ok 1063
ok 1064
ok 1065
ok 1066
ok 1067
ok 1068
ok 1069
ok 1070
ok 1071
ok 1072
ok 1073
ok 1074
ok 1075
ok 1076
ok 1077
ok 1078
ok 1079
ok 1080
ok 1081
ok 1082
ok 1083
ok 1084
ok 1085
ok 1086
ok 1087
ok 1088
ok 1089
ok 1090
ok 1091
ok 1092
ok 1093
ok 1094
ok 1095
ok 1096
ok 1097
ok 1098
ok 1099
ok 1100
ok 1101
ok 1102
ok 1103
ok 1104
ok 1105
ok 1106
ok 1107
ok 1108
ok 1109
ok 1110
ok 1111
ok 1112
ok 1113
ok 1114
ok 1115
ok 1116
ok 1117
ok 1118
ok 1119
ok 1120
ok 1121
ok 1122
ok 1123 - correct number of loops for T10
ok 1124 - correct number of loops for T11a
ok 1125 - correct number of loops for T11
ok 1126
ok 1127
ok 1128
ok 1129
ok 1130
ok 1131
ok 1132
ok 1133
ok 1134
ok 1135
ok 1136
ok 1137
ok 1138
ok 1139
ok 1140
ok 1141 - correct number of loops for T15
ok 1142
ok 1143
ok 1144
ok 1145
ok 1146
ok 1147 - correct number of loops for T3
ok 1148 - correct number of loops for T4
ok 1149
ok 1150 - correct number of loops for T5
ok 1151
ok 1152 - correct number of loops for T6
ok 1153
ok 1154
ok 1155
ok 1156
ok 1157 - correct number of loops for T7
ok 1158
ok 1159 - correct number of loops for T8
ok 1160
ok 1161 - correct number of loops for T10
ok 1162 - correct number of loops for T11a
ok 1163 - correct number of loops for T11
ok 1164
ok 1165
ok 1166
ok 1167
ok 1168
ok 1169
ok 1170
ok 1171
ok 1172
ok 1173
ok 1174
ok 1175
ok 1176 - correct number of loops for T15
ok 1177
ok 1178
ok 1179
ok 1180
ok 1181 - correct number of loops for T3
ok 1182 - correct number of loops for T4
ok 1183 - correct number of loops for T5
ok 1184 - correct number of loops for T6
ok 1185
ok 1186
ok 1187
ok 1188 - correct number of loops for T7
ok 1189
ok 1190 - correct number of loops for T8
ok 1191
ok 1192 - correct number of loops for T10
ok 1193 - correct number of loops for T11a
ok 1194 - correct number of loops for T11
ok 1195
ok 1196
ok 1197
ok 1198
ok 1199
ok 1200
ok 1201
ok 1202
ok 1203
ok 1204
ok 1205
ok 1206
ok 1207
ok 1208
ok 1209
ok 1210
ok 1211
ok 1212
ok 1213
ok 1214
ok 1215
ok 1216
ok 1217
ok 1218
ok 1219
ok 1220
ok 1221 - correct number of loops for T13/14
ok 1222
ok 1223
ok 1224
ok 1225
ok 1226
ok 1227
ok 1228
ok 1229
ok 1230
ok 1231 - correct number of loops for T15
ok 1232
ok 1233
ok 1234
ok 1235
ok 1236
ok 1237 - correct number of loops for T3
ok 1238
ok 1239 - correct number of loops for T4
ok 1240
ok 1241 - correct number of loops for T5
ok 1242
ok 1243 - correct number of loops for T6
ok 1244
ok 1245 - correct number of loops for T7
ok 1246
ok 1247 - correct number of loops for T8
ok 1248
ok 1249
ok 1250
ok 1251 - correct number of loops for T10
ok 1252 - correct number of loops for T11a
ok 1253 - correct number of loops for T11
ok 1254
ok 1255
ok 1256
ok 1257
ok 1258
ok 1259
ok 1260
ok 1261
ok 1262
ok 1263
ok 1264
ok 1265
ok 1266
ok 1267 - correct number of loops for T15
ok 1268
ok 1269
ok 1270
ok 1271
ok 1272 - correct number of loops for T3
ok 1273 - correct number of loops for T4
ok 1274 - correct number of loops for T5
ok 1275
ok 1276 - correct number of loops for T6
ok 1277
ok 1278
ok 1279 - correct number of loops for T7
ok 1280 - correct number of loops for T8
ok 1281
ok 1282 - correct number of loops for T10
ok 1283 - correct number of loops for T11a
ok 1284 - correct number of loops for T11a
ok 1285 - correct number of loops for T11a
ok 1286 - correct number of loops for T11a
ok 1287 - correct number of loops for T11
ok 1288
ok 1289
ok 1290
ok 1291
ok 1292 - correct number of loops for T15
ok 1293
ok 1294
ok 1295
ok 1296
ok 1297 - correct number of loops for T3
ok 1298 - correct number of loops for T4
ok 1299 - correct number of loops for T5
ok 1300 - correct number of loops for T6
ok 1301
ok 1302
ok 1303 - correct number of loops for T7
ok 1304 - correct number of loops for T8
ok 1305
ok 1306 - correct number of loops for T10
ok 1307 - correct number of loops for T11a
ok 1308 - correct number of loops for T11a
ok 1309 - correct number of loops for T11a
ok 1310 - correct number of loops for T11a
ok 1311 - correct number of loops for T11
ok 1312
ok 1313
ok 1314
ok 1315
ok 1316 - correct number of loops for T15
ok 1317
ok 1318
ok 1319
ok 1320
ok 1321
ok 1322 - correct number of loops for T3
ok 1323 - correct number of loops for T4
ok 1324 - correct number of loops for T5
ok 1325
ok 1326 - correct number of loops for T6
ok 1327
ok 1328
ok 1329
ok 1330 - correct number of loops for T7
ok 1331 - correct number of loops for T8
ok 1332
ok 1333 - correct number of loops for T10
ok 1334 - correct number of loops for T11a
ok 1335 - correct number of loops for T11a
ok 1336 - correct number of loops for T11a
ok 1337 - correct number of loops for T11a
ok 1338 - correct number of loops for T11
ok 1339
ok 1340
ok 1341
ok 1342
ok 1343
ok 1344
ok 1345
ok 1346
ok 1347 - correct number of loops for T15
ok 1348
ok 1349
ok 1350
ok 1351
ok 1352 - correct number of loops for T3
ok 1353 - correct number of loops for T4
ok 1354 - correct number of loops for T5
ok 1355 - correct number of loops for T6
ok 1356
ok 1357
ok 1358 - correct number of loops for T7
ok 1359 - correct number of loops for T8
ok 1360
ok 1361 - correct number of loops for T10
ok 1362
ok 1363 - correct number of loops for T11a
ok 1364 - correct number of loops for T11a
ok 1365 - correct number of loops for T11a
ok 1366 - correct number of loops for T11a
ok 1367 - correct number of loops for T11
ok 1368
ok 1369
ok 1370
ok 1371
ok 1372 - correct number of loops for T15
ok 1373
ok 1374
ok 1375
ok 1376
ok 1377
ok 1378 - correct number of loops for T3
ok 1379
ok 1380 - correct number of loops for T4
ok 1381 - correct number of loops for T5
ok 1382 - correct number of loops for T6
ok 1383
ok 1384
ok 1385 - correct number of loops for T7
ok 1386 - correct number of loops for T8
ok 1387
ok 1388 - correct number of loops for T10
ok 1389 - correct number of loops for T11a
ok 1390 - correct number of loops for T11a
ok 1391
ok 1392 - correct number of loops for T11a
ok 1393 - correct number of loops for T11a
ok 1394 - correct number of loops for T11
ok 1395
ok 1396
ok 1397
ok 1398
ok 1399 - correct number of loops for T15
ok 1400 - looped through correct number of sequences
ok 1401
ok 1402
ok 1403
ok 1404
ok 1405
ok 1406
ok 1407
ok 1408
ok 1409
ok 1410
ok 1411
ok 1412
ok 1413
ok 1414
ok 1415
ok 1416
ok 1417
ok 1418
ok 1419
ok 1420
ok 1421
ok 1422 - correct number of loops for T18
ok
t/SeqIO/excel.t ........................ 
1..4
ok 1 - use Bio::SeqIO::excel;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::excel->can('next_seq')
ok 4 - Bio::SeqIO::excel->can('write_seq')
ok
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t ........................ 
1..22
ok 1 - use Bio::SeqIO::fasta;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::fasta->can('next_seq')
ok 4 - Bio::SeqIO::fasta->can('write_seq')
ok 5 - The object isa Bio::Seq
ok 6 - sequence
ok 7 - length
ok 8 - primary_id
ok 9 - description
ok 10 - The object isa Bio::Seq
ok 11 - sequence
ok 12 - length
ok 13 - primary_id
ok 14 - description
ok 15 - use Algorithm::Diff;
ok 16 - use IO::ScalarArray;
ok 17 - use IO::String;
ok 18 - fasta format can round-trip
ok 19 - dies with roa1.genbank
ok 20 - dies with test.gcg
ok 21 - dies with test.ace
ok 22 - dies with test.raw
ok
t/SeqIO/fastq.t ........................ 
1..140
ok 1 - use Bio::SeqIO::fastq;
ok 2 - use Bio::Seq::Quality;
ok 3 - bug2335 parses
ok 4 - correct num. seqs in bug2335
ok 5 - sample sequence obtained
ok 6 - The object isa Bio::Seq::Quality
ok 7 - seq() matches bug2335
ok 8 - desc() matches bug2335
ok 9 - display_id() matches bug2335
ok 10 - qual() matches bug2335
ok 11
ok 12 - evil_wrapping parses
ok 13 - correct num. seqs in evil_wrapping
ok 14 - sample sequence obtained
ok 15 - The object isa Bio::Seq::Quality
ok 16 - seq() matches evil_wrapping
ok 17 - desc() matches evil_wrapping
ok 18 - display_id() matches evil_wrapping
ok 19 - qual() matches evil_wrapping
ok 20
ok 21 - example parses
ok 22 - correct num. seqs in example
ok 23 - sample sequence obtained
ok 24 - The object isa Bio::Seq::Quality
ok 25 - seq() matches example
ok 26 - desc() matches example
ok 27 - display_id() matches example
ok 28 - qual() matches example
ok 29
ok 30 - illumina_faked parses
ok 31 - correct num. seqs in illumina_faked
ok 32 - sample sequence obtained
ok 33 - The object isa Bio::Seq::Quality
ok 34 - seq() matches illumina_faked
ok 35 - desc() matches illumina_faked
ok 36 - display_id() matches illumina_faked
ok 37 - qual() matches illumina_faked
ok 38
ok 39 - sanger_93 parses
ok 40 - correct num. seqs in sanger_93
ok 41 - sample sequence obtained
ok 42 - The object isa Bio::Seq::Quality
ok 43 - seq() matches sanger_93
ok 44 - desc() matches sanger_93
ok 45 - display_id() matches sanger_93
ok 46 - qual() matches sanger_93
ok 47
ok 48 - sanger_faked parses
ok 49 - correct num. seqs in sanger_faked
ok 50 - sample sequence obtained
ok 51 - The object isa Bio::Seq::Quality
ok 52 - seq() matches sanger_faked
ok 53 - desc() matches sanger_faked
ok 54 - display_id() matches sanger_faked
ok 55 - qual() matches sanger_faked
ok 56
ok 57 - solexa_example parses
ok 58 - correct num. seqs in solexa_example
ok 59 - sample sequence obtained
ok 60 - The object isa Bio::Seq::Quality
ok 61 - seq() matches solexa_example
ok 62 - desc() matches solexa_example
ok 63 - display_id() matches solexa_example
ok 64 - qual() matches solexa_example
ok 65
ok 66 - solexa_faked parses
ok 67 - correct num. seqs in solexa_faked
ok 68 - sample sequence obtained
ok 69 - The object isa Bio::Seq::Quality
ok 70 - seq() matches solexa_faked
ok 71 - desc() matches solexa_faked
ok 72 - display_id() matches solexa_faked
ok 73 - qual() matches solexa_faked
ok 74
ok 75 - test1_sanger parses
ok 76 - correct num. seqs in test1_sanger
ok 77 - sample sequence obtained
ok 78 - The object isa Bio::Seq::Quality
ok 79 - seq() matches test1_sanger
ok 80 - desc() matches test1_sanger
ok 81 - display_id() matches test1_sanger
ok 82 - qual() matches test1_sanger
ok 83
ok 84 - test2_solexa parses
ok 85 - correct num. seqs in test2_solexa
ok 86 - sample sequence obtained
ok 87 - The object isa Bio::Seq::Quality
ok 88 - seq() matches test2_solexa
ok 89 - desc() matches test2_solexa
ok 90 - display_id() matches test2_solexa
ok 91 - qual() matches test2_solexa
ok 92
ok 93 - test3_illumina parses
ok 94 - correct num. seqs in test3_illumina
ok 95 - sample sequence obtained
ok 96 - The object isa Bio::Seq::Quality
ok 97 - seq() matches test3_illumina
ok 98 - desc() matches test3_illumina
ok 99 - display_id() matches test3_illumina
ok 100 - qual() matches test3_illumina
ok 101
ok 102 - tricky parses
ok 103 - correct num. seqs in tricky
ok 104 - sample sequence obtained
ok 105 - The object isa Bio::Seq::Quality
ok 106 - seq() matches tricky
ok 107 - desc() matches tricky
ok 108 - display_id() matches tricky
ok 109 - qual() matches tricky
ok 110
ok 111 - Conversion from illumina to sanger
ok 112 - Conversion from illumina to illumina
ok 113 - Conversion from illumina to solexa
ok 114 - Conversion from sanger to sanger
ok 115 - Conversion from sanger to illumina
ok 116 - Conversion from sanger to solexa
ok 117 - Conversion from solexa to sanger
ok 118 - Conversion from solexa to illumina
ok 119 - Conversion from solexa to solexa
ok 120 - Exception caught for error_diff_ids
ok 121 - Exception caught for error_long_qual
ok 122 - Exception caught for error_no_qual
ok 123 - Exception caught for error_qual_del
ok 124 - Exception caught for error_qual_escape
ok 125 - Exception caught for error_qual_null
ok 126 - Exception caught for error_qual_space
ok 127 - Exception caught for error_qual_tab
ok 128 - Exception caught for error_qual_unit_sep
ok 129 - Exception caught for error_qual_vtab
ok 130 - Exception caught for error_short_qual
ok 131 - Exception caught for error_spaces
ok 132 - Exception caught for error_tabs
ok 133 - Exception caught for error_trunc_at_plus
ok 134 - Exception caught for error_trunc_at_qual
ok 135 - Exception caught for error_trunc_at_seq
ok 136 - Exception caught for error_trunc_in_plus
ok 137 - Exception caught for error_trunc_in_qual
ok 138 - Exception caught for error_trunc_in_seq
ok 139 - Exception caught for error_trunc_in_title
ok 140 - edge case; single 0 in quality fails
ok
t/SeqIO/flybase_chadoxml.t ............. 
