wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
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# = bio/db/prosite.rb - PROSITE database class
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#
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# Copyright:: Copyright (C) 2001 Toshiaki Katayama <k@bioruby.org>
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# Licence:: Ruby's
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#
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# $Id: prosite.rb,v 0.16 2006/09/19 06:03:51 k Exp $
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#
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require 'bio/db'
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module Bio
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class PROSITE < EMBLDB
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# Delimiter
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DELIMITER = "\n//\n"
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# Delimiter
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RS = DELIMITER
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# Bio::DB API
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TAGSIZE = 5
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def initialize(entry)
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super(entry, TAGSIZE)
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end
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# ID Identification (Begins each entry; 1 per entry)
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#
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# ID ENTRY_NAME; ENTRY_TYPE. (ENTRY_TYPE : PATTERN, MATRIX, RULE)
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#
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# Returns
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def name
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unless @data['ID']
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@data['ID'], @data['TYPE'] = fetch('ID').chomp('.').split('; ')
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end
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@data['ID']
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end
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# Returns
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def division
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unless @data['TYPE']
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name
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end
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@data['TYPE']
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end
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# AC Accession number (1 per entry)
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#
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# AC PSnnnnn;
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#
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# Returns
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def ac
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unless @data['AC']
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@data['AC'] = fetch('AC').chomp(';')
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end
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@data['AC']
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end
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alias entry_id ac
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# DT Date (1 per entry)
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#
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# DT MMM-YYYY (CREATED); MMM-YYYY (DATA UPDATE); MMM-YYYY (INFO UPDATE).
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#
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# Returns
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def dt
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field_fetch('DT')
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end
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alias date dt
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# DE Short description (1 per entry)
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#
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# DE Description.
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#
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# Returns
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def de
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field_fetch('DE')
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end
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alias definition de
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# PA Pattern (>=0 per entry)
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#
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# see - pa2re method
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#
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# Returns
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def pa
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field_fetch('PA')
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@data['PA'] = fetch('PA') unless @data['PA']
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@data['PA'].gsub!(/\s+/, '') if @data['PA']
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@data['PA']
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end
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alias pattern pa
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# MA Matrix/profile (>=0 per entry)
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#
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# see - ma2re method
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#
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# Returns
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def ma
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field_fetch('MA')
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end
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alias profile ma
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# RU Rule (>=0 per entry)
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#
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# RU Rule_Description.
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#
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# The rule is described in ordinary English and is free-format.
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#
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# Returns
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def ru
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field_fetch('RU')
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end
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alias rule ru
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# NR Numerical results (>=0 per entry)
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#
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# - SWISS-PROT scan statistics of true and false positives/negatives
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#
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# /RELEASE SWISS-PROT release number and total number of sequence
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# entries in that release.
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# /TOTAL Total number of hits in SWISS-PROT.
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# /POSITIVE Number of hits on proteins that are known to belong to the
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# set in consideration.
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# /UNKNOWN Number of hits on proteins that could possibly belong to
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# the set in consideration.
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# /FALSE_POS Number of false hits (on unrelated proteins).
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# /FALSE_NEG Number of known missed hits.
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# /PARTIAL Number of partial sequences which belong to the set in
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# consideration, but which are not hit by the pattern or
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# profile because they are partial (fragment) sequences.
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#
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# Returns
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def nr
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unless @data['NR']
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hash = {} # temporal hash
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fetch('NR').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
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if v =~ /^(\d+)\((\d+)\)$/
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hits = $1.to_i # the number of hits
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seqs = $2.to_i # the number of sequences
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v = [hits, seqs]
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elsif v =~ /([\d\.]+),(\d+)/
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sprel = $1 # the number of SWISS-PROT release
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spseq = $2.to_i # the number of SWISS-PROT sequences
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v = [sprel, spseq]
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else
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v = v.to_i
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end
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hash[k] = v
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end
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@data['NR'] = hash
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end
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@data['NR']
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end
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alias statistics nr
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# Returns
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def release
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statistics['RELEASE']
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end
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# Returns
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def swissprot_release_number
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release.first
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end
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# Returns
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def swissprot_release_sequences
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release.last
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end
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# Returns
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def total
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statistics['TOTAL']
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end
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# Returns
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def total_hits
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total.first
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end
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# Returns
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def total_sequences
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total.last
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end
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# Returns
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def positive
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statistics['POSITIVE']
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end
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# Returns
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def positive_hits
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positive.first
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end
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# Returns
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def positive_sequences
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positive.last
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end
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# Returns
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def unknown
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statistics['UNKNOWN']
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end
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# Returns
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def unknown_hits
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unknown.first
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end
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# Returns
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def unknown_sequences
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unknown.last
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end
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# Returns
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def false_pos
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statistics['FALSE_POS']
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end
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# Returns
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def false_positive_hits
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false_pos.first
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end
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# Returns
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def false_positive_sequences
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false_pos.last
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end
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# Returns
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def false_neg
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statistics['FALSE_NEG']
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end
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alias false_negative_hits false_neg
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# Returns
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def partial
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statistics['PARTIAL']
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end
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# CC Comments (>=0 per entry)
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#
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# CC /QUALIFIER=data; /QUALIFIER=data; .......
