wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- 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
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- 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
data/lib/bio/db/fasta.rb
ADDED
@@ -0,0 +1,410 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/fasta.rb - FASTA format class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2001, 2002
|
5
|
+
# Naohisa Goto <ng@bioruby.org>,
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: fasta.rb,v 1.28.2.3 2008/06/20 13:43:36 ngoto Exp $
|
10
|
+
#
|
11
|
+
# == Description
|
12
|
+
#
|
13
|
+
# FASTA format class.
|
14
|
+
#
|
15
|
+
# == Examples
|
16
|
+
#
|
17
|
+
# See documents of Bio::FastaFormat class.
|
18
|
+
#
|
19
|
+
# == References
|
20
|
+
#
|
21
|
+
# * FASTA format (WikiPedia)
|
22
|
+
# http://en.wikipedia.org/wiki/FASTA_format
|
23
|
+
#
|
24
|
+
# * Fasta format description (NCBI)
|
25
|
+
# http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
|
26
|
+
#
|
27
|
+
|
28
|
+
require 'bio/db'
|
29
|
+
require 'bio/sequence'
|
30
|
+
require 'bio/sequence/dblink'
|
31
|
+
require 'bio/db/fasta/defline'
|
32
|
+
|
33
|
+
module Bio
|
34
|
+
|
35
|
+
|
36
|
+
# Treats a FASTA formatted entry, such as:
|
37
|
+
#
|
38
|
+
# >id and/or some comments <== comment line
|
39
|
+
# ATGCATGCATGCATGCATGCATGCATGCATGCATGC <== sequence lines
|
40
|
+
# ATGCATGCATGCATGCATGCATGCATGCATGCATGC
|
41
|
+
# ATGCATGCATGC
|
42
|
+
#
|
43
|
+
# The precedent '>' can be omitted and the trailing '>' will be removed
|
44
|
+
# automatically.
|
45
|
+
#
|
46
|
+
# === Examples
|
47
|
+
#
|
48
|
+
# f_str = <<END_OF_STRING
|
49
|
+
# >sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
|
50
|
+
# MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
|
51
|
+
# VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
|
52
|
+
# GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
|
53
|
+
# KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
|
54
|
+
# IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
|
55
|
+
# QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
|
56
|
+
# >sce:YBR274W CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
|
57
|
+
# MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
|
58
|
+
# TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
|
59
|
+
# GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
|
60
|
+
# DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
|
61
|
+
# DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
|
62
|
+
# EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
|
63
|
+
# AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
|
64
|
+
# QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
|
65
|
+
# CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
|
66
|
+
# FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
|
67
|
+
# KTGDPLEWRRLFKKISTICRDIILIPN
|
68
|
+
# END_OF_STRING
|
69
|
+
#
|
70
|
+
# f = Bio::FastaFormat.new(f_str)
|
71
|
+
# puts "### FastaFormat"
|
72
|
+
# puts "# entry"
|
73
|
+
# puts f.entry
|
74
|
+
# puts "# entry_id"
|
75
|
+
# p f.entry_id
|
76
|
+
# puts "# definition"
|
77
|
+
# p f.definition
|
78
|
+
# puts "# data"
|
79
|
+
# p f.data
|
80
|
+
# puts "# seq"
|
81
|
+
# p f.seq
|
82
|
+
# puts "# seq.type"
|
83
|
+
# p f.seq.type
|
84
|
+
# puts "# length"
|
85
|
+
# p f.length
|
86
|
+
# puts "# aaseq"
|
87
|
+
# p f.aaseq
|
88
|
+
# puts "# aaseq.type"
|
89
|
+
# p f.aaseq.type
|
90
|
+
# puts "# aaseq.composition"
|
91
|
+
# p f.aaseq.composition
|
92
|
+
# puts "# aalen"
|
93
|
+
# p f.aalen
|
94
|
+
#
|
95
|
+
# === References
|
96
|
+
#
|
97
|
+
# * FASTA format (WikiPedia)
|
98
|
+
# http://en.wikipedia.org/wiki/FASTA_format
|
99
|
+
#
|
100
|
+
class FastaFormat < DB
|
101
|
+
|
102
|
+
# Entry delimiter in flatfile text.
|
103
|
+
DELIMITER = RS = "\n>"
|
104
|
+
|
105
|
+
# (Integer) excess read size included in DELIMITER.
|
106
|
+
DELIMITER_OVERRUN = 1 # '>'