1..8
ok 1 - use Bio::SeqIO::flybase_chadoxml;
not ok 2 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
ok
t/SeqIO/game.t ......................... 
1..24
ok 1 - use Bio::SeqIO::game;
ok 2 - The object isa Bio::SeqIO
ok 3 - The object isa Bio::Seq::RichSeq
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/SeqIO/gbxml.t ........................ 
1..14
ok 1 - use Bio::SeqIO::gbxml;
ok 2 - The object isa Bio::SeqIO
ok 3 - molecule
ok 4 - alphabet
ok 5 - primary_id
ok 6 - display_id
ok 7 - version
ok 8 - is_circular
ok 9 - description
ok 10 - sequence
ok 11 - classification
ok 12 - feat - clone_lib
ok 13 - feat - db_xref
ok 14 - feat - lab_host
ok
t/SeqIO/gcg.t .......................... 
1..17
ok 1 - use Bio::SeqIO::gcg;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::gcg->can('next_seq')
ok 4 - Bio::SeqIO::gcg->can('write_seq')
ok 5 - The object isa Bio::Seq
ok 6 - The object isa Bio::Seq::RichSeq
ok 7 - sequence
ok 8 - length
not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id?
#   Failed (TODO) test 'primary_id'
#   at t/SeqIO/gcg.t line 54.
#          got: 'Bio::PrimarySeq=HASH(0x100ba89e8)'
#     expected: 'roa1_drome'
ok 10 - description
ok 11
ok 12 - The object isa Bio::SeqI
ok 13
ok 14 - use Algorithm::Diff;
ok 15 - use IO::ScalarArray;
ok 16 - use IO::String;
ok 17 - gcg format can round-trip
ok
t/SeqIO/genbank.t ...................... 
1..282
ok 1 - use Bio::SeqIO::genbank;
ok 2 - The object isa Bio::SeqIO
ok 3 - AI129902
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - NT_021877
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - BAB68554
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28 - operator overloading in AnnotationI is deprecated
ok 29 - NC_006346
ok 30
ok 31
ok 32 - U71225
ok 33
ok 34 - AB077698
ok 35
ok 36 - DQ018368
ok 37 - D10483
ok 38
ok 39
ok 40
ok 41 - bug 1487
ok 42
ok 43 - bug 1647
ok 44
ok 45
ok 46 - bug 1673
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52 - AF165282
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61 - species parsing incorrect for genbank
ok 62 - genus duplicated in genbank parsing
ok 63
ok 64
ok 65 - species parsing incorrect for genbank
ok 66 - genus duplicated in genbank parsing
ok 67
ok 68
ok 69 - species parsing incorrect for genbank
ok 70 - genus duplicated in genbank parsing
ok 71
ok 72 - streaming
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78 - Total number of sequences in test file
ok 79
ok 80 - Fuzzy in
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92 - Fuzzy out
ok 93 - BK000016
ok 94
ok 95 - BK000016
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110 - BK000016
ok 111 - roundtrip
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129 - revcomp split location
ok 130 - Bug 1925
ok 131
ok 132
ok 133 - wgs
ok 134
ok 135 - wgs_scafld
ok 136
ok 137 - wgs_scafld
ok 138
ok 139
ok 140 - BC000007
ok 141 - BK000016-tpa.gbk
ok 142 - ay116458.gb
ok 143 - ay149291.gb
ok 144 - NC_006346.gb
ok 145 - ay007676.gb
ok 146 - dq519393.gb
ok 147
ok 148 - swissprot:K1C9_HUMAN
ok 149
ok 150 - swissprot
ok 151
ok 152 - GenBank:Z29074.1
ok 153
ok 154 - GenBank
ok 155
ok 156 - GenPept:CAA82315.1
ok 157
ok 158 - GenPept
ok 159
ok 160 - GenBank:S69510.1
ok 161
ok 162 - GenBank
ok 163
ok 164 - GenPept:AAC60619.1
ok 165
ok 166 - GenPept
ok 167
ok 168 - GenBank:X75015.1
ok 169
ok 170 - GenBank
ok 171
ok 172 - GenPept:CAA52924.1
ok 173
ok 174 - GenPept
ok 175
ok 176 - GenBank:AB001594.1
ok 177
ok 178 - GenBank
ok 179
ok 180 - GenPept:BAA19418.1
ok 181
ok 182 - GenPept
ok 183
ok 184 - GenBank:I37984
ok 185
ok 186 - GenBank
ok 187
ok 188 - HSSP:P08670
ok 189
ok 190 - HSSP
ok 191
ok 192 - IntAct:P35527
ok 193
ok 194 - IntAct
ok 195
ok 196 - Ensembl:ENSG00000171403
ok 197
ok 198 - Ensembl
ok 199
ok 200 - KEGG:hsa:3857
ok 201
ok 202 - KEGG
ok 203
ok 204 - HGNC:6447
ok 205
ok 206 - HGNC
ok 207
ok 208 - MIM:144200
ok 209
ok 210 - MIM
ok 211
ok 212 - MIM:607606
ok 213
ok 214 - MIM
ok 215
ok 216 - ArrayExpress:P35527
ok 217
ok 218 - ArrayExpress
ok 219
ok 220 - GO:0005200
ok 221
ok 222 - GO
ok 223
ok 224 - GO:0008544
ok 225
ok 226 - GO
ok 227
ok 228 - InterPro:IPR011000
ok 229
ok 230 - InterPro
ok 231
ok 232 - InterPro:IPR001664
ok 233
ok 234 - InterPro
ok 235
ok 236 - InterPro:IPR002957
ok 237
ok 238 - InterPro
ok 239
ok 240 - Pfam:PF00038
ok 241
ok 242 - Pfam
ok 243
ok 244 - PRINTS:PR01248
ok 245
ok 246 - PRINTS
ok 247
ok 248 - PROSITE:PS00226
ok 249
ok 250 - PROSITE
ok 251
ok 252 - Bug 2195
ok 253 - Bug 2195
ok 254 - The object isa Bio::Annotation::SimpleValue
ok 255
ok 256 - The object isa Bio::Annotation::SimpleValue
ok 257
ok 258 - P39765
ok 259 - P39765
ok 260 - P39765
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270 - operator overloading in AnnotationI is deprecated
ok 271
ok 272
ok 273
ok 274
ok 275 - bug3375 database is BioProject
ok 276 - bug3375 primary_id is PRJNA15288
ok 277
ok 278
ok 279
ok 280
ok 281
ok 282 - Label is the same
ok
t/SeqIO/interpro.t ..................... 
1..20
ok 1 - use Bio::SeqIO::interpro;
ok 2 - The object isa Bio::SeqIO
ok 3 - seq obj is defined
ok 4 - The object isa Bio::Seq::RichSeq
ok 5 - right number of SeqFeatures
ok 6 - The object isa Bio::SeqFeature::Generic
ok 7 - display_name()
ok 8 - seq object is defined
ok 9 - right number of SeqFeatures
ok 10 - there is no next_seq (correctly)
ok 11 - bug 1908
ok 12 - right number of SeqFeatures
ok 13 - primary_tag()
ok 14 - display_name()
ok 15 - location->end()
ok 16 - right number of dblinks
ok 17 - first primary_id
ok 18 - second primary_id
ok 19 - right number of dblinks
ok 20 - primary_id via dblinks
ok
t/SeqIO/kegg.t ......................... 
1..16
ok 1 - use Bio::SeqIO::kegg;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - The object isa Bio::Seq::RichSeq
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
t/SeqIO/largefasta.t ................... 
1..16
ok 1 - use Bio::SeqIO::largefasta;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
t/SeqIO/lasergene.t .................... 
1..13
ok 1 - use Bio::SeqIO::lasergene;
ok 2
ok 3 - The object isa Bio::SeqIO
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/SeqIO/locuslink.t .................... 
1..26
ok 1 - use Bio::SeqIO::locuslink;
ok 2 - use Bio::SeqFeature::Generic;
ok 3 - use Bio::SeqFeature::AnnotationAdaptor;
ok 4
ok 5 - The object isa Bio::SeqIO
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
t/SeqIO/mbsout.t ....................... 
1..74
ok 1 - use Bio::SeqIO::mbsout;
ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3
ok 3 - The object isa Bio::SeqIO::mbsout
ok 4 - The object isa Bio::SeqIO::mbsout
ok 5 - Get NSITES
ok 6 - Get TRAJ_FILENAME
ok 7 - Get SELPOS
ok 8 - Get TOT_RUN_HAPS
ok 9 - Get MBS_INFO_LINE
ok 10 - Get NFILES
ok 11 - Get POP_MUT_PARAM_PER_SITE
ok 12 - Get POP_RECOMB_PARAM_PER_SITE
ok 13 - Get NEXT_RUN_NUM
ok 14 - Get CURRENT_RUN_SEGSITES
ok 15 - Get RUNS
ok 16 - Get LAST_READ_HAP_NUM
ok 17 - Get NREPS
ok 18 - Get POSITIONS
ok 19 - Get SEGSITES
ok 20 - Get next_hap at beginning of run
ok 21 - Get next_hap after beginning of run
ok 22 - Get next_pop after beginning of pop
ok 23 - Get next_hap
ok 24 - Get next_hap
ok 25 - Get next_run after beginning of run
ok 26 - Get next_run at beginning of run
ok 27 - Get next_run at beginning of run
ok 28 - have all lines been read?
ok 29 - The object isa Bio::SeqIO::mbsout
ok 30 - Get NSITES
ok 31 - Get TRAJ_FILENAME
ok 32 - Get SELPOS
ok 33 - Get TOT_RUN_HAPS
ok 34 - Get MBS_INFO_LINE
ok 35 - Get NFILES
ok 36 - Get POP_MUT_PARAM_PER_SITE
ok 37 - Get POP_RECOMB_PARAM_PER_SITE
ok 38 - Get NEXT_RUN_NUM
ok 39 - Get CURRENT_RUN_SEGSITES
ok 40 - Get RUNS
ok 41 - Get LAST_READ_HAP_NUM
ok 42 - Get NREPS
ok 43 - Get POSITIONS
ok 44 - Get SEGSITES
ok 45 - Get next_hap at beginning of run
ok 46 - Get next_hap after beginning of run
ok 47 - Testing mbsout::outgroup
ok 48 - Get next_run after beginning of run
ok 49 - Get next_run after beginning of run
ok 50 - Get next_run at beginning of run
ok 51 - Get next_hap at beginning of run 2
ok 52 - Get next_run after hap
ok 53 - next run should be 5.
ok 54 - The object isa Bio::SeqIO::mbsout
ok 55 - Get NSITES
ok 56 - Get TRAJ_FILENAME
ok 57 - Get SELPOS
ok 58 - Get TOT_RUN_HAPS
ok 59 - Get MBS_INFO_LINE
ok 60 - Get NFILES
ok 61 - Get POP_MUT_PARAM_PER_SITE
ok 62 - Get POP_RECOMB_PARAM_PER_SITE
ok 63 - Get NEXT_RUN_NUM
ok 64 - Get CURRENT_RUN_SEGSITES
ok 65 - Get RUNS
ok 66 - Get LAST_READ_HAP_NUM
ok 67 - Get NREPS
ok 68 - Get POSITIONS
ok 69 - Get SEGSITES
ok 70 - Get next_run at end/beginning of run
ok 71 - have all lines been read?
ok 72 - Get next_run at eof
ok 73 - Get next_hap at eof
ok 74 - Get next_seq at eof
ok
t/SeqIO/metafasta.t .................... 