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#
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# /TAXO-RANGE Taxonomic range.
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# /MAX-REPEAT Maximum known number of repetitions of the pattern in a
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# single protein.
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# /SITE Indication of an `interesting' site in the pattern.
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# /SKIP-FLAG Indication of an entry that can be, in some cases, ignored
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# by a program (because it is too unspecific).
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#
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# Returns
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def cc
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unless @data['CC']
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hash = {} # temporal hash
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fetch('CC').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
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hash[k] = v
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end
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@data['CC'] = hash
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end
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@data['CC']
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end
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alias comment cc
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# Returns
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def taxon_range(expand = nil)
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range = comment['TAXO-RANGE']
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if range and expand
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expand = []
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range.scan(/./) do |x|
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case x
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when 'A'; expand.push('archaebacteria')
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when 'B'; expand.push('bacteriophages')
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when 'E'; expand.push('eukaryotes')
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when 'P'; expand.push('prokaryotes')
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when 'V'; expand.push('eukaryotic viruses')
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end
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end
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range = expand
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end
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return range
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end
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# Returns
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def max_repeat
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comment['MAX-REPEAT'].to_i
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end
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# Returns
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def site
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if comment['SITE']
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num, desc = comment['SITE'].split(',')
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end
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return [num.to_i, desc]
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end
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# Returns
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def skip_flag
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if comment['SKIP-FLAG'] == 'TRUE'
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return true
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end
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end
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# DR Cross-references to SWISS-PROT (>=0 per entry)
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#
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# DR AC_NB, ENTRY_NAME, C; AC_NB, ENTRY_NAME, C; AC_NB, ENTRY_NAME, C;
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#
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# - `AC_NB' is the SWISS-PROT primary accession number of the entry to
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# which reference is being made.
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# - `ENTRY_NAME' is the SWISS-PROT entry name.
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# - `C' is a one character flag that can be one of the following:
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#
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# T For a true positive.
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# N For a false negative; a sequence which belongs to the set under
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# consideration, but which has not been picked up by the pattern or
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# profile.
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# P For a `potential' hit; a sequence that belongs to the set under
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# consideration, but which was not picked up because the region(s) that
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# are used as a 'fingerprint' (pattern or profile) is not yet available
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# in the data bank (partial sequence).
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# ? For an unknown; a sequence which possibly could belong to the set under
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# consideration.
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# F For a false positive; a sequence which does not belong to the set in
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# consideration.
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#
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# Returns
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def dr
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unless @data['DR']
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hash = {} # temporal hash
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if fetch('DR')
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fetch('DR').scan(/(\w+)\s*, (\w+)\s*, (.);/).each do |a, e, c|
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hash[a] = [e, c] # SWISS-PROT : accession, entry, true/false
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end
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end
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@data['DR'] = hash
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end
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@data['DR']
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end
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alias sp_xref dr
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# Returns
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def list_xref(flag, by_name = nil)
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ary = []
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sp_xref.each do |sp_acc, value|
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if value[1] == flag
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if by_name
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sp_name = value[0]
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ary.push(sp_name)
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else
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ary.push(sp_acc)
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end
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end
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end
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return ary
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end
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# Returns
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381
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def list_truepositive(by_name = nil)
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list_xref('T', by_name)
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end
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|
+
|
385
|
+
# Returns
|
386
|
+
def list_falsenegative(by_name = nil)
|
387
|
+
list_xref('F', by_name)
|
388
|
+
end
|
389
|
+
|
390
|
+
# Returns
|
391
|
+
def list_falsepositive(by_name = nil)
|
392
|
+
list_xref('P', by_name)
|
393
|
+
end
|
394
|
+
|
395
|
+
# Returns
|
396
|
+
def list_potentialhit(by_name = nil)
|
397
|
+
list_xref('P', by_name)
|
398
|
+
end
|
399
|
+
|
400
|
+
# Returns
|
401
|
+
def list_unknown(by_name = nil)
|
402
|
+
list_xref('?', by_name)