|
107
|
+
|
108
|
+
# The comment line of the FASTA formatted data.
|
109
|
+
attr_accessor :definition
|
110
|
+
|
111
|
+
# The seuqnce lines in text.
|
112
|
+
attr_accessor :data
|
113
|
+
|
114
|
+
attr_reader :entry_overrun
|
115
|
+
|
116
|
+
# Stores the comment and sequence information from one entry of the
|
117
|
+
# FASTA format string. If the argument contains more than one
|
118
|
+
# entry, only the first entry is used.
|
119
|
+
def initialize(str)
|
120
|
+
@definition = str[/.*/].sub(/^>/, '').strip # 1st line
|
121
|
+
@data = str.sub(/.*/, '') # rests
|
122
|
+
@data.sub!(/^>.*/m, '') # remove trailing entries for sure
|
123
|
+
@entry_overrun = $&
|
124
|
+
end
|
125
|
+
|
126
|
+
# Returns the stored one entry as a FASTA format. (same as to_s)
|
127
|
+
def entry
|
128
|
+
@entry = ">#{@definition}\n#{@data.strip}\n"
|
129
|
+
end
|
130
|
+
alias to_s entry
|
131
|
+
|
132
|
+
|
133
|
+
# Executes FASTA/BLAST search by using a Bio::Fasta or a Bio::Blast
|
134
|
+
# factory object.
|
135
|
+
#
|
136
|
+
# #!/usr/bin/env ruby
|
137
|
+
# require 'bio'
|
138
|
+
#
|
139
|
+
# factory = Bio::Fasta.local('fasta34', 'db/swissprot.f')
|
140
|
+
# flatfile = Bio::FlatFile.open(Bio::FastaFormat, 'queries.f')
|
141
|
+
# flatfile.each do |entry|
|
142
|
+
# p entry.definition
|
143
|
+
# result = entry.fasta(factory)
|
144
|
+
# result.each do |hit|
|
145
|
+
# print "#{hit.query_id} : #{hit.evalue}\t#{hit.target_id} at "
|
146
|
+
# p hit.lap_at
|
147
|
+
# end
|
148
|
+
# end
|
149
|
+
#
|
150
|
+
def query(factory)
|
151
|
+
factory.query(@entry)
|
152
|
+
end
|
153
|
+
alias fasta query
|
154
|
+
alias blast query
|
155
|
+
|
156
|
+
# Returns a joined sequence line as a String.
|
157
|
+
def seq
|
158
|
+
unless defined?(@seq)
|
159
|
+
unless /\A\s*^\#/ =~ @data then
|
160
|
+
@seq = Sequence::Generic.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
|
161
|
+
else
|
162
|
+
a = @data.split(/(^\#.*$)/)
|
163
|
+
i = 0
|
164
|
+
cmnt = {}
|
165
|
+
s = []
|
166
|
+
a.each do |x|
|
167
|
+
if /^# ?(.*)$/ =~ x then
|
168
|
+
cmnt[i] ? cmnt[i] << "\n" << $1 : cmnt[i] = $1
|
169
|
+
else
|
170
|
+
x.tr!(" \t\r\n0-9", '') # lazy clean up
|
171
|
+
i += x.length
|
172
|
+
s << x
|
173
|
+
end
|
174
|
+
end
|
175
|
+
@comment = cmnt
|
176
|
+
@seq = Bio::Sequence::Generic.new(s.join(''))
|
177
|
+
end
|
178
|
+
end
|
179
|
+
@seq
|
180
|
+
end
|
181
|
+
|
182
|
+
# Returns comments.
|
183
|
+
def comment
|
184
|
+
seq
|
185
|
+
@comment
|
186
|
+
end
|
187
|
+
|
188
|
+
# Returns sequence length.
|
189
|
+
def length
|
190
|
+
seq.length
|
191
|
+
end
|
192
|
+
|
193
|
+
# Returens the Bio::Sequence::NA.
|
194
|
+
def naseq
|
195
|
+
Sequence::NA.new(seq)
|
196
|
+
end
|
197
|
+
|
198
|
+
# Returens the length of Bio::Sequence::NA.
|
199
|
+
def nalen
|
200
|
+
self.naseq.length
|
201
|
+
end
|
202
|
+
|
203
|
+
# Returens the Bio::Sequence::AA.
|
204
|
+
def aaseq
|
205
|
+
Sequence::AA.new(seq)
|
206
|
+
end
|
207
|
+
|
208
|
+
# Returens the length of Bio::Sequence::AA.
|
209
|
+
def aalen
|
210
|
+
self.aaseq.length
|
211
|
+
end
|
212
|
+
|
213
|
+
# Returns sequence as a Bio::Sequence object.
|
214
|
+
#
|
215
|
+
# Note: If you modify the returned Bio::Sequence object,
|
216
|
+
# the sequence or definition in this FastaFormat object
|
217
|
+
# might also be changed (but not always be changed)
|
218
|
+
# because of efficiency.
|
219
|
+
#
|
220
|
+
def to_biosequence
|
221
|
+
Bio::Sequence.adapter(self, Bio::Sequence::Adapter::FastaFormat)
|
222
|
+
end
|
223
|
+
alias to_seq to_biosequence
|
224
|
+
|
225
|
+
# Parsing FASTA Defline, and extract IDs.
|
226
|
+
# IDs are NSIDs (NCBI standard FASTA sequence identifiers)
|
227
|
+
# or ":"-separated IDs.
|
228
|
+
# It returns a Bio::FastaDefline instance.
|
229
|
+
def identifiers
|
230
|
+
unless defined?(@ids) then
|
231
|
+
@ids = FastaDefline.new(@definition)