1..6
ok 1 - use Bio::SeqIO::metafasta;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - The object isa Bio::Seq::Meta
ok 5
ok 6
ok
t/SeqIO/msout.t ........................ 
1..165
ok 1 - use Bio::SeqIO::msout;
ok 2 - Bio::SeqIO::msout is at least api version 1.1.5
ok 3 - The object isa Bio::SeqIO::msout
ok 4 - Get N_SITES
ok 5 - Get TOT_RUN_HAPS
ok 6 - Get POPS
ok 7 - Get CURRENT_RUN_SEGSITES
ok 8 - Get NEXT_RUN_NUM
ok 9 - Get RUNS
ok 10 - Get MS_INFO_LINE
ok 11 - Get LAST_READ_HAP_NUM
ok 12 - Get POSITIONS
ok 13 - Get SEGSITES
ok 14 - Get SEEDS
ok 15 - Get next_hap at beginning of run
ok 16 - Get next_hap after beginning of run
ok 17 - Testing msout::outgroup
ok 18 - Get next_pop after beginning of pop
ok 19 - Get next_pop at beginning of pop
ok 20 - Get next_run after beginning of run
ok 21 - Get next_pop at beginning of run
ok 22 - Get next_hap after pop
ok 23 - Get next_run after pop and hap
ok 24 - Get next_run at beginning of run
ok 25 - have all lines been read?
ok 26 - The object isa Bio::SeqIO::msout
ok 27 - Get N_SITES
ok 28 - Get TOT_RUN_HAPS
ok 29 - Get POPS
ok 30 - Get CURRENT_RUN_SEGSITES
ok 31 - Get NEXT_RUN_NUM
ok 32 - Get RUNS
ok 33 - Get MS_INFO_LINE
ok 34 - Get LAST_READ_HAP_NUM
ok 35 - Get POSITIONS
ok 36 - Get SEGSITES
ok 37 - Get SEEDS
ok 38 - Get next_hap at beginning of run
ok 39 - Get next_hap after beginning of run
ok 40 - Testing msout::outgroup
ok 41 - Get next_pop after beginning of pop
ok 42 - Get next_pop at beginning of pop/run
ok 43 - Get next_run at beginning of run
ok 44 - Get next_hap at beginning of run 2
ok 45 - Get next_run after hap
ok 46 - next run should be 5.
ok 47 - Get last hap through next_hap
ok 48 - The object isa Bio::SeqIO::msout
ok 49 - Get TOT_RUN_HAPS
ok 50 - Get POPS
ok 51 - Get CURRENT_RUN_SEGSITES
ok 52 - Get NEXT_RUN_NUM
ok 53 - Get RUNS
ok 54 - Get MS_INFO_LINE
ok 55 - Get LAST_READ_HAP_NUM
ok 56 - Get POSITIONS
ok 57 - Get SEGSITES
ok 58 - Get SEEDS
ok 59 - Get next_pop at end of run
ok 60 - have all lines been read?
ok 61 - Get next_pop at eof
ok 62 - Get next_run at eof
ok 63 - Get next_hap at eof
ok 64 - Get next_seq at eof
ok 65 - The object isa Bio::SeqIO::msout
ok 66 - Get N_SITES
ok 67 - Get TOT_RUN_HAPS
ok 68 - Get POPS
ok 69 - Get CURRENT_RUN_SEGSITES
ok 70 - Get NEXT_RUN_NUM
ok 71 - Get LAST_READ_HAP_NUM
ok 72 - Get MS_INFO_LINE
ok 73 - Get RUNS
ok 74 - Get POSITIONS
ok 75 - Get SEGSITES
ok 76 - Get SEEDS
ok 77 - Get next_hap at beginning of run
ok 78 - Get next_hap after beginning of run
ok 79 - Testing msout::outgroup
ok 80 - Get next_pop after beginning of pop
ok 81 - Get next_pop at beginning of pop
ok 82 - Get next_run after beginning of run
ok 83 - Get next_pop at beginning of run
ok 84 - Get next_hap after pop
ok 85 - Get next_run after pop and hap
ok 86 - Get next_run at beginning of run
ok 87 - have all lines been read?
ok 88 - The object isa Bio::SeqIO::msout
ok 89 - Caught error in bad msout file 1
ok 90 - The object isa Bio::SeqIO::msout
ok 91 - Caught error in bad msout file 2
ok 92 - The object isa Bio::SeqIO::msout
ok 93 - Get N_SITES
ok 94 - Get TOT_RUN_HAPS
ok 95 - Get POPS
ok 96 - Get CURRENT_RUN_SEGSITES
ok 97 - Get NEXT_RUN_NUM
ok 98 - Get LAST_READ_HAP_NUM
ok 99 - Get MS_INFO_LINE
ok 100 - Get RUNS
ok 101 - Get POSITIONS
ok 102 - Get SEGSITES
ok 103 - Get SEEDS
ok 104 - Get next_hap at beginning of run
ok 105 - Get next_hap after beginning of run
ok 106 - Testing msout::outgroup
ok 107 - Get next_pop after beginning of pop
ok 108 - Get next_pop at beginning of pop
ok 109 - Get next_run after beginning of run
ok 110 - Get next_pop at beginning of run
ok 111 - Get next_hap after pop
ok 112 - Get next_run after pop and hap
ok 113 - Get next_run at beginning of run
ok 114 - have all lines been read?
ok 115 - The object isa Bio::SeqIO::msout
ok 116 - Get N_SITES
ok 117 - Get TOT_RUN_HAPS
ok 118 - Get POPS
ok 119 - Get CURRENT_RUN_SEGSITES
ok 120 - Get NEXT_RUN_NUM
ok 121 - Get LAST_READ_HAP_NUM
ok 122 - Get MS_INFO_LINE
ok 123 - Get RUNS
ok 124 - Get POSITIONS
ok 125 - Get SEGSITES
ok 126 - Get SEEDS
ok 127 - Get next_hap at beginning of run
ok 128 - Get next_hap after beginning of run
ok 129 - Testing msout::outgroup
ok 130 - Get next_pop after beginning of pop
ok 131 - Get next_pop at beginning of pop/run
ok 132 - Get next_run at beginning of run
ok 133 - Get next_hap at beginning of run 2
ok 134 - Get next_run after hap
ok 135 - next run should be 5.
ok 136 - Get last hap through next_hap
ok 137 - The object isa Bio::SeqIO::msout
ok 138 - Get N_SITES
ok 139 - Get TOT_RUN_HAPS
ok 140 - Get POPS
ok 141 - Get CURRENT_RUN_SEGSITES
ok 142 - Get NEXT_RUN_NUM
ok 143 - Get LAST_READ_HAP_NUM
ok 144 - Get MS_INFO_LINE
ok 145 - Get RUNS
ok 146 - Get POSITIONS
ok 147 - Get SEGSITES
ok 148 - Get SEEDS
ok 149 - Get next_hap at beginning of run
ok 150 - Get next_hap after beginning of run
ok 151 - Testing msout::outgroup
ok 152 - Get next_pop after beginning of pop
ok 153 - Get next_pop at beginning of pop
ok 154 - Get next_run after beginning of run
ok 155 - Get next_pop at beginning of run
ok 156 - Get next_hap after pop
ok 157 - Get next_run after pop and hap
ok 158 - Get next_run at beginning of run
ok 159 - have all lines been read?
ok 160 - The object isa Bio::SeqIO::msout
ok 161 - Caught error in bad msout file 1
ok 162 - The object isa Bio::SeqIO::msout
ok 163 - Caught error in bad msout file 2
ok 164 - threw Regexp ((?^:first argument needs to be a positive integer. argument supplied: -1))
ok 165 - too few n_sites failed OK
ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/SeqIO/nexml.t ........................ 
1..126
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqIO::nexml;
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 126 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok
t/SeqIO/phd.t .......................... 
1..21
ok 1 - use Bio::SeqIO::phd;
ok 2 - The object isa Bio::SeqIO::phd
ok 3 - Did you get the 'QUALITY_LEVELS' comment?
ok 4 - The object isa Bio::Seq::Quality
ok 5 - The object isa Bio::SeqIO::phd
ok 6
ok 7 - $seq->subseq()
ok 8 - $seq->subqual_tex()
ok 9 - $seq->subqual_tex()
ok 10 - $phd->chromat_file()
ok 11 - $phd->chromat_file()
ok 12
ok 13 - $seq->subseq()
ok 14 - $seq->subqual_tex()
ok 15 - $seq->subqual_tex()
ok 16
ok 17 - $seq->subseq()
ok 18 - $seq->subqual_tex()
ok 19 - $seq->subqual_tex()
ok 20 - The object isa Bio::SeqIO::phd
ok 21
ok
t/SeqIO/pir.t .......................... 
1..9
ok 1 - use Bio::SeqIO::pir;
ok 2 - new instance is defined 
ok 3 - The object isa Bio::SeqIO
ok 4 - checked length
ok 5 - checked length
ok 6 - checked length
ok 7 - checked length
ok 8 - checked length
ok 9 - checked length
ok
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ......................... 
1..18
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::PrimaryQual;
ok 3
ok 4 - The object isa Bio::Seq::PrimaryQual
ok 5
ok 6 - The object isa Bio::Seq::PrimaryQual
ok 7 - The object isa Bio::Seq::PrimaryQual
ok 8 - The object isa Bio::Seq::PrimaryQual
ok 9 - The object isa Bio::Seq::PrimaryQual
ok 10 - The object isa Bio::Seq::PrimaryQual
ok 11 - The object isa Bio::Seq::PrimaryQual
ok 12 - The object isa Bio::Seq::PrimaryQual
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/SeqIO/raw.t .......................... 
1..25
ok 1 - use Bio::SeqIO::raw;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - Bio::SeqIO::raw->can('next_seq')
ok 5 - Bio::SeqIO::raw->can('write_seq')
ok 6 - The object isa Bio::Seq
ok 7 - sequence
ok 8 - length
ok 9 - The object isa Bio::Seq
ok 10 - sequence
ok 11 - length
ok 12 - use Algorithm::Diff;
ok 13 - raw format can round-trip
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
t/SeqIO/scf.t .......................... 