|
403
|
+
end
|
404
|
+
|
405
|
+
|
406
|
+
# 3D Cross-references to PDB (>=0 per entry)
|
407
|
+
#
|
408
|
+
# 3D name; [name2;...]
|
409
|
+
#
|
410
|
+
# Returns
|
411
|
+
def pdb_xref
|
412
|
+
unless @data['3D']
|
413
|
+
@data['3D'] = fetch('3D').split(/; */)
|
414
|
+
end
|
415
|
+
@data['3D']
|
416
|
+
end
|
417
|
+
|
418
|
+
|
419
|
+
# DO Pointer to the documentation file (1 per entry)
|
420
|
+
#
|
421
|
+
# DO PDOCnnnnn;
|
422
|
+
#
|
423
|
+
# Returns
|
424
|
+
def pdoc_xref
|
425
|
+
@data['DO'] = fetch('DO').chomp(';')
|
426
|
+
end
|
427
|
+
|
428
|
+
|
429
|
+
### prosite pattern to regular expression
|
430
|
+
#
|
431
|
+
# prosite/prosuser.txt:
|
432
|
+
#
|
433
|
+
# The PA (PAttern) lines contains the definition of a PROSITE pattern. The
|
434
|
+
# patterns are described using the following conventions:
|
435
|
+
#
|
436
|
+
# 0) The standard IUPAC one-letter codes for the amino acids are used.
|
437
|
+
# 0) Ambiguities are indicated by listing the acceptable amino acids for a
|
438
|
+
# given position, between square parentheses `[ ]'. For example: [ALT]
|
439
|
+
# stands for Ala or Leu or Thr.
|
440
|
+
# 1) A period ends the pattern.
|
441
|
+
# 2) When a pattern is restricted to either the N- or C-terminal of a
|
442
|
+
# sequence, that pattern either starts with a `<' symbol or respectively
|
443
|
+
# ends with a `>' symbol.
|
444
|
+
# 3) Ambiguities are also indicated by listing between a pair of curly
|
445
|
+
# brackets `{ }' the amino acids that are not accepted at a given
|
446
|
+
# position. For example: {AM} stands for any amino acid except Ala and
|
447
|
+
# Met.
|
448
|
+
# 4) Repetition of an element of the pattern can be indicated by following
|
449
|
+
# that element with a numerical value or a numerical range between
|
450
|
+
# parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to
|
451
|
+
# x-x or x-x-x or x-x-x-x.
|
452
|
+
# 5) The symbol `x' is used for a position where any amino acid is accepted.
|
453
|
+
# 6) Each element in a pattern is separated from its neighbor by a `-'.
|
454
|
+
#
|
455
|
+
# Examples:
|
456
|
+
#
|
457
|
+
# PA [AC]-x-V-x(4)-{ED}.
|
458
|
+
#
|
459
|
+
# This pattern is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any
|
460
|
+
# but Glu or Asp}
|
461
|
+
#
|
462
|
+
# PA <A-x-[ST](2)-x(0,1)-V.
|
463
|
+
#
|
464
|
+
# This pattern, which must be in the N-terminal of the sequence (`<'), is
|
465
|
+
# translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
|
466
|
+
#
|
467
|
+
def self.pa2re(pattern)
|
468
|
+
pattern.gsub!(/\s/, '') # remove white spaces
|
469
|
+
pattern.sub!(/\.$/, '') # (1) remove trailing '.'