|
232
|
+
end
|
233
|
+
@ids
|
234
|
+
end
|
235
|
+
|
236
|
+
# Parsing FASTA Defline (using #identifiers method), and
|
237
|
+
# shows a possibly unique identifier.
|
238
|
+
# It returns a string.
|
239
|
+
def entry_id
|
240
|
+
identifiers.entry_id
|
241
|
+
end
|
242
|
+
|
243
|
+
# Parsing FASTA Defline (using #identifiers method), and
|
244
|
+
# shows GI/locus/accession/accession with version number.
|
245
|
+
# If a entry has more than two of such IDs,
|
246
|
+
# only the first ID are shown.
|
247
|
+
# It returns a string or nil.
|
248
|
+
def gi
|
249
|
+
identifiers.gi
|
250
|
+
end
|
251
|
+
|
252
|
+
# Returns an accession number.
|
253
|
+
def accession
|
254
|
+
identifiers.accession
|
255
|
+
end
|
256
|
+
|
257
|
+
# Parsing FASTA Defline (using #identifiers method), and
|
258
|
+
# shows accession numbers.
|
259
|
+
# It returns an array of strings.
|
260
|
+
def accessions
|
261
|
+
identifiers.accessions
|
262
|
+
end
|
263
|
+
|
264
|
+
# Returns accession number with version.
|
265
|
+
def acc_version
|
266
|
+
identifiers.acc_version
|
267
|
+
end
|
268
|
+
|
269
|
+
# Returns locus.
|
270
|
+
def locus
|
271
|
+
identifiers.locus
|
272
|
+
end
|
273
|
+
|
274
|
+
end #class FastaFormat
|
275
|
+
|
276
|
+
# Treats a FASTA formatted numerical entry, such as:
|
277
|
+
#
|
278
|
+
# >id and/or some comments <== comment line
|
279
|
+
# 24 15 23 29 20 13 20 21 21 23 22 25 13 <== numerical data
|
280
|
+
# 22 17 15 25 27 32 26 32 29 29 25
|
281
|
+
#
|
282
|
+
# The precedent '>' can be omitted and the trailing '>' will be removed
|
283
|
+
# automatically.
|
284
|
+
#
|
285
|
+
# --- Bio::FastaNumericFormat.new(entry)
|
286
|
+
#
|
287
|
+
# Stores the comment and the list of the numerical data.
|
288
|
+
#
|
289
|
+
# --- Bio::FastaNumericFormat#definition
|
290
|
+
#
|
291
|
+
# The comment line of the FASTA formatted data.
|
292
|
+
#
|
293
|
+
# * FASTA format (Wikipedia)
|
294
|
+
# http://en.wikipedia.org/wiki/FASTA_format
|
295
|
+
class FastaNumericFormat < FastaFormat
|
296
|
+
|
297
|
+
# Returns the list of the numerical data (typically the quality score
|
298
|
+
# of its corresponding sequence) as an Array.
|
299
|
+
def data
|
300
|
+
unless @list
|
301
|
+
@list = @data.strip.split(/\s+/).map {|x| x.to_i}
|
302
|
+
end
|
303
|
+
@list
|
304
|
+
end
|
305
|
+
|
306
|
+
# Returns the number of elements in the numerical data.
|
307
|
+
def length
|
308
|
+
data.length
|
309
|
+
end
|
310
|
+
|
311
|
+
# Yields on each elements of the numerical data.
|
312
|
+
def each
|
313
|
+
data.each do |x|
|
314
|
+
yield x
|
315
|
+
end
|
316
|
+
end
|
317
|
+
|
318
|
+
# Returns the n-th element.
|
319
|
+
def [](n)
|
320
|
+
data[n]
|
321
|
+
end
|
322
|
+
|
323
|
+
undef query, blast, fasta, seq, naseq, nalen, aaseq, aalen
|
324
|
+
|
325
|
+
end #class FastaNumericFormat
|
326
|
+
|
327
|
+
end #module Bio
|
328
|
+
|
329
|
+
if __FILE__ == $0
|
330
|
+
|
331
|
+
f_str = <<END
|
332
|
+
>sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
|
333
|
+
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
|
334
|
+
VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
|
335
|
+
GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
|
336
|
+
KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
|
337
|
+
IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
|
338
|
+
QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
|
339
|
+
>sce:YBR274W CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
|
340
|
+
MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
|
341
|
+
TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
|
342
|
+
GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
|
343
|
+
DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
|
344
|
+
DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
|
345
|
+
EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
|
346
|
+
AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
|
347
|
+
QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
|
348
|
+
CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
|
349
|
+
FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
|
350
|
+
KTGDPLEWRRLFKKISTICRDIILIPN
|
351
|
+
END
|
352
|
+
|
353
|
+
f = Bio::FastaFormat.new(f_str)
|
354
|
+
puts "### FastaFormat"
|
355
|
+
puts "# entry"
|
356
|
+
puts f.entry
|
357
|
+
puts "# entry_id"
|
358
|
+
p f.entry_id
|
359
|
+
puts "# definition"
|
360
|
+
p f.definition
|
361
|
+
puts "# data"
|
362
|
+
p f.data
|
363
|
+
puts "# seq"
|
364
|
+
p f.seq
|
365
|
+
puts "# seq.type"
|
366
|
+
p f.seq.type
|
367
|
+
puts "# length"
|
368
|
+
p f.length
|
369
|
+
puts "# aaseq"
|
370
|
+
p f.aaseq
|
371
|
+
puts "# aaseq.type"
|
372
|
+
p f.aaseq.type
|
373
|
+
puts "# aaseq.composition"
|
374
|
+
p f.aaseq.composition
|
375
|
+
puts "# aalen"
|
376
|
+
p f.aalen
|
377
|
+
|
378
|
+
puts
|
379
|
+
|
380
|
+
n_str = <<END
|
381
|
+
>CRA3575282.F
|
382
|
+
24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26
|
383
|
+
32 29 29 25
|
384
|
+
END
|
385
|
+
|
386
|
+
n = Bio::FastaNumericFormat.new(n_str)
|
387
|
+
puts "### FastaNumericFormat"
|
388
|
+
puts "# entry"
|
389
|
+
puts n.entry
|
390
|
+
puts "# entry_id"
|
391
|
+
p n.entry_id
|
392
|
+
puts "# definition"
|
393
|
+
p n.definition
|
394
|
+
puts "# data"
|
395
|
+
p n.data
|
396
|
+
puts "# length"
|
397
|
+
p n.length
|
398
|
+
puts "# percent to ratio by yield"
|
399
|
+
n.each do |x|
|
400
|
+
p x/100.0
|
401
|
+
end
|
402
|
+
puts "# first three"
|
403
|
+
p n[0]
|
404
|
+
p n[1]
|
405
|
+
p n[2]
|
406
|
+
puts "# last one"
|
407
|
+
p n[-1]
|
408
|
+
|
409
|
+
end
|
410
|
+
|
@@ -0,0 +1,532 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/fasta/defline.rb - FASTA defline parser class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2001, 2002