1..80
ok 1 - use Bio::SeqIO::scf;
ok 2 - use Bio::Seq::SequenceTrace;
ok 3
ok 4 - The object isa Bio::Seq::SequenceTrace
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::Quality
ok 14 - The object isa Bio::Seq::Quality
ok 15 - alphabet
ok 16 - display_id
ok 17 - primary_id is the stringified memory position
ok 18 - set primary_id
ok 19 - accession_number
ok 20 - desc
ok 21 - desc
ok 22 - id
ok 23 - id
ok 24 - seq
ok 25 - subseq
ok 26 - baseat
ok 27 - qualat
ok 28 - trace_value_at
not ok 29 - accuracies # TODO documentation and code for accuracies() do not match
#   Failed (TODO) test 'accuracies'
#   at t/SeqIO/scf.t line 78.
#          got: 'ARRAY(0x100c1bb70)'
#     expected: '482'
ok 30
ok 31 - sub_peak_index
ok 32 - peak_index_at
ok 33
ok 34
ok 35 - The object isa Bio::Seq::SequenceTrace
ok 36 - accuracy_at
ok 37 - The object isa Bio::Seq::SequenceTrace
ok 38
ok 39
ok 40
ok 41 - The object isa Bio::Annotation::Collection
ok 42
ok 43 - The object isa Bio::Annotation::Collection
ok 44
ok 45
ok 46 - The object isa Bio::Annotation::Collection
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54 - The object isa Bio::Seq::SequenceTrace
ok 55 - The object isa Bio::Annotation::Collection
ok 56
ok 57
ok 58
ok 59
ok 60 - The object isa Bio::Seq::SequenceTrace
ok 61
ok 62 - The object isa Bio::Seq::SequenceTrace
ok 63 - qual scores match
ok 64 - The object isa Bio::Seq::SequenceTrace
ok 65
ok 66 - The object isa Bio::Seq::SequenceTrace
not ok 67 - display_id matches # TODO display_id doesn't round trip yet

#   Failed (TODO) test 'display_id matches'
#   at t/SeqIO/scf.t line 285.
#          got: 'ML4942R'
#     expected: undef
ok 68 - qual scores match
ok 69 - The object isa Bio::Seq::SequenceTrace
ok 70
ok 71 - The object isa Bio::Seq::SequenceTrace
not ok 72 - display_id matches # TODO display_id doesn't round trip yet

#   Failed (TODO) test 'display_id matches'
#   at t/SeqIO/scf.t line 285.
#          got: 'IIABP1D4373'
#     expected: undef
ok 73 - qual scores match
ok 74 - The object isa Bio::Seq::SequenceTrace
ok 75
ok 76 - The object isa Bio::Seq::SequenceTrace
not ok 77 - display_id matches # TODO display_id doesn't round trip yet

#   Failed (TODO) test 'display_id matches'
#   at t/SeqIO/scf.t line 285.
#          got: 'IIABP1D4373'
#     expected: undef
ok 78 - qual scores match
ok 79 - Bio::Sequence::Quality matches
ok 80 - Bio::Sequence::Quality matches
ok
t/SeqIO/seqxml.t ....................... 
1..61
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::PrimarySeq;
ok 3 - use Bio::SeqIO::seqxml;
ok 4 - stream ok
ok 5 - seqXML version
ok 6 - source
ok 7 - source version
ok 8 - The object isa Bio::Seq
ok 9 - display id
ok 10 - primary id
ok 11 - description
ok 12 - sequence
ok 13 - length
ok 14 - entry source
ok 15 - species isa Bio::Species
ok 16 - species name
ok 17 - NCBI tax id
ok 18 - The object isa Bio::Annotation::DBLink
ok 19 - dblink source
ok 20 - dblink ID
ok 21 - The object isa Bio::Annotation::SimpleValue
ok 22 - boolean property
ok 23 - The object isa Bio::Annotation::SimpleValue
ok 24 - property with value
ok 25 - writer ok
ok 26 - outfile is created
ok 27 - seqXML version
ok 28 - source
ok 29 - source version
ok 30 - schemaLocation
ok 31 - The object isa Bio::Seq
ok 32 - display id
ok 33 - primary id
ok 34 - description
ok 35 - sequence
ok 36 - length
ok 37 - entry source
ok 38 - species isa Bio::Species
ok 39 - species name
ok 40 - NCBI tax id
ok 41 - The object isa Bio::Annotation::DBLink
ok 42 - dblink source
ok 43 - dblink ID
ok 44 - The object isa Bio::Annotation::SimpleValue
ok 45 - property with value
ok 46 - The object isa Bio::Annotation::SimpleValue
ok 47 - boolean property
ok 48 - outfile is created
ok 49 - seqXML version
ok 50 - source
ok 51 - source version
ok 52 - display id
ok 53 - primary id
ok 54 - description
ok 55 - sequence
ok 56 - length
ok 57 - display id
ok 58 - primary id
ok 59 - description
ok 60 - sequence
ok 61 - length
ok
t/SeqIO/strider.t ...................... 
1..8
ok 1 - use Bio::SeqIO::strider;
not ok 2 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for strider format -- no sample file to test against
ok
t/SeqIO/swiss.t ........................ 
1..247
ok 1 - use Bio::SeqIO::swiss;
ok 2 - The object isa Bio::SeqIO
ok 3 - The object isa Bio::Species
ok 4
ok 5
ok 6 - operator overloading in AnnotationI is deprecated
ok 7 - dates
ok 8 - dates
ok 9 - dates
ok 10
ok 11 - The object isa Bio::Seq::RichSeqI
ok 12
ok 13
ok 14
ok 15 - operator overloading in AnnotationI is deprecated
ok 16
ok 17
ok 18
ok 19
ok 20 - id is ROA1_HUMAN
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28 - operator overloading in AnnotationI is deprecated
ok 29
ok 30
ok 31
ok 32
ok 33 - The object isa Bio::Seq::RichSeqI
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46
ok 47 - GC1QBP
ok 48 - HABP1
ok 49 - SF2P32
ok 50 - C1QBP
ok 51
ok 52 - The object isa Bio::Seq::RichSeqI
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - F54H12.1
ok 60 - The object isa Bio::Seq::RichSeqI
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - The object isa Bio::Seq::RichSeqI
ok 73
ok 74
ok 75
ok 76
ok 77 - The object isa Bio::Seq::RichSeqI
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 - The object isa Bio::Seq::RichSeqI
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
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ok 175 - The object isa Bio::Species
ok 176
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ok 178 - operator overloading in AnnotationI is deprecated
ok 179
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ok 207 - The object isa Bio::Species
ok 208
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ok 211
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ok 240
ok 241 - Converting to fasta seqids match
ok 242 - Converting to fasta sequences match
ok 243 - Can parse generated swiss
ok 244 - Roundtrip, seqids match
ok 245 - Roundtrip, sequences match
ok 246
ok 247
ok
t/SeqIO/tab.t .......................... 
1..8
ok 1 - use Bio::SeqIO::tab;
ok 2 - The object isa Bio::SeqIO
ok 3 - seq is defined
ok 4 - check seq length
ok 5 - check matching
ok 6 - seq is defined
ok 7 - check seq length
ok 8 - check matching
ok
t/SeqIO/table.t ........................ 
1..450
ok 1 - use Bio::Tools::CodonTable;
ok 2 - use Bio::SeqIO::table;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
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ok
t/SeqIO/tigr.t ......................... 
1..8
ok 1 - use Bio::SeqIO::tigr;
not ok 2 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for tigr format -- no sample file to test against
ok
t/SeqIO/tigrxml.t ...................... 
1..49
ok 1 - use Bio::SeqIO::tigrxml;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 49
ok
t/SeqIO/tinyseq.t ...................... 
1..16
ok 1 - use Bio::SeqIO::tinyseq;
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/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. 
1..8
ok 1 - use Bio::Tools::SeqPattern::Backtranslate;
ok 2 - Bio::Tools::SeqPattern::Backtranslate->can('_reverse_translate_motif')
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8 - threw Regexp ((?^:syntax token))
ok
t/SeqTools/CodonTable.t ................ 
1..61
ok 1 - use Bio::Tools::CodonTable;
ok 2 - use Bio::CodonUsage::IO;
ok 3
ok 4 - The object isa Bio::Tools::CodonTable
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
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ok 34
ok 35
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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
t/SeqTools/ECnumber.t .................. 
1..27
ok 1 - use Bio::Tools::ECnumber;
ok 2 - The object isa Bio::Tools::ECnumber
ok 3 - The object isa Bio::Tools::ECnumber
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/SeqTools/GuessSeqFormat.t ............ 
1..52
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::Tools::GuessSeqFormat;
ok 4
ok 5
ok 6
ok 7 - Guessed:ace
ok 8 - The object isa Bio::PrimarySeqI
ok 9 - Guessed:embl
ok 10 - The object isa Bio::SeqI
ok 11 - Guessed:fasta
ok 12 - The object isa Bio::SeqI
ok 13 - Guessed:fastq
ok 14 - The object isa Bio::SeqI
ok 15 - Guessed:gcg
ok 16 - The object isa Bio::SeqI
ok 17 - Guessed:genbank
ok 18 - The object isa Bio::SeqI
ok 19 - Guessed:mase
ok 20 - Guessed:pfam
ok 21 - Guessed:pir
ok 22 - The object isa Bio::SeqI
ok 23 - Guessed:raw
ok 24 - The object isa Bio::SeqI
ok 25 - Guessed:swiss
ok 26 - The object isa Bio::SeqI
ok 27 - Guessed:tab
ok 28 - The object isa Bio::SeqI
ok 29 - Guessed:game
ok 30 - The object isa Bio::SeqI
ok 31 - clustalw
ok 32 - The object isa Bio::Align::AlignI
ok 33 - fasta
ok 34 - The object isa Bio::Align::AlignI
ok 35 - fastq
ok 36 - mase
ok 37 - The object isa Bio::Align::AlignI
ok 38 - msf
ok 39 - The object isa Bio::Align::AlignI
ok 40 - nexus
ok 41 - The object isa Bio::Align::AlignI
ok 42 - pfam
ok 43 - The object isa Bio::Align::AlignI
ok 44 - phylip
ok 45 - The object isa Bio::Align::AlignI
ok 46 - prodom
ok 47 - The object isa Bio::Align::AlignI
ok 48 - stockholm
ok 49 - The object isa Bio::Align::AlignI
ok 50
ok 51
ok 52 - fasta
ok
t/SeqTools/OddCodes.t .................. 
1..11
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::OddCodes;
ok 3 - The object isa Bio::Tools::OddCodes
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
t/SeqTools/SeqPattern.t ................ 
1..28
ok 1 - use Bio::Tools::SeqPattern;
ok 2
ok 3 - The object isa Bio::Tools::SeqPattern
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Tools::SeqPattern
ok 8
ok 9
ok 10 - The object isa Bio::Tools::SeqPattern
ok 11
ok 12 - threw Regexp ((?^:revcom for .+ sequence types))
ok 13 - threw Regexp ((?^:backtranslate for .+ sequence types))
ok 14 - The object isa Bio::Tools::SeqPattern
ok 15 - The object isa Bio::Tools::SeqPattern
ok 16
ok 17 - The object isa Bio::Tools::SeqPattern
ok 18 - The object isa Bio::Tools::SeqPattern
ok 19
ok 20 - The object isa Bio::Tools::SeqPattern
ok 21 - The object isa Bio::Tools::SeqPattern
ok 22
ok 23 - The object isa Bio::Tools::SeqPattern
ok 24 - The object isa Bio::Tools::SeqPattern
ok 25
ok 26 - The object isa Bio::Tools::SeqPattern
ok 27 - The object isa Bio::Tools::SeqPattern
ok 28
ok
t/SeqTools/SeqStats.t .................. 
1..47
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Tools::SeqStats;
ok 3 - new Bio::Root::IO object
ok 4 - new Bio::Tools:SeqStats object
ok 5 - count_monomers()
ok 6 - count_codons()
ok 7 - get_mol_wt()
ok 8
ok 9 - The object isa Bio::Tools::SeqStats
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/SeqTools/SeqUtils.t .................. 