|
470
|
+
pattern.sub!(/^</, '^') # (2) restricted to the N-terminal : `<'
|
471
|
+
pattern.sub!(/>$/, '$') # (2) restricted to the C-terminal : `>'
|
472
|
+
pattern.gsub!(/\{(\w+)\}/) { |m|
|
473
|
+
'[^' + $1 + ']' # (3) not accepted at a given position : '{}'
|
474
|
+
}
|
475
|
+
pattern.gsub!(/\(([\d,]+)\)/) { |m|
|
476
|
+
'{' + $1 + '}' # (4) repetition of an element : (n), (n,m)
|
477
|
+
}
|
478
|
+
pattern.tr!('x', '.') # (5) any amino acid is accepted : 'x'
|
479
|
+
pattern.tr!('-', '') # (6) each element is separated by a '-'
|
480
|
+
Regexp.new(pattern, Regexp::IGNORECASE)
|
481
|
+
end
|
482
|
+
|
483
|
+
def pa2re(pattern)
|
484
|
+
self.class.pa2re(pattern)
|
485
|
+
end
|
486
|
+
|
487
|
+
def re
|
488
|
+
self.class.pa2re(self.pa)
|
489
|
+
end
|
490
|
+
|
491
|
+
|
492
|
+
### prosite profile to regular expression
|
493
|
+
#
|
494
|
+
# prosite/profile.txt:
|
495
|
+
#
|
496
|
+
# Returns
|
497
|
+
def ma2re(matrix)
|
498
|
+
raise NotImplementedError
|
499
|
+
end
|
500
|
+
|
501
|
+
end # PROSITE
|
502
|
+
|
503
|
+
end # Bio
|
504
|
+
|
505
|
+
|
506
|
+
if __FILE__ == $0
|
507
|
+
|
508
|
+
begin
|
509
|
+
require 'pp'
|
510
|
+
alias p pp
|
511
|
+
rescue LoadError
|
512
|
+
end
|
513
|
+
|
514
|
+
ps = Bio::PROSITE.new(ARGF.read)
|
515
|
+
|
516
|
+
list = %w(
|
517
|
+
name
|
518
|
+
division
|
519
|
+
ac
|
520
|
+
entry_id
|
521
|
+
dt
|
522
|
+
date
|
523
|
+
de
|
524
|
+
definition
|
525
|
+
pa
|
526
|
+
pattern
|
527
|
+
ma
|
528
|
+
profile
|
529
|
+
ru
|
530
|
+
rule
|
531
|
+
nr
|
532
|
+
statistics
|
533
|
+
release
|
534
|
+
swissprot_release_number
|
535
|
+
swissprot_release_sequences
|
536
|
+
total
|
537
|
+
total_hits
|
538
|
+
total_sequences
|
539
|
+
positive
|
540
|
+
positive_hits
|
541
|
+
positive_sequences
|
542
|
+
unknown
|
543
|
+
unknown_hits
|
544
|
+
unknown_sequences
|
545
|
+
false_pos
|
546
|
+
false_positive_hits
|
547
|
+
false_positive_sequences
|
548
|
+
false_neg
|
549
|
+
false_negative_hits
|
550
|
+
partial
|
551
|
+
cc
|
552
|
+
comment
|
553
|
+
max_repeat
|
554
|
+
site
|
555
|
+
skip_flag
|
556
|
+
dr
|
557
|
+
sp_xref
|
558
|
+
pdb_xref
|
559
|
+
pdoc_xref
|
560
|
+
)
|
561
|
+
|
562
|
+
list.each do |method|
|
563
|
+
puts ">>> #{method}"
|
564
|
+
p ps.send(method)
|
565
|
+
end
|
566
|
+
|
567
|
+
puts ">>> taxon_range"
|
568
|
+
p ps.taxon_range
|
569
|
+
puts ">>> taxon_range(expand)"
|
570
|
+
p ps.taxon_range(true)
|
571
|
+
|
572
|
+
puts ">>> list_truepositive"
|
573
|
+
p ps.list_truepositive
|
574
|
+
puts ">>> list_truepositive(by_name)"
|
575
|
+
p ps.list_truepositive(true)
|
576
|
+
|
577
|
+
puts ">>> list_falsenegative"
|
578
|
+
p ps.list_falsenegative
|
579
|
+
puts ">>> list_falsenegative(by_name)"
|
580
|
+
p ps.list_falsenegative(true)
|
581
|
+
|
582
|
+
puts ">>> list_falsepositive"
|
583
|
+
p ps.list_falsepositive
|
584
|
+
puts ">>> list_falsepositive(by_name)"
|
585
|
+
p ps.list_falsepositive(true)
|
586
|
+
|
587
|
+
puts ">>> list_potentialhit"
|
588
|
+
p ps.list_potentialhit
|
589
|
+
puts ">>> list_potentialhit(by_name)"
|
590
|
+
p ps.list_potentialhit(true)
|
591
|
+
|
592
|
+
puts ">>> list_unknown"
|
593
|
+
p ps.list_unknown
|
594
|
+
puts ">>> list_unknown(by_name)"
|
595
|
+
p ps.list_unknown(true)
|
596
|
+
|
597
|
+
end
|