|
5
|
+
# GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>,
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $
|
10
|
+
#
|
11
|
+
# == Description
|
12
|
+
#
|
13
|
+
# Bio::FastaDefline is a parser class for definition line (defline)
|
14
|
+
# of the FASTA format.
|
15
|
+
#
|
16
|
+
# == Examples
|
17
|
+
#
|
18
|
+
# rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
|
19
|
+
# rub.entry_id ==> 'gi|671595'
|
20
|
+
# rub.get('emb') ==> 'CAA85678.1'
|
21
|
+
# rub.emb ==> 'CAA85678.1'
|
22
|
+
# rub.gi ==> '671595'
|
23
|
+
# rub.accession ==> 'CAA85678'
|
24
|
+
# rub.accessions ==> [ 'CAA85678' ]
|
25
|
+
# rub.acc_version ==> 'CAA85678.1'
|
26
|
+
# rub.locus ==> nil
|
27
|
+
# rub.list_ids ==> [["gi", "671595"],
|
28
|
+
# ["emb", "CAA85678.1", nil],
|
29
|
+
# ["Perovskia abrotanoides"]]
|
30
|
+
#
|
31
|
+
# ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
|
32
|
+
# ckr.entry_id ==> "gi|2495000"
|
33
|
+
# ckr.sp ==> "CCKR_CAVPO"
|
34
|
+
# ckr.pir ==> "I51898"
|
35
|
+
# ckr.gb ==> "AAB29504.1"
|
36
|
+
# ckr.gi ==> "2495000"
|
37
|
+
# ckr.accession ==> "AAB29504"
|
38
|
+
# ckr.accessions ==> ["Q63931", "AAB29504"]
|
39
|
+
# ckr.acc_version ==> "AAB29504.1"
|
40
|
+
# ckr.locus ==> nil
|
41
|
+
# ckr.description ==>
|
42
|
+
# "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
|
43
|
+
# ckr.descriptions ==>
|
44
|
+
# ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
|
45
|
+
# "cholecystokinin A receptor - guinea pig",
|
46
|
+
# "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
|
47
|
+
# ckr.words ==>
|
48
|
+
# ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
|
49
|
+
# "receptor", "type"]
|
50
|
+
# ckr.id_strings ==>
|
51
|
+
# ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
|
52
|
+
# "544724", "AAB29504.1", "Cavia"]
|
53
|
+
# ckr.list_ids ==>
|
54
|
+
# [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
|
55
|
+
# ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
|
56
|
+
# ["gb", "AAB29504.1", nil], ["Cavia"]]
|
57
|
+
#
|
58
|
+
# == References
|
59
|
+
#
|
60
|
+
# * FASTA format (WikiPedia)
|
61
|
+
# http://en.wikipedia.org/wiki/FASTA_format
|
62
|
+
#
|
63
|
+
# * Fasta format description (NCBI)
|
64
|
+
# http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
|
65
|
+
#
|
66
|
+
|
67
|
+
module Bio
|
68
|
+
|
69
|
+
#--
|
70
|
+
# split from fasta.rb revision 1.28
|
71
|
+
#++
|
72
|
+
|
73
|
+
# Parsing FASTA Defline, and extract IDs and other informations.
|
74
|
+
# IDs are NSIDs (NCBI standard FASTA sequence identifiers)
|
75
|
+
# or ":"-separated IDs.
|
76
|
+
#
|
77
|
+
# specs are described in:
|
78
|
+
# ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
|
79
|
+
# http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
|
80
|
+
#
|
81
|
+
# === Examples
|
82
|
+
#
|
83
|
+
# rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
|
84
|
+
# rub.entry_id ==> 'gi|671595'
|
85
|
+
# rub.get('emb') ==> 'CAA85678.1'
|
86
|
+
# rub.emb ==> 'CAA85678.1'
|
87
|
+
# rub.gi ==> '671595'
|
88
|
+
# rub.accession ==> 'CAA85678'
|
89
|
+
# rub.accessions ==> [ 'CAA85678' ]
|
90
|
+
# rub.acc_version ==> 'CAA85678.1'
|
91
|
+
# rub.locus ==> nil
|
92
|
+
# rub.list_ids ==> [["gi", "671595"],
|
93
|
+
# ["emb", "CAA85678.1", nil],
|
94
|
+
# ["Perovskia abrotanoides"]]
|
95
|
+
#
|
96
|
+
# ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
|
97
|
+
# ckr.entry_id ==> "gi|2495000"
|
98
|
+
# ckr.sp ==> "CCKR_CAVPO"
|
99
|
+
# ckr.pir ==> "I51898"
|
100
|
+
# ckr.gb ==> "AAB29504.1"
|
101
|
+
# ckr.gi ==> "2495000"
|
102
|
+