1..133
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqUtils;
ok 3 - use Bio::LiveSeq::Mutation;
ok 4 - use Bio::SeqFeature::Generic;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Collection;
ok 7 - use Bio::Annotation::Comment;
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 - cat - has expected tags
ok 37 - cat - has expected tag values
ok 38 - cat - note tag transfered (no throw)
ok 39 - cat - note tag values transfered (correct count)
ok 40 - get correct start of feature before 'cat'
ok 41 - get correct start of feature after 'cat'
ok 42 - different alphabets
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - trunc_with_features - has expected tags
ok 49 - trunc_with_features - has expected tag values
ok 50
ok 51 - primary_tag matches original feature...
ok 52 - but tagged sf is now revcom
ok 53 - primary_tag matches original feature...
ok 54 - but tagged sf is now revcom
ok 55 - primary_tag matches original feature...
ok 56 - but tagged sf is now revcom
ok 57 - revcom_with_features - has expected tags
ok 58 - revcom_with_features - has expected tag values
ok 59 - still not circular
ok 60 - still circular
ok 61 - No error thrown when deleting a segment of the sequence
ok 62 - annotation of whole sequence has been moved to new molecule
ok 63 - the product has an additional 'misc_feature' and the note specifies the lengths of the deletion'
ok 64 - The composite feature is still present
ok 65 - The object isa Bio::SeqFeature::Generic
ok 66 - a composite feature that spanned the deletion site has been split up, Location isa Bio::Location::Split
ok 67 - one of the sub-eatures of the composite feature has been deleted completely
ok 68 - sub-feature 1 of the composite feature is still present
ok 69 - the original end of sf1 is 12
ok 70 - after deletion, the end of sf1 is 1nt before the deletion site
ok 71 - the original end location of sf1 EXACT
ok 72 - annotation of subeature 1 has been moved to new molecule
ok 73 - feature1 is till present
ok 74 - feature1 location has now been split by the deletion and location object isa Bio::Location::Split
ok 75 - feature1 has two locations after the deletion
ok 76 - feature1 start is unaffected by the deletion
ok 77 - feature1 end of first split is 1nt before deletion site
ok 78 - feature1 start of second split is 1nt after deletion site
ok 79 - feature1 end of second split has been adjusted correctly
ok 80 - split feature now has a note
ok 81 - got the expected note about length and position of deletion
ok 82 - feature3 is till present
ok 83 - a feature downstream of the deletion site is shifted entirely by 10nt to the left
ok 84 - feature4 is till present
ok 85 - a feature upstream of the deletion site is not repositioned by the deletion
ok 86 - feature2 is till present
ok 87 - start pos of a feature that started in the deletion site has been altered accordingly
ok 88 - feature 2 now has a note
ok 89 - note added to feature2 about deletion at 3' end
ok 90 - a feature that was completely positioned inside the deletion site is not present on the new molecule
ok 91 - feature6 is till present
ok 92 - start pos of a feature that started in the deletion site has been altered accordingly
ok 93 - end pos of a feature that started in the deletion site has been altered accordingly
ok 94 - No error thrown when inserting a fragment into recipient sequence
ok 95 - annotation of whole sequence has been moved to new molecule
ok 96 - The composite feature is still present
ok 97 - The object isa Bio::SeqFeature::Generic
ok 98 - a composite feature that spanned the insertion site has been split up, Location isa Bio::Location::Split
ok 99 - all of the parts of the composite feature are still present
ok 100 - sub-feature 1 of the composite feature is still present
ok 101 - the original end of sf1 is 12
ok 102 - after insertion, the end of sf1 has been shifted by the length of the insertion
ok 103 - sub-feature 1 (spans insertion site) is now split up and isa Bio::Location::Split
ok 104 - the start and end position types of sub-feature1 have not changed
ok 105 - annotation of subeature 1 has been moved to new molecule
ok 106 - split feature now has a note
ok 107 - got the expected note about length and position of insertion
ok 108 - feature3 is till present
ok 109 - a feature downstream of the insertion site is shifted entirely to the left by the length of the insertion
ok 110 - feature4 is till present
ok 111 - a feature upstream of the insertion site is not repositioned
ok 112 - a feature on the inserted fragment is present on the product molecule
ok 113 - position of the feature on the insert has been adjusted to product coordinates
ok 114 - strand of the feature on insert has not changed
ok 115 - desctription of the product contains description of the fragment
ok 116 - desctription of the product contains description of the recipient
ok 117 - the product has an additional 'misc_feature' with note='inserted fragment'
ok 118 - No error thrown using 'ligate' of fragment into recipient
ok 119 - product has the expected length
ok 120 - the sequence of the fragment is inserted into the product
ok 121 - we have a feature annotating the ligated fragment
ok 122 - coordinates of the feature annotating the ligated feature are correct
ok 123 - the fragment feature1 is now a feature of the product
ok 124 - start and end of a feature on the fragment are correct after insertion with "flip" option
ok 125 - Trying to delete from an object of a custom Bio::Seq subclass that doesn't allow calling 'new' throws an error
ok 126 - Deleting from Bio::Seq::Foo does not throw an error when using the 'clone_obj' option to clone instead of calling 'new'
ok 127 - The object isa Bio::Seq::Foo
ok 128 - the product has an additional 'misc_feature' and the note specifies the lengths of the deletion'
ok 129 - The composite feature is still present
ok 130 - The object isa Bio::SeqFeature::Generic
ok 131 - a composite feature that spanned the deletion site has been split up, Location isa Bio::Location::Split
ok 132 - 'ligate' without clone_obj option dies with a Bio::Seq::Foo object that can't call new
ok 133 - 'ligate' with clone_obj option works with a Bio::Seq::Foo object that can't call new
ok
t/SeqTools/SeqWords.t .................. 
1..22
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Tools::SeqWords;
ok 3 - new Bio::Root::IO object
ok 4 - new Bio::Tools::SeqWords object
ok 5 - count_words
ok 6
ok 7 - The object isa Bio::Tools::SeqWords
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::Tools::SeqWords
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok
t/Species.t ............................ 
1..23
ok 1 - use Bio::Species;
ok 2 - use Bio::DB::Taxonomy;
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 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22
ok 23
ok
t/Structure/IO.t ....................... 
1..14
ok 1 - use Bio::Structure::IO;
ok 2
ok 3
ok 4 - The object isa Bio::Structure::Entry
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Structure/Structure.t ................ 
1..51
ok 1 - use Bio::Structure::Entry;
ok 2 - use Bio::Structure::Model;
ok 3 - use Bio::Structure::Chain;
ok 4 - use Bio::Structure::Residue;
ok 5 - use Bio::Structure::Atom;
ok 6
ok 7 - The object isa Bio::Structure::Entry
ok 8
ok 9 - The object isa Bio::Structure::Model
ok 10
ok 11 - The object isa Bio::Structure::Chain
ok 12
ok 13 - The object isa Bio::Structure::Residue
ok 14
ok 15 - The object isa Bio::Structure::Atom
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - The object isa Bio::Structure::Model
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Structure::Chain
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Structure::Residue
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/Symbol.t ............................. 
1..9
ok 1 - use Bio::Symbol::Symbol;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
t/TaxonTree.t .......................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
t/Tools/Alignment/Consed.t ............. 
1..15
ok 1 - use Bio::Tools::Alignment::Consed;
ok 2 - new CSM::Consed object was created
ok 3 - The object isa Bio::Tools::Alignment::Consed
ok 4 - singlets can be successfully set
ok 5 - singlets can be retrieved
ok 6 - doublets can be set
ok 7 - doublets can be retreived
ok 8 - doublets can be retrieved
ok 9 - pairs can be retrieved
ok 10 - multiplets can be retrieved
ok 11 - singletons can be retrieved
ok 12 - how many sequences there are in the acefile _and_ in the singlets file
ok 13 - statistics from the Bio::Tools::Alignment::Consed object to compare the total number of sequences accounted for there to the number of sequences found via grep
ok 14
ok 15
ok
t/Tools/AmpliconSearch.t ............... 
1..185
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqFeature::Primer;
ok 3 - use Bio::Tools::AmpliconSearch;
ok 4 - Basic
ok 5 - The object isa Bio::Tools::AmpliconSearch
ok 6 - Forward primer only
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Seq
ok 11
ok 12
ok 13 - The object isa Bio::SeqFeature::Amplicon
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - Reverse primer only
ok 26
ok 27
ok 28
ok 29
ok 30 - The object isa Bio::SeqFeature::Amplicon
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38 - Two primers, no match
ok 39
ok 40
ok 41
ok 42
ok 43 - Two degenerate primers from a file
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::SeqFeature::Amplicon
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54 - RNA template
ok 55
ok 56
ok 57
ok 58
ok 59 - The object isa Bio::SeqFeature::Amplicon
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65 - Forward primer from file
ok 66
ok 67
ok 68
ok 69
ok 70 - The object isa Bio::Seq
ok 71
ok 72
ok 73 - The object isa Bio::SeqFeature::Amplicon
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - Multiple amplicons
ok 80
ok 81 - The object isa Bio::SeqFeature::Amplicon
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87 - The object isa Bio::SeqFeature::Amplicon
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93 - Amplicon on reverse strand
ok 94
ok 95 - The object isa Bio::SeqFeature::Amplicon
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101 - The object isa Bio::SeqFeature::Amplicon
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107 - Overlapping amplicons (1)
ok 108
ok 109 - The object isa Bio::SeqFeature::Amplicon
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115 - Overlapping amplicons (2)
ok 116
ok 117 - The object isa Bio::SeqFeature::Amplicon
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - Overlapping amplicons (3)
ok 124
ok 125 - The object isa Bio::SeqFeature::Amplicon
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131 - Amplicons on both strands
ok 132
ok 133 - The object isa Bio::SeqFeature::Amplicon
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139 - The object isa Bio::SeqFeature::Amplicon
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145 - Overlapping amplicons on both strands
ok 146
ok 147 - The object isa Bio::SeqFeature::Amplicon
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153 - Annotated template
ok 154
ok 155 - The object isa Bio::Seq
ok 156 - The object isa Bio::SeqFeature::Amplicon
ok 157 - The object isa Bio::SeqFeature::Amplicon
ok 158
ok 159
ok 160 - Update primers
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 - Update template
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Mitoprot.t .... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Scansite.t .... 
1..14
ok 1 - use Bio::Tools::Analysis::Protein::Scansite;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::WebAgent;
ok 4
ok 5
ok 6
ok 7
ok 8
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/Tools/Analysis/Protein/Sopma.t ....... 
1..16
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::Analysis::Protein::Sopma;
ok 3
ok 4
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/Tools/EMBOSS/Palindrome.t ............ 
1..13
ok 1 - use Bio::Tools::EMBOSS::Palindrome;
ok 2 - use Bio::Tools::GFF;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/Tools/Est2Genome.t ................... 
1..61
ok 1 - use Bio::Tools::Est2Genome;
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
t/Tools/FootPrinter.t .................. 
1..27
ok 1 - use Bio::Tools::FootPrinter;
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
t/Tools/GFF.t .......................... 
1..34
ok 1 - use Bio::Tools::GFF;
ok 2 - use Bio::SeqFeature::Generic;
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
t/Tools/Geneid.t ....................... 
1..26
ok 1 - use Bio::Tools::Geneid;
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
t/Tools/Genewise.t ..................... 
1..33
ok 1 - use Bio::Tools::Genewise;
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
t/Tools/Genomewise.t ................... 
1..21
ok 1 - use Bio::Tools::Genomewise;
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
t/Tools/Genpred.t ...................... 
1..185
ok 1 - use Bio::Tools::Fgenesh;
ok 2 - use Bio::Tools::Genscan;
ok 3 - use Bio::Tools::Genemark;
ok 4 - use Bio::Tools::Glimmer;
ok 5 - use Bio::Tools::MZEF;
ok 6 - use Bio::SeqIO;
ok 7
ok 8
ok 9
ok 10 - strand match (-1  and -1)
ok 11 - score match (1.05 and 1.05)
ok 12
ok 13 - predicted and extracted protein seqs match
ok 14 - strand match (1 and 1)
ok 15 - score match (4.46 and 4.46)
ok 16
ok 17 - predicted and extracted protein seqs match
ok 18 - initial exons 0
ok 19 - score match 1.74
ok 20
ok 21 - predicted and extracted protein seqs match
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 - Genemark tests
ok 43
ok 44
ok 45
ok 46 - The object isa Bio::Location::Fuzzy
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55 - The object isa Bio::Location::Fuzzy
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 - The object isa Bio::Location::SplitLocationI
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 - The object isa Bio::Location::SplitLocationI
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 - The object isa Bio::Location::Fuzzy
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161 - The object isa Bio::Location::Fuzzy
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
t/Tools/GuessSeqFormat.t ............... 
1..4
ok 1 - use Bio::Tools::GuessSeqFormat;
ok 2
ok 3 - The object isa Bio::Tools::GuessSeqFormat
ok 4
ok
t/Tools/Hmmer.t ........................ 
1..29
ok 1 - use Bio::Tools::HMMER::Domain;
ok 2 - use Bio::Tools::HMMER::Set;
ok 3 - use Bio::Tools::HMMER::Results;
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
t/Tools/IUPAC.t ........................ 
1..46
ok 1 - use Bio::Tools::IUPAC;
ok 2 - use Bio::Seq;
ok 3 - use Bio::PrimarySeq;
ok 4
ok 5
ok 6 - Regexp
ok 7
ok 8 - Regexp
ok 9 - Count
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 - Regexp matches ambiguous sequences
ok 28
ok 29 - Nucleic IUPAC
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36 - Proteic IUPAC
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok
t/Tools/Lucy.t ......................... 
1..22
ok 1 - use Bio::Tools::Lucy;
ok 2 - The object isa Bio::Tools::Lucy
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
t/Tools/Match.t ........................ 