# ckr.accession ==> "AAB29504"
|
103
|
+
# ckr.accessions ==> ["Q63931", "AAB29504"]
|
104
|
+
# ckr.acc_version ==> "AAB29504.1"
|
105
|
+
# ckr.locus ==> nil
|
106
|
+
# ckr.description ==>
|
107
|
+
# "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
|
108
|
+
# ckr.descriptions ==>
|
109
|
+
# ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
|
110
|
+
# "cholecystokinin A receptor - guinea pig",
|
111
|
+
# "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
|
112
|
+
# ckr.words ==>
|
113
|
+
# ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
|
114
|
+
# "receptor", "type"]
|
115
|
+
# ckr.id_strings ==>
|
116
|
+
# ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
|
117
|
+
# "544724", "AAB29504.1", "Cavia"]
|
118
|
+
# ckr.list_ids ==>
|
119
|
+
# [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
|
120
|
+
# ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
|
121
|
+
# ["gb", "AAB29504.1", nil], ["Cavia"]]
|
122
|
+
#
|
123
|
+
# === Refereneces
|
124
|
+
#
|
125
|
+
# * Fasta format description (NCBI)
|
126
|
+
# http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
|
127
|
+
#
|
128
|
+
# * Frequently Asked Questions: Indexing of Sequence Identifiers (by Warren R. Gish.)
|
129
|
+
# http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
|
130
|
+
#
|
131
|
+
# * README.formatdb
|
132
|
+
# ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
|
133
|
+
#
|
134
|
+
class FastaDefline
|
135
|
+
|
136
|
+
NSIDs = {
|
137
|
+
# NCBI and WU-BLAST
|
138
|
+
'gi' => [ 'gi' ], # NCBI GI
|
139
|
+
'gb' => [ 'acc_version', 'locus' ], # GenBank
|
140
|
+
'emb' => [ 'acc_version', 'locus' ], # EMBL
|
141
|
+
'dbj' => [ 'acc_version', 'locus' ], # DDBJ
|
142
|
+
'sp' => [ 'accession', 'entry_id' ], # SWISS-PROT
|
143
|
+
'pdb' => [ 'entry_id', 'chain' ], # PDB
|
144
|
+
'bbs' => [ 'number' ], # GenInfo Backbone Id
|
145
|
+
'gnl' => [ 'database' , 'entry_id' ], # General database identifier
|
146
|
+
'ref' => [ 'acc_version' , 'locus' ], # NCBI Reference Sequence
|
147
|
+
'lcl' => [ 'entry_id' ], # Local Sequence identifier
|
148
|
+
|
149
|
+
# WU-BLAST and NCBI
|
150
|
+
'pir' => [ 'accession', 'entry_id' ], # PIR
|
151
|
+
'prf' => [ 'accession', 'entry_id' ], # Protein Research Foundation
|
152
|
+
'pat' => [ 'country', 'number', 'serial' ], # Patents
|
153
|
+
|
154
|
+
# WU-BLAST only
|
155
|
+
'bbm' => [ 'number' ], # NCBI GenInfo Backbone database identifier
|
156
|
+
'gim' => [ 'number' ], # NCBI GenInfo Import identifier
|
157
|
+
'gp' => [ 'acc_version', 'locus' ], # GenPept
|
158
|
+
'oth' => [ 'accession', 'name', 'release' ], # Other (user-definable) identifier
|
159
|
+
'tpd' => [ 'accession', 'name' ], # Third party annotation, DDBJ
|
160
|
+
'tpe' => [ 'accession', 'name' ], # Third party annotation, EMBL
|
161
|
+
'tpg' => [ 'accession', 'name' ], # Third party annotation, GenBank
|
162
|
+
|
163
|
+
# Original
|
164
|
+
'ri' => [ 'entry_id', 'rearray_id', 'len' ], # RIKEN FANTOM DB
|
165
|
+
}
|
166
|
+
|
167
|
+
# Shows array that contains IDs (or ID-like strings).
|
168
|
+
# Returns an array of arrays of strings.
|
169
|
+
attr_reader :list_ids
|
170
|
+
|
171
|
+
# Shows a possibly unique identifier.
|
172
|
+
# Returns a string.
|
173
|
+
attr_reader :entry_id
|
174
|
+
|
175
|
+
# Parses given string.
|
176
|
+
def initialize(str)
|
177
|
+
@deflines = []
|
178
|
+
@info = {}
|
179
|
+
@list_ids = []
|
180
|
+
|
181
|
+
@entry_id = nil
|
182
|
+
|
183
|
+
lines = str.split("\x01")
|
184
|
+
lines.each do |line|
|
185
|
+
add_defline(line)
|
186
|
+
end
|
187
|
+
end #def initialize
|
188
|
+
|
189
|
+
# Parses given string and adds parsed data.
|
190
|
+
def add_defline(str)
|
191
|
+
case str
|
192
|
+
when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/
|
193
|
+
# NSIDs
|
194
|
+
# examples:
|
195
|
+
# >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P
|
196
|
+
#
|
197
|
+
# note: regexp (:?) means grouping without backreferences
|
198
|
+
i = $1
|
199
|
+
d = $2
|
200
|
+
tks = i.split('|')
|
201
|
+
tks << '' if i[-1,1] == '|'
|
202
|
+
a = parse_NSIDs(tks)
|
203
|
+
i = a[0].join('|')
|
204
|
+
a.unshift('|')
|
205
|
+
d = tks.join('|') + ' ' + d unless tks.empty?
|
206
|
+
a << d
|
207
|
+
this_line = a
|
208
|
+
match_EC(d)
|
209
|
+
parse_square_brackets(d).each do |x|
|
210
|
+
if !match_EC(x, false) and x =~ /\A[A-Z]/ then
|
211
|
+
di = [ x ]
|
212
|
+
@list_ids << di
|
213
|
+
@info['organism'] = x unless @info['organism']
|
214
|
+
end
|
215
|
+
end
|
216
|
+
|
217
|
+
when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/
|
218
|
+
# examples:
|
219
|
+
# >sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
|
220
|
+
# >emb:CACDC28 [X80034] C.albicans CDC28 gene
|
221
|
+
i = $1
|
222
|
+
d = $2
|
223
|
+
a = parse_ColonSepID(i)
|
224
|
+
i = a.join(':')
|
225
|
+
this_line = [ ':', a , d ]
|
226
|
+
match_EC(d)
|
227
|
+
parse_square_brackets(d).each do |x|
|
228
|
+
if !match_EC(x, false) and x =~ /:/ then
|
229
|
+
parse_ColonSepID(x)
|
230
|
+
elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then
|
231
|
+
@list_ids << [ $1 ]
|
232
|
+
end
|
233
|
+
end
|
234
|
+
|
235
|
+
when /^\>?\s*(\S+)(?:\s+(.+))?$/
|
236
|
+
# examples:
|
237
|
+
# >ABC12345 this is test
|
238
|
+
i = $1
|
239
|
+
d = $2.to_s
|
240
|
+
@list_ids << [ i.chomp('.') ]
|
241
|
+
this_line = [ '', [ i ], d ]
|
242
|
+
match_EC(d)
|
243
|
+
else
|
244
|
+
i = str
|
245
|
+
d = ''
|
246
|
+
match_EC(i)
|
247
|
+
this_line = [ '', [ i ], d ]
|
248
|
+
end
|
249
|
+
|
250
|
+
@deflines << this_line
|
251
|
+
@entry_id = i unless @entry_id
|
252
|
+
end
|
253
|
+
|
254
|
+
def match_EC(str, write_flag = true)
|
255
|
+
di = nil
|
256
|
+
str.scan(/EC\:((:?[\-\d]+\.){3}(:?[\-\d]+))/i) do |x|
|
257
|
+
di = [ 'EC', $1 ]
|
258
|
+
if write_flag then
|
259
|
+
@info['ec'] = di[1] if (!@info['ec'] or @info['ec'].to_s =~ /\-/)
|
260
|
+
@list_ids << di
|
261
|
+
end
|
262
|
+
end
|
263
|
+
di
|
264
|
+
end
|
265
|
+
private :match_EC
|
266
|
+
|
267
|
+
def parse_square_brackets(str)
|
268
|
+
r = []
|
269
|
+
str.scan(/\[([^\]]*)\]/) do |x|
|
270
|
+
r << x[0]
|
271
|
+
end
|
272
|
+
r
|
273
|
+
end
|
274
|
+
private :parse_square_brackets
|
275
|
+
|
276
|
+
def parse_ColonSepID(str)
|
277
|
+
di = str.split(':', 2)
|
278
|
+
di << nil if di.size <= 1
|
279
|
+
@list_ids << di
|
280
|
+
di
|
281
|
+
end
|
282
|
+
private :parse_ColonSepID
|
283
|
+
|
284
|
+
def parse_NSIDs(ary)
|
285
|
+
# this method destroys ary
|
286
|
+
data = []
|
287
|
+
while token = ary.shift
|
288
|
+
if labels = self.class::NSIDs[token] then
|
289
|
+
di = [ token ]
|
290
|
+
idtype = token
|
291
|
+
labels.each do |x|
|
292
|
+
token = ary.shift
|
293
|
+
break unless token
|
294
|
+
if self.class::NSIDs[token] then
|
295
|
+
ary.unshift(token)
|
296
|
+
break #each
|
297
|
+
end
|
298
|
+
if token.length > 0 then
|
299
|
+
di << token
|
300
|
+
else
|
301
|
+
di << nil
|
302
|
+
end
|
303
|
+
end
|
304
|
+
data << di
|
305
|
+
else
|
306
|
+
if token.length > 0 then
|
307
|
+
# UCID (uncontrolled identifiers)
|
308
|
+
di = [ token ]
|
309
|
+
data << di
|
310
|
+
@info['ucid'] = token unless @info['ucid']