1..38
ok 1 - use Bio::Tools::Match;
ok 2
ok 3 - The object isa Bio::SeqFeature::Generic
ok 4 - correct source
ok 5 - feature start correct
ok 6 - feature end correct
ok 7 - feature core score correct
ok 8 - feature matrix score correct
ok 9 - feature matrix id correct
ok 10 - The object isa Bio::SeqFeature::Generic
ok 11 - correct source
ok 12 - feature start correct
ok 13 - feature end correct
ok 14 - feature core score correct
ok 15 - feature matrix score correct
ok 16 - feature matrix id correct
ok 17 - The object isa Bio::SeqFeature::Generic
ok 18 - correct source
ok 19 - feature start correct
ok 20 - feature end correct
ok 21 - feature core score correct
ok 22 - feature matrix score correct
ok 23 - feature matrix id correct
ok 24 - The object isa Bio::SeqFeature::Generic
ok 25 - correct source
ok 26 - feature start correct
ok 27 - feature end correct
ok 28 - feature core score correct
ok 29 - feature matrix score correct
ok 30 - feature matrix id correct
ok 31 - The object isa Bio::SeqFeature::Generic
ok 32 - correct source
ok 33 - feature start correct
ok 34 - feature end correct
ok 35 - feature core score correct
ok 36 - feature matrix score correct
ok 37 - feature matrix id correct
ok 38 - correct number of results managed to get tested
ok
t/Tools/Phylo/Gerp.t ................... 
1..33
ok 1 - use Bio::Tools::Phylo::Gerp;
ok 2
ok 3 - The object isa Bio::SeqFeature::Generic
ok 4 - correct source
ok 5 - feature start correct
ok 6 - feature end correct
ok 7 - feature score correct
ok 8 - feature pvalue correct
ok 9 - The object isa Bio::SeqFeature::Generic
ok 10 - correct source
ok 11 - feature start correct
ok 12 - feature end correct
ok 13 - feature score correct
ok 14 - feature pvalue correct
ok 15 - The object isa Bio::SeqFeature::Generic
ok 16 - correct source
ok 17 - feature start correct
ok 18 - feature end correct
ok 19 - feature score correct
ok 20 - feature pvalue correct
ok 21 - The object isa Bio::SeqFeature::Generic
ok 22 - correct source
ok 23 - feature start correct
ok 24 - feature end correct
ok 25 - feature score correct
ok 26 - feature pvalue correct
ok 27 - The object isa Bio::SeqFeature::Generic
ok 28 - correct source
ok 29 - feature start correct
ok 30 - feature end correct
ok 31 - feature score correct
ok 32 - feature pvalue correct
ok 33 - correct number of results parsed out
ok
t/Tools/Phylo/Molphy.t ................. 
1..18
ok 1 - use Bio::Tools::Phylo::Molphy;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/Tools/Phylo/PAML.t ................... 
1..256
ok 1 - use Bio::Tools::Phylo::PAML;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163 - node\#8 reconstructed seq
ok 164 - ancestral AA
ok 165 - ancestral AA
ok 166 - derived AA
ok 167 - ancestral AA
ok 168 - ancestral AA
ok 169 - derived AA
ok 170 - derived AA
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 - codeml 4.3 runmode=-2
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215 - codeml 4.3 two NSSites models
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 - NEB positively selected sites
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251 - bug 3040
ok 252 - bug 3365
ok 253 - bug 3366
ok 254 - bug 3367
ok 255 - bug 3332
ok 256 - bug 3331
ok
t/Tools/Phylo/Phylip/ProtDist.t ........ 
1..47
ok 1 - use Bio::Tools::Phylo::Phylip::ProtDist;
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
t/Tools/Primer3.t ...................... 
1..14
ok 1 - use Bio::Tools::Primer3;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Seq::PrimedSeq
ok 11
ok 12
ok 13
ok 14 - bug 2862
ok
t/Tools/Promoterwise.t ................. 
1..7
ok 1 - use Bio::Tools::Promoterwise;
ok 2 - The object isa Bio::Tools::Promoterwise
ok 3
ok 4
ok 5
ok 6
ok 7
ok
t/Tools/Pseudowise.t ................... 
1..21
ok 1 - use Bio::Tools::Pseudowise;
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
t/Tools/QRNA.t ......................... 
1..30
ok 1 - use Bio::Tools::QRNA;
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
t/Tools/RandDistFunctions.t ............ 
1..5
ok 1 - use Bio::Tools::RandomDistFunctions;
ok 2
ok 3
ok 4
ok 5
ok
t/Tools/RepeatMasker.t ................. 
1..28
ok 1 - use Bio::Tools::RepeatMasker;
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/Tools/Run/RemoteBlast.t .............. skipped: Network tests have not been requested
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
t/Tools/Run/StandAloneBlast.t .......... 
1..45
ok 1 - use Bio::Tools::Run::StandAloneBlast;
ok 2 - use Bio::SeqIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tools::Run::StandAloneBlast
ok 14 - The object isa Bio::Tools::Run::StandAloneNCBIBlast
ok 15 - The object isa Bio::Tools::Run::StandAloneBlast
ok 16 - The object isa Bio::Tools::Run::StandAloneWUBlast
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 # skip blastall not installed, skipping tests
ok 35 # skip blastall not installed, skipping tests
ok 36 # skip blastall not installed, skipping tests
ok 37 # skip blastall not installed, skipping tests
ok 38 # skip blastall not installed, skipping tests
ok 39 # skip blastall not installed, skipping tests
ok 40 # skip blastall not installed, skipping tests
ok 41 # skip blastall not installed, skipping tests
ok 42 # skip blastall not installed, skipping tests
ok 43 # skip blastall not installed, skipping tests
ok 44 # skip blastall not installed, skipping tests
ok 45 # skip blastall not installed, skipping tests
ok
t/Tools/Run/WBCommandExts.t ............ 
1..25
ok 1 - use Dummy::Config;
ok 2 - use Dummy;
ok 3 - use Bio::Tools::Run::WrapperBase;
ok 4 - use Bio::Tools::Run::WrapperBase::CommandExts;
ok 5 - make factory
ok 6 - parm changed flag set
ok 7 - correct prog name
ok 8 - is pseudo
ok 9 - correct parm set
ok 10 - parm flag cleared
ok 11 - translate opts to command line
ok 12 - translate opts to command line
ok 13 - translate opts to command line
ok 14 - translate opts to command line # TODO Determine whether the order of the parameters should be set somehow; this sporadically breaks hash randomization introduced in perl 5.17+
ok 15 - parm reset
ok 16 - parm cleared after reset
ok 17 - avail parms
ok 18 - avail switches
ok 19 - avail commands
ok 20 - make composite cmd factory
ok 21 - comp cmd parm set
ok 22 - make subfactories
ok 23 - subfactory 1 parm correct
ok 24 - subfactory 2 parm correct
ok 25 - find in syspath
ok
t/Tools/Run/WrapperBase.t .............. 
1..27
ok 1 - use Bio::Tools::Run::WrapperBase;
ok 2 - The object isa Bio::Tools::Run::WrapperBase
ok 3 - run() exists
ok 4 - program_dir() exists
ok 5 - program_name() exists
ok 6 - version() exists
ok 7 - error_string could be set
ok 8 - arguments could be set
ok 9 - no_param_checks could be set
ok 10 - save_tempfiles could be set
ok 11 - outfile_name could be set
ok 12 - quiet could be set
ok 13 - tempdir created a directory
ok 14 - could create file in tempdir
ok 15 - following cleanup() with save_tempfiles unset, tempdir was deleted
ok 16 - The object isa Bio::Root::IO
ok 17 - io() always returns the same instance of IO
ok 18 - program_path was correct
ok 19 - pretend program name not found as executable
ok 20 - perl found as executable
ok 21 - params string correct
ok 22 - params string correct
ok 23 - params string correct
ok 24 - params string correct
ok 25 - params string correct
ok 26 - params string correct
ok 27 - params string correct
ok
t/Tools/Seg.t .......................... 
1..15
ok 1 - use Bio::Tools::Seg;
ok 2 - parser defined
ok 3
ok 4 - seq id for seq 0 identified
ok 5 - start for seq 0 identified
ok 6 - end for seq 0 identified
ok 7 - score for seq 0 identified
ok 8 - seq id for seq 1 identified
ok 9 - start for seq 1 identified
ok 10 - end for seq 1 identified
ok 11 - score for seq 1 identified
ok 12 - seq id for seq 2 identified
ok 13 - start for seq 2 identified
ok 14 - end for seq 2 identified
ok 15 - score for seq 2 identified
ok
t/Tools/SiRNA.t ........................ 
1..11
ok 1 - use Bio::Tools::SiRNA;
ok 2 - use Bio::Seq;
ok 3 - use Bio::SeqIO;
ok 4 - The object isa Bio::SeqIO
ok 5 - The object isa Bio::Tools::SiRNA
ok 6 - CDS only: got 65
ok 7
ok 8
ok 9 - The object isa Bio::Seq
ok 10
ok 11
ok
t/Tools/Sigcleave.t .................... 
1..18
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::Sigcleave;
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 - unable to get raw sigcleave results
ok 16
ok 17 - unable to get raw sigcleave results
ok 18
ok
t/Tools/Signalp.t ...................... 
1..11
ok 1 - use Bio::Tools::Signalp;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
t/Tools/Signalp/ExtendedSignalp.t ...... 
1..185
ok 1 - use Bio::Tools::Signalp::ExtendedSignalp;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok
t/Tools/Sim4.t ......................... 
1..27
ok 1 - use Bio::Tools::Sim4::Results;
ok 2 - new Sim4 results instance
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - new Sim4 results instance
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/Tools/Spidey/Spidey.t ................ 
1..26
ok 1 - use Bio::Tools::Spidey::Results;
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
t/Tools/TandemRepeatsFinder.t .......... 
1..66
ok 1 - use Bio::Tools::TandemRepeatsFinder;
ok 2 - Parser created  successfully
ok 3 - empty results file correctly returns no results
ok 4 - Second parser created  successfully
ok 5 - seq_id for first result correctly parsed
ok 6 - start for first result correctly parsed
ok 7 - end for first result correctly parsed
ok 8 - source tag for first result correctly parsed
ok 9 - primary tag for first result correctly parsed
ok 10 - score for first result correctly parsed
ok 11 - sequence description correctly parsed.
ok 12 - correctly parsed all run parameters
ok 13 - correctly parsed period_size for first result
ok 14 - correctly parsed copy_number for first result
ok 15 - correctly parsed consensus_size for first result
ok 16 - correctly parsed percent_matches for first result
ok 17 - correctly parsed percent_indels for first result
ok 18 - correctly parsed percent_a for first result
ok 19 - correctly parsed percent_c for first result
ok 20 - correctly parsed percent_g for first result
ok 21 - correctly parsed percent_t for first result
ok 22 - correctly parsed entropy for first result
ok 23 - correctly parsed repeat_sequence for first result
ok 24 - correctly parsed consensus_sequence for first result
ok 25 - seq_id for second result correctly parsed
ok 26 - start for second result correctly parsed
ok 27 - end for second result correctly parsed
ok 28 - source tag for first result correctly parsed
ok 29 - primary tag for first result correctly parsed
ok 30 - score for first result correctly parsed
ok 31 - sequence description correctly parsed.
ok 32 - correctly reatained all run parameters for second feature
ok 33 - correctly parsed period_size for second result
ok 34 - correctly parsed copy_number for second result
ok 35 - correctly parsed consensus_size for second result
ok 36 - correctly parsed percent_matches for second result
ok 37 - correctly parsed percent_indels for second result
ok 38 - correctly parsed percent_a for second result
ok 39 - correctly parsed percent_c for second result
ok 40 - correctly parsed percent_g for second result
ok 41 - correctly parsed percent_t for second result
ok 42 - correctly parsed entropy for second result
ok 43 - correctly parsed repeat_sequence for second result
ok 44 - correctly parsed consensus_sequence for second result
ok 45 - seq_id for first result correctly parsed
ok 46 - start for first result correctly parsed
ok 47 - end for first result correctly parsed
ok 48 - source tag for first result correctly parsed
ok 49 - primary tag for first result correctly parsed
ok 50 - score for first result correctly parsed
ok 51 - sequence description correctly parsed.
ok 52 - correctly reatained all run parameters for third feature
ok 53 - correctly parsed period_size for third result
ok 54 - correctly parsed copy_number for third result
ok 55 - correctly parsed consensus_size for third result
ok 56 - correctly parsed percent_matches for third result
ok 57 - correctly parsed percent_indels for third result
ok 58 - correctly parsed percent_a for third result
ok 59 - correctly parsed percent_c for third result
ok 60 - correctly parsed percent_g for third result
ok 61 - correctly parsed percent_t for third result
ok 62 - correctly parsed entropy for third result
ok 63 - correctly parsed repeat_sequence for third result
ok 64 - correctly parsed consensus_sequence for third result
ok 65 - correctly return undef when no features are left
ok 66 - Correctly parsed seq_id even if description does not exist
ok
t/Tools/TargetP.t ...................... 
1..124
ok 1 - use Bio::Tools::TargetP;
ok 2
ok 3
ok 4
ok 5 - good SeqID
ok 6 - good Seqlength
ok 7 - correct Mitochondrion cutoff
ok 8 - correct signalpPeptide cutoff
ok 9 - correct other cutoff
ok 10 - correct location
ok 11 - correct Reliability class score
ok 12 - No peptide signal length reported
ok 13 - good SeqID
ok 14 - good Seqlength
ok 15 - correct Mitochondrion cutoff
ok 16 - correct signalpPeptide cutoff
ok 17 - correct other cutoff
ok 18 - correct location
ok 19 - correct Reliability class score
ok 20 - correct peptide signal length
ok 21 - good SeqID
ok 22 - good Seqlength
ok 23 - correct Mitochondrion cutoff
ok 24 - correct signalpPeptide cutoff
ok 25 - correct other cutoff
ok 26 - correct location
ok 27 - correct Reliability class score
ok 28 - correct peptide signal length
ok 29 - good SeqID
ok 30 - good Seqlength
ok 31 - correct Mitochondrion cutoff
ok 32 - correct signalpPeptide cutoff
ok 33 - correct other cutoff
ok 34 - correct location
ok 35 - correct Reliability class score
ok 36 - No peptide signal length reported
ok 37 - good SeqID
ok 38 - good Seqlength
ok 39 - correct Mitochondrion cutoff
ok 40 - correct signalpPeptide cutoff
ok 41 - correct other cutoff
ok 42 - correct location
ok 43 - correct Reliability class score
ok 44 - No peptide signal length reported
ok 45 - good SeqID
ok 46 - good Seqlength
ok 47 - correct Mitochondrion cutoff
ok 48 - correct signalpPeptide cutoff
ok 49 - correct other cutoff
ok 50 - correct location
ok 51 - correct Reliability class score
ok 52 - No peptide signal length reported
ok 53 - good SeqID
ok 54 - good Seqlength
ok 55 - correct Mitochondrion cutoff
ok 56 - correct signalpPeptide cutoff
ok 57 - correct other cutoff
ok 58 - correct location
ok 59 - correct Reliability class score
ok 60 - No peptide signal length reported
ok 61 - good SeqID
ok 62 - good Seqlength
ok 63 - correct Mitochondrion cutoff
ok 64 - correct signalpPeptide cutoff
ok 65 - correct other cutoff
ok 66 - correct location
ok 67 - correct Reliability class score
ok 68 - correct peptide signal length
ok 69 - good SeqID
ok 70 - good Seqlength
ok 71 - correct Mitochondrion cutoff
ok 72 - correct signalpPeptide cutoff
ok 73 - correct other cutoff
ok 74 - correct location
ok 75 - correct Reliability class score
ok 76 - No peptide signal length reported
ok 77 - good SeqID
ok 78 - good Seqlength
ok 79 - correct Mitochondrion cutoff
ok 80 - correct signalpPeptide cutoff
ok 81 - correct other cutoff
ok 82 - correct location
ok 83 - correct Reliability class score
ok 84 - No peptide signal length reported
ok 85 - good SeqID
ok 86 - good Seqlength
ok 87 - correct Mitochondrion cutoff
ok 88 - correct signalpPeptide cutoff
ok 89 - correct other cutoff
ok 90 - correct location
ok 91 - correct Reliability class score
ok 92 - No peptide signal length reported
ok 93 - good SeqID
ok 94 - good Seqlength
ok 95 - correct Mitochondrion cutoff
ok 96 - correct signalpPeptide cutoff
ok 97 - correct other cutoff
ok 98 - correct location
ok 99 - correct Reliability class score
ok 100 - No peptide signal length reported
ok 101 - good SeqID
ok 102 - good Seqlength
ok 103 - correct Mitochondrion cutoff
ok 104 - correct signalpPeptide cutoff
ok 105 - correct other cutoff
ok 106 - correct location
ok 107 - correct Reliability class score
ok 108 - correct peptide signal length
ok 109 - good SeqID
ok 110 - good Seqlength
ok 111 - correct Mitochondrion cutoff
ok 112 - correct signalpPeptide cutoff
ok 113 - correct other cutoff
ok 114 - correct location
ok 115 - correct Reliability class score
ok 116 - No peptide signal length reported
ok 117 - good SeqID
ok 118 - good Seqlength
ok 119 - correct Mitochondrion cutoff
ok 120 - correct signalpPeptide cutoff
ok 121 - correct other cutoff
ok 122 - correct location
ok 123 - correct Reliability class score
ok 124 - No peptide signal length reported
ok
t/Tools/Tmhmm.t ........................ 
1..12
ok 1 - use Bio::Tools::Tmhmm;
ok 2 - new()
ok 3 - got 3 feat
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/Tools/ePCR.t ......................... 
1..27
ok 1 - use Bio::Tools::EPCR;
ok 2 - use Bio::SeqIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26 - got 3 forward strand ePCR hits
ok 27 - got 3 reverse strand ePCR hits
ok
t/Tools/pICalculator.t ................. 
1..38
ok 1 - use Bio::Seq;
ok 2 - use Bio::Tools::pICalculator;
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
t/Tools/rnamotif.t ..................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
t/Tools/tRNAscanSE.t ................... 
1..14
ok 1 - use Bio::Tools::tRNAscanSE;
ok 2 - The object isa Bio::Tools::tRNAscanSE
ok 3
ok 4 - seq_id
ok 5 - codon
ok 6 - start
ok 7 - end
ok 8 - strand
ok 9 - exons
ok 10 - end
ok 11 - start
ok 12 - start
ok 13 - end
ok 14 - seq_id
ok
t/Tree/Compatible.t .................... 
1..5
ok 1 - use Bio::Tree::Compatible;
ok 2 - use Bio::TreeIO;
ok 3
ok 4
ok 5
ok
t/Tree/Node.t .......................... 
1..40
ok 1 - use Bio::Tree::Node;
ok 2 - use Bio::Tree::AlleleNode;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - retrieve the first value
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 - with fake node
ok 37 - after reroot on fake node
ok 38 - reroot on B
ok 39 - remove fake node, reroot on former B anc
ok 40 - roundtrip
ok
t/Tree/PhyloNetwork/Factory.t .......... 
1..70
ok 1 - use Bio::PhyloNetwork::Factory;
ok 2 - The object isa Bio::PhyloNetwork::Factory
ok 3 - factory
ok 4 - seen all the data lines
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok 20 - found
ok 21 - found
ok 22 - found
ok 23 - found
ok 24 - found
ok 25 - found
ok 26 - found
ok 27 - found
ok 28 - found
ok 29 - found
ok 30 - found
ok 31 - found
ok 32 - found
ok 33 - found
ok 34 - found
ok 35 - found
ok 36 - found
ok 37 - found
ok 38 - found
ok 39 - found
ok 40 - found
ok 41 - found
ok 42 - found
ok 43 - found
ok 44 - found
ok 45 - found
ok 46 - found
ok 47 - found
ok 48 - found
ok 49 - found
ok 50 - found
ok 51 - found
ok 52 - found
ok 53 - found
ok 54 - found
ok 55 - found
ok 56 - found
ok 57 - found
ok 58 - found
ok 59 - found
ok 60 - found
ok 61 - found
ok 62 - found
ok 63 - found
ok 64 - found
ok 65 - found
ok 66 - found
ok 67 - found
ok 68 - found
ok 69 - found
ok 70 - found
ok
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module GraphViz (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... 
1..8
ok 1 - use Bio::PhyloNetwork::muVector;
ok 2 - The object isa Bio::PhyloNetwork::muVector
ok 3 - The object isa Bio::PhyloNetwork::muVector
ok 4 - arithmetic
ok 5 - display
ok 6 - is_positive
ok 7 - geq_poset
ok 8 - geq_poset
ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... 
1..30
ok 1 - use Bio::PhyloNetwork;
ok 2 - The object isa Bio::PhyloNetwork
ok 3 - is_leaf
ok 4 - is_tree_node
ok 5 - is_hybrid_node
ok 6 - is_root
ok 7 - is_tree_child
ok 8 - nodes
ok 9 - leaves
ok 10 - internal_nodes
ok 11 - edges
ok 12 - tree_edges
ok 13 - hybrid_edges
ok 14 - mudata
ok 15 - build from mudata
ok 16 - heights
ok 17 - mu_distance
ok 18 - time_consistent
ok 19 - temporal_representation
ok 20 - tripartitions
ok 21 - tripartitions
ok 22 - tripartition_error
ok 23 - weight (manhattan)
ok 24 - optimal_alignment (manhattan)
ok 25 - weight (hamming)
ok 26 - optimal_alignment (hamming)
ok 27 - eNewick
ok 28 - eNewick_full
ok 29 - explode
ok 30 - The object isa Bio::Tree::Tree
ok
t/Tree/PhyloNetwork/RandomFactory.t .... 
1..70
ok 1 - use Bio::PhyloNetwork::RandomFactory;
ok 2 - The object isa Bio::PhyloNetwork::RandomFactory
ok 3 - random factory
ok 4
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok 20 - found
ok 21 - found
ok 22 - found
ok 23 - found
ok 24 - found
ok 25 - found
ok 26 - found
ok 27 - found
ok 28 - found
ok 29 - found
ok 30 - found
ok 31 - found
ok 32 - found
ok 33 - found
ok 34 - found
ok 35 - found
ok 36 - found
ok 37 - found
ok 38 - found
ok 39 - found
ok 40 - found
ok 41 - found
ok 42 - found
ok 43 - found
ok 44 - found
ok 45 - found
ok 46 - found
ok 47 - found
ok 48 - found
ok 49 - found
ok 50 - found
ok 51 - found
ok 52 - found
ok 53 - found
ok 54 - found
ok 55 - found
ok 56 - found
ok 57 - found
ok 58 - found
ok 59 - found
ok 60 - found
ok 61 - found
ok 62 - found
ok 63 - found
ok 64 - found
ok 65 - found
ok 66 - found
ok 67 - found
ok 68 - found
ok 69 - found
ok 70 - found
ok
t/Tree/PhyloNetwork/TreeFactory.t ...... 
1..19
ok 1 - use Bio::PhyloNetwork::TreeFactory;
ok 2 - The object isa Bio::PhyloNetwork::TreeFactory
ok 3 - tree factory
ok 4 - seen all the data lines
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok
t/Tree/RandomTreeFactory.t ............. 
1..5
ok 1 - use Bio::Tree::RandomFactory;
ok 2 - use Bio::TreeIO;
ok 3 - use Bio::Tree::Statistics;
ok 4
ok 5
ok
t/Tree/Tree.t .......................... 
1..66
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7 - retrieve the first value
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - Number of nodes that have ADH2 as name
ok 15 - Test Monophyly
ok 16 - Height
ok 17 - Depth
ok 18 - non-monophyletic group
ok 19 - not a binary tree
ok 20 - 12 nodes
ok 21 - after force_binary() it is
ok 22 - and there are more nodes (17)
ok 23 - B,C are Monophyletic
ok 24 - A,B are Monophyletic
ok 25 - B,F are not Monophyletic
ok 26 - A,B are Monophyletic
ok 27 - A,B,C are not Monophyletic w D as outgroup
ok 28 - A,F,E are monophyletic with I as outgroup
ok 29 - subtree_length() without attributes is an alias to total_branch_lenght()
ok 30 - Length of the tree is larger that lenght of a subtree
ok 31 - Can re-root with A as outgroup
ok 32 - Count the number of nodes
ok 33 - same length
ok 34 - Root node is A
ok 35 - Root node is A's ancestor
ok 36 - Can reroot with C's ancsestor
ok 37 - Node count correct
ok 38 - Total original branch length is what it is supposed to be
ok 39 - Updated total branch length after the reroot
ok 40 - Make sure root is really what we asked for
ok 41 - Testing for failed re-rerooting
ok 42 - Test that rooting succeeded
ok 43 - Test that re-rooted tree has proper number of nodes after re-rooting
ok 44 - Branch length before rerooting
ok 45 - Branch length after rerooting
ok 46 - Root is really the ancestor we asked for
ok 47 - BFS traversal order
ok 48 - DFS travfersal order
ok 49 - DFS traversal after removing H
ok 50 - DFS traversal after removing G
ok 51 - DFS traversal after removing E
ok 52 - DFS after removing all but 0,1,2,A,B,C,D
ok 53 - Testing bootstrap copy
ok 54 - Testing bootstrap copy
ok 55 - Testing bootstrap copy
ok 56 - Testing bootstrap copy
ok 57 - Testing bootstrap copy
ok 58 - Testing bootstrap copy
ok 59 - Testing bootstrap copy
ok 60 - Testing bootstrap copy
ok 61 - Testing auto-boostrap copy during parse
ok 62 - Testing auto-boostrap copy during parse
ok 63 - Testing auto-boostrap copy during parse
ok 64 - Testing auto-boostrap copy during parse
ok 65
ok 66
ok
t/Tree/TreeIO.t ........................ 