|
311
|
+
end
|
312
|
+
break #while
|
313
|
+
end
|
314
|
+
end #while
|
315
|
+
@list_ids.concat data
|
316
|
+
data
|
317
|
+
end #def parse_NSIDs
|
318
|
+
private :parse_NSIDs
|
319
|
+
|
320
|
+
|
321
|
+
# Shows original string.
|
322
|
+
# Note that the result of this method may be different from
|
323
|
+
# original string which is given in FastaDefline.new method.
|
324
|
+
def to_s
|
325
|
+
@deflines.collect { |a|
|
326
|
+
s = a[0]
|
327
|
+
(a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip
|
328
|
+
}.join("\x01")
|
329
|
+
end
|
330
|
+
|
331
|
+
# Shows description.
|
332
|
+
def description
|
333
|
+
@deflines[0].to_a[-1]
|
334
|
+
end
|
335
|
+
|
336
|
+
# Returns descriptions.
|
337
|
+
def descriptions
|
338
|
+
@deflines.collect do |a|
|
339
|
+
a[-1]
|
340
|
+
end
|
341
|
+
end
|
342
|
+
|
343
|
+
# Shows ID-like strings.
|
344
|
+
# Returns an array of strings.
|
345
|
+
def id_strings
|
346
|
+
r = []
|
347
|
+
@list_ids.each do |a|
|
348
|
+
if a.size >= 2 then
|
349
|
+
r.concat a[1..-1].find_all { |x| x }
|
350
|
+
else
|
351
|
+
if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/
|
352
|
+
r << a[0]
|
353
|
+
end
|
354
|
+
end
|
355
|
+
end
|
356
|
+
r.concat( words(true, []).find_all do |x|
|
357
|
+
x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or
|
358
|
+
x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
|
359
|
+
end)
|
360
|
+
r
|
361
|
+
end
|
362
|
+
|
363
|
+
KillWords = [
|
364
|
+
'an', 'the', 'this', 'that',
|
365
|
+
'is', 'are', 'were', 'was', 'be', 'can', 'may', 'might',
|
366
|
+
'as', 'at', 'by', 'for', 'in', 'of', 'on', 'to', 'with',
|
367
|
+
'from', 'and', 'or', 'not',
|
368
|
+
'dna', 'rna', 'mrna', 'cdna', 'orf',
|
369
|
+
'aa', 'nt', 'pct', 'id', 'ec', 'sp', 'subsp',
|
370
|
+
'similar', 'involved', 'identical', 'identity',
|
371
|
+
'cds', 'clone', 'library', 'contig', 'contigs',
|
372
|
+
'homolog', 'homologue', 'homologs', 'homologous',
|
373
|
+
'protein', 'proteins', 'gene', 'genes',
|
374
|
+
'product', 'products', 'sequence', 'sequences',
|
375
|
+
'strain', 'strains', 'region', 'regions',
|
376
|
+
]
|
377
|
+
KillWordsHash = {}
|
378
|
+
KillWords.each { |x| KillWordsHash[x] = true }
|
379
|
+
|
380
|
+
KillRegexpArray = [
|
381
|
+
/\A\d{1,3}\%?\z/,
|
382
|
+
/\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/,
|
383
|
+
/\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
|
384
|
+
]
|
385
|
+
|
386
|
+
# Shows words used in the defline. Returns an Array.
|
387
|
+
def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
|
388
|
+
kwhash = self.class::KillWordsHash)
|
389
|
+
a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\x00-\x1f\x7f]+/)
|
390
|
+
a.collect! do |x|
|
391
|
+
x.sub!(/\A[\$\*\-\+]+/, '')
|
392
|
+
x.sub!(/[\$\*\-\=]+\z/, '')
|
393
|
+
if x.size <= 1 then
|
394
|
+
nil
|
395
|
+
elsif kwhash[x.downcase] then
|
396
|
+
nil
|
397
|
+
else
|
398
|
+
if kill_regexp.find { |expr| expr =~ x } then
|
399
|
+
nil
|
400
|
+
else
|
401
|
+
x
|
402
|
+
end
|
403
|
+
end
|
404
|
+
end
|
405
|
+
a.compact!