1..78
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tree::TreeI
ok 14
ok 15
ok 16
ok 17
ok 18 - Saw SINFRUP0000006110 as expected
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::Tree::TreeI
ok 23 - Total Nodes
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Tree::TreeI
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - The object isa Bio::Tree::TreeI
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Tree::TreeI
ok 43 - Leaf nodes
ok 44 - All nodes
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 - bug 2356
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Tree::NodeI
ok 76
ok 77 - The object isa Bio::Tree::NodeI
not ok 78 # TODO The nodes are garbage-collected away b/c Tree isn't retained in memory

#   Failed (TODO) test at t/Tree/TreeIO.t line 342.
#          got: '0'
#     expected: '198'
ok
t/Tree/TreeIO/lintree.t ................ 
1..24
ok 1 - use Bio::TreeIO;
ok 2 - The object isa Bio::Tree::TreeI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Tree::TreeI
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Tree::TreeI
ok 18 - Leaf nodes
ok 19 - All nodes
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/Tree/TreeIO/newick.t ................. 
1..49
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tree::TreeI
ok 14
ok 15
ok 16
ok 17
ok 18 - Saw SINFRUP0000006110 as expected
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - Round trip: simple newick
ok 26 - Round trip: Root node branch length
ok 27 - Round trip: Root node branch length
ok 28 - Round trip: from Wikipedia
ok 29 - Branch length on root
ok 30 - Tiny branch length on root
ok 31 - Zero branch lenghts
ok 32 - wkp blank tree
ok 33 - wkp only leaves labeled
ok 34 - wkp all nodes labeled
ok 35 - wkp branch lengths, no labels
ok 36 - wkp branch lengths, including root
ok 37 - wkp distances and leaf names
ok 38 - wkp distances and all names
ok 39 - wkp rooted on leaf node
ok 40 - phylip simple tree
ok 41 - phylip no labels
ok 42 - phylip w/ branch lengths
ok 43 - phylip w/ internal label
ok 44 - phylip raccoon tree
ok 45 - phylip mammal tree
ok 46 - phylip mammal tree w/ underbars
ok 47 - phylip single node
ok 48 - phylip_quartet
ok 49 - phylip greek
ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
# Begin tests for writing tree files
t/Tree/TreeIO/nexml.t .................. 
1..46
ok 1 - use Bio::Tree::Tree;
ok 2 - use Bio::TreeIO;
ok 3 - use Bio::TreeIO::nexml;
ok 4
ok 5 - tree obj read
ok 6 - The object isa Bio::Tree::Tree
ok 7 - root node
ok 8 - number of nodes
ok 9
ok 10 - branch length
ok 11 - anc id
ok 12 - anc bl
ok 13
ok 14 - number of leaf nodes
ok 15 - n2 exists
ok 16 - n2 taxon
ok 17 - n5 exists
ok 18 - n5 taxon
ok 19 - n6 exists
ok 20 - n6 taxon
ok 21 - n8 exists
ok 22 - n8 taxon
ok 23 - n9 exists
ok 24 - n9 taxon
ok 25 - out stream
ok 26 - write tree
ok 27 - read tree obj (rt)
ok 28 - The object isa Bio::Tree::Tree
ok 29 - root node (rt)
ok 30 - number of nodes (rt)
ok 31
ok 32 - branch length (rt)
ok 33 - anc id (rt)
ok 34 - anc bl (rt)
ok 35
ok 36 - number of leaf nodes (rt)
ok 37 - n2 exists (rt)
ok 38 - n2 taxon (rt)
ok 39 - n5 exists (rt)
ok 40 - n5 taxon (rt)
ok 41 - n6 exists (rt)
ok 42 - n6 taxon (rt)
ok 43 - n8 exists (rt)
ok 44 - n8 taxon (rt)
ok 45 - n9 exists (rt)
ok 46 - n9 taxon (rt)
ok
t/Tree/TreeIO/nexus.t .................. 
1..24
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - bug 2356
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/Tree/TreeIO/nhx.t .................... 
1..19
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4 - Total Nodes
ok 5
ok 6
ok 7
ok 8 - Roundtrip: simple newick
ok 9 - Roundtrip: bug 1471 test
ok 10 - Roundtrip: different combinations of label, NHX, and branch length
ok 11 - Roundtrip: doot node branch length
ok 12 - Roundtrip: Example from Wikipedia
ok 13 - Roundtrip: ADH NHX tree
ok 14 - Roundtrip: notung nhx example http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html
ok 15 - Roundtrip: notung nhx bootstrap http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html
ok 16 - Roundtrip: r-sig-phylo mailing list http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00516.html
ok 17 - Roundtrip: treebest example nhx
ok 18 - Roundtrip: Wellcome Trust ToL (from http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html)
ok 19 - Roundtrip: Biorecipes NHX file (http://www.biorecipes.com/Orthologues/StatusPage/pics/TreeEukaryota.nt)
ok
t/Tree/TreeIO/phyloxml.t ............... 
1..98
ok 1 - use Bio::TreeIO;
ok 2 - use Bio::TreeIO::phyloxml;
ok 3
ok 4 - The object isa Bio::Tree::TreeI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::Tree::TreeI
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - The object isa Bio::Tree::TreeI
ok 24
ok 25
ok 26
ok 27
ok 28 - The object isa Bio::Tree::TreeI
ok 29 - The object isa Bio::Annotation::Collection
ok 30 - The object isa Bio::Annotation::Collection
ok 31
ok 32 - The object isa Bio::Annotation::Collection
ok 33
ok 34 - The object isa Bio::SeqI
ok 35 - The object isa Bio::Annotation::Collection
ok 36
ok 37
ok 38 - The object isa Bio::Tree::TreeI
ok 39
ok 40 - The object isa Bio::SeqI
ok 41 - The object isa Bio::Annotation::Relation
ok 42
ok 43 - The object isa Bio::SeqI
ok 44 - The object isa Bio::Annotation::Relation
ok 45
ok 46 - The object isa Bio::SeqI
ok 47
ok 48 - The object isa Bio::Tree::TreeI
ok 49 - The object isa Bio::SeqI
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::SeqI
ok 54
ok 55 - The object isa Bio::Tree::TreeI
ok 56 - The object isa Bio::Annotation::Relation
ok 57
ok 58 - The object isa Bio::Tree::AnnotatableNode
ok 59
ok 60
ok 61
ok 62 - The object isa Bio::Tree::TreeI
ok 63 - The object isa Bio::Tree::AnnotatableNode
ok 64 - The object isa Bio::AnnotationCollectionI
ok 65 - The object isa Bio::Annotation::Collection
ok 66
ok 67
ok 68
ok 69 - The object isa Bio::Tree::TreeI
ok 70 - The object isa Bio::Tree::AnnotatableNode
ok 71 - The object isa Bio::AnnotationCollectionI
ok 72 - The object isa Bio::Annotation::Collection
ok 73
ok 74
ok 75
ok 76 - The object isa Bio::Tree::TreeI
ok 77
ok 78 - The object isa Bio::Tree::TreeI
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84 - The object isa Bio::Tree::TreeI
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90 - The object isa Bio::Tree::TreeI
ok 91
ok 92 - The object isa Bio::Tree::AnnotatableNode
ok 93
ok 94
ok 95
ok 96
ok 97 - The object isa Bio::Tree::TreeI
ok 98
ok
t/Tree/TreeIO/svggraph.t ............... 
1..4
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok
t/Tree/TreeIO/tabtree.t ................ 
1..24
ok 1 - use Bio::TreeIO;
ok 2 - The object isa Bio::Tree::TreeI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Tree::TreeI
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Tree::TreeI
ok 18 - Leaf nodes
ok 19 - All nodes
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/Tree/TreeStatistics.t ................ 
1..42
ok 1 - use Bio::TreeIO;
ok 2 - use Bio::Tree::Statistics;
ok 3 - cherries
ok 4 - cherries
ok 5 - read traits
ok 6
ok 7
ok 8 - parsimony score
ok 9 - subtree parsimony score
ok 10 - ps value
ok 11 - fitch_down
ok 12 - ps value after fitch_down
ok 13 - persistence of a leaf
ok 14 - persistence of an internal node value 
ok 15 - persistence of an internal node value
ok 16 - persistence of an internal node value
ok 17 - leaf node: number of clusters = 0 
ok 18 - number of clusters 
ok 19 - number of clusters 
ok 20 - number of clusters 
ok 21 - number of leaves in phylotype 
ok 22 - number of leaves in phylotype 
ok 23 - number of leaves in phylotype 
ok 24 - number of leaves in phylotype 
ok 25 - phylotype length
ok 26 - phylotype length
ok 27 - phylotype length
ok 28 - phylotype length
ok 29 - phylotype length
ok 30 - sum of leaf distances
ok 31 - sum of leaf distances
ok 32 - sum of leaf distances
ok 33 - sum of leaf distances
ok 34 - sum of leaf distances
ok 35 - genetic diversity
ok 36 - separation
ok 37 - association index
ok 38 - subtree association index
ok 39 - monophyletic clade size
ok 40 - monophyletic clade size
ok 41 - monophyletic clade size
ok 42 - monophyletic clade size
ok
t/Variation/AAChange.t ................. 
1..27
ok 1 - use Bio::Variation::Allele;
ok 2 - use Bio::Variation::AAChange;
ok 3 - use Bio::Variation::RNAChange;
ok 4
ok 5 - The object isa Bio::Variation::AAChange
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 - Trivial name is [V3A]
ok 27
ok
t/Variation/AAReverseMutate.t .......... 
1..16
ok 1 - use Bio::Variation::AAReverseMutate;
ok 2
ok 3 - The object isa Bio::Variation::AAReverseMutate
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Variation::RNAChange
ok 11
ok 12
ok 13
ok 14 - Codon_ori is |ttc|
ok 15
ok 16
ok
t/Variation/Allele.t ................... 
1..14
ok 1 - use Bio::Variation::Allele;
ok 2 - The object isa Bio::Variation::Allele
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/Variation/DNAMutation.t .............. 
1..37
ok 1 - use Bio::Variation::DNAMutation;
ok 2 - use Bio::Variation::Allele;
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
t/Variation/RNAChange.t ................ 
1..31
ok 1 - use Bio::Variation::Allele;
ok 2 - use Bio::Variation::RNAChange;
ok 3 - use Bio::Variation::AAChange;
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 - label ismissense
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - Codon_ori is |gaa|
ok 26 - Codon_mut is |aaa|
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/Variation/SNP.t ...................... 
1..13
ok 1 - use Bio::Variation::SNP;
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
t/Variation/SeqDiff.t .................. 
1..44
ok 1 - use Bio::Variation::SeqDiff;
ok 2 - use Bio::Variation::DNAMutation;
ok 3 - use Bio::Variation::Allele;
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 - The object isa Bio::Variation::VariantI
ok 34 - The object isa Bio::Variation::VariantI
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeq
ok 43
ok 44
ok
t/Variation/Variation_IO.t ............. 
1..26
ok 1 - use Bio::Variation::IO;
ok 2
ok 3
ok 4
ok 5
ok 6 - test output file compared to input
ok 7
ok 8
ok 9
ok 10
ok 11 - test output file compared to input
ok 12
ok 13
ok 14
ok 15
ok 16 - test output file compared to input
ok 17
ok 18
ok 19
ok 20
ok 21 - test output file compared to input
ok 22
ok 23
ok 24
ok 25
ok 26 - test output file compared to input
ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/nexml.t .............................. 
1..125
ok 1 - use Bio::NexmlIO;
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

Test Summary Report
-------------------
t/Map/Physical.t                     (Wstat: 0 Tests: 40 Failed: 0)
  TODO passed:   40
t/RemoteDB/Taxonomy.t                (Wstat: 3328 Tests: 5 Failed: 0)
  Non-zero exit status: 13
  Parse errors: Bad plan.  You planned 191 tests but ran 5.
t/Tools/Run/WBCommandExts.t          (Wstat: 0 Tests: 25 Failed: 0)
  TODO passed:   14
Files=337, Tests=22955, 201 wallclock secs ( 3.68 usr  1.52 sys + 177.07 cusr 15.81 csys = 198.08 CPU)
Result: FAIL
Failed 1/337 test programs. 0/22955 subtests failed.
  CJFIELDS/BioPerl-1.6.921.tar.gz
  ./Build test verbose=1 -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.921.tar.gz
Finished 2013-09-11T01:07:05