|
406
|
+
a.collect! { |x| x.downcase } unless case_sensitive
|
407
|
+
a.sort!
|
408
|
+
a.uniq!
|
409
|
+
a
|
410
|
+
end
|
411
|
+
|
412
|
+
# Returns identifires by a database name.
|
413
|
+
def get(dbname)
|
414
|
+
db = dbname.to_s
|
415
|
+
r = nil
|
416
|
+
unless r = @info[db] then
|
417
|
+
di = @list_ids.find { |x| x[0] == db.to_s }
|
418
|
+
if di and di.size <= 2 then
|
419
|
+
r = di[-1]
|
420
|
+
elsif di then
|
421
|
+
labels = self.class::NSIDs[db]
|
422
|
+
[ 'acc_version', 'entry_id',
|
423
|
+
'locus', 'accession', 'number'].each do |x|
|
424
|
+
if i = labels.index(x) then
|
425
|
+
r = di[i+1]
|
426
|
+
break if r
|
427
|
+
end
|
428
|
+
end
|
429
|
+
r = di[1..-1].find { |x| x } unless r
|
430
|
+
end
|
431
|
+
@info[db] = r if r
|
432
|
+
end
|
433
|
+
r
|
434
|
+
end
|
435
|
+
|
436
|
+
# Returns an identifier by given type.
|
437
|
+
def get_by_type(type_str)
|
438
|
+
@list_ids.each do |x|
|
439
|
+
if labels = self.class::NSIDs[x[0]] then
|
440
|
+
if i = labels.index(type_str) then
|
441
|
+
return x[i+1]
|
442
|
+
end
|
443
|
+
end
|
444
|
+
end
|
445
|
+
nil
|
446
|
+
end
|
447
|
+
|
448
|
+
# Returns identifiers by given type.
|
449
|
+
def get_all_by_type(*type_strarg)
|
450
|
+
d = []
|
451
|
+
@list_ids.each do |x|
|
452
|
+
if labels = self.class::NSIDs[x[0]] then
|
453
|
+
type_strarg.each do |y|
|
454
|
+
if i = labels.index(y) then
|
455
|
+
d << x[i+1] if x[i+1]
|
456
|
+
end
|
457
|
+
end
|
458
|
+
end
|
459
|
+
end
|
460
|
+
d
|
461
|
+
end
|
462
|
+
|
463
|
+
# Shows locus.
|
464
|
+
# If the entry has more than two of such IDs,
|
465
|
+
# only the first ID are shown.
|
466
|
+
# Returns a string or nil.
|
467
|
+
def locus
|
468
|
+
unless defined?(@locus)
|
469
|
+
@locus = get_by_type('locus')
|
470
|
+
end
|
471
|
+
@locus
|
472
|
+
end
|
473
|
+
|
474
|
+
# Shows GI.
|
475
|
+
# If the entry has more than two of such IDs,
|
476
|
+
# only the first ID are shown.
|
477
|
+
# Returns a string or nil.
|
478
|
+
def gi
|
479
|
+
unless defined?(@gi) then
|
480
|
+
@gi = get_by_type('gi')
|
481
|
+
end
|
482
|
+
@gi
|
483
|
+
end
|
484
|
+
|
485
|
+
# Shows accession with version number.
|
486
|
+
# If the entry has more than two of such IDs,
|
487
|
+
# only the first ID are shown.
|
488
|
+
# Returns a string or nil.
|
489
|
+
def acc_version
|
490
|
+
unless defined?(@acc_version) then
|
491
|
+
@acc_version = get_by_type('acc_version')
|
492
|
+
end
|
493
|
+
@acc_version
|
494
|
+
end
|
495
|
+
|
496
|
+
# Shows accession numbers.
|
497
|
+
# Returns an array of strings.
|
498
|
+
def accessions
|
499
|
+
unless defined?(@accessions) then
|
500
|
+
@accessions = get_all_by_type('accession', 'acc_version')
|
501
|
+
@accessions.collect! { |x| x.sub(/\..*\z/, '') }
|
502
|
+
end
|
503
|
+
@accessions
|
504
|
+
end
|
505
|
+
|
506
|
+
# Shows an accession number.
|
507
|
+
def accession
|
508
|
+
unless defined?(@accession) then
|
509
|
+
if acc_version then
|
510
|
+
@accession = acc_version.split('.')[0]
|
511
|
+
else
|
512
|
+
@accession = accessions[0]
|
513
|
+
end
|
514
|
+
end
|
515
|
+
@accession
|
516
|
+
end
|
517
|
+
|
518
|
+
def method_missing(name, *args)
|
519
|
+
# raise ArgumentError,
|
520
|
+
# "wrong # of arguments(#{args.size} for 1)" if args.size >= 2
|
521
|
+
r = get(name, *args)
|
522
|
+
if !r and !(self.class::NSIDs[name.to_s]) then
|
523
|
+
raise "NameError: undefined method `#{name.inspect}'"
|
524
|
+
end
|
525
|
+
r
|
526
|
+
end
|
527
|
+
|
528
|
+
|
529
|
+
end #class FastaDefline
|
530
|
+
|
531
|
+
end #module Bio
|
532
|
+
|