jandot-bio 1.2.1
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- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +282 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/KEGG_API.rd +1843 -0
- data/doc/KEGG_API.rd.ja +1834 -0
- data/doc/Tutorial.rd +1296 -0
- data/doc/Tutorial.rd.ja +2640 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +279 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +351 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/report.rb +516 -0
- data/lib/bio/appl/blast/rexml.rb +135 -0
- data/lib/bio/appl/blast/rpsblast.rb +176 -0
- data/lib/bio/appl/blast/wublast.rb +550 -0
- data/lib/bio/appl/blast/xmlparser.rb +228 -0
- data/lib/bio/appl/blat/report.rb +489 -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 +237 -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/phylip/alignment.rb +129 -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 +457 -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 +222 -0
- data/lib/bio/command.rb +337 -0
- data/lib/bio/data/aa.rb +349 -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/embl/common.rb +336 -0
- data/lib/bio/db/embl/embl.rb +402 -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 +599 -0
- data/lib/bio/db/fasta.rb +907 -0
- data/lib/bio/db/genbank/common.rb +290 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/genbank.rb +215 -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 +174 -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 +170 -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 +323 -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 +457 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/feature.rb +226 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +581 -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 +181 -0
- data/lib/bio/io/flatfile.rb +1309 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/index.rb +1371 -0
- data/lib/bio/io/flatfile/indexer.rb +787 -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 +256 -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 +365 -0
- data/lib/bio/location.rb +772 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +854 -0
- data/lib/bio/reference.rb +623 -0
- data/lib/bio/sequence.rb +475 -0
- data/lib/bio/sequence/aa.rb +125 -0
- data/lib/bio/sequence/common.rb +333 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/format.rb +181 -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 +850 -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 +199 -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/sample/any2fasta.rb +59 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +91 -0
- data/sample/dbget +37 -0
- data/sample/enzymes.rb +78 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fastagrep.rb +72 -0
- data/sample/fastasort.rb +54 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +30 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +303 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/na2aa.rb +34 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +214 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -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/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/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -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/io/test_ensembl.rb +186 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -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_report.rb +417 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +388 -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/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 +163 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_pts1.rb +140 -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_sptr.rb +1775 -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 +127 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +360 -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/io/test_ddbjxml.rb +75 -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 +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +103 -0
- data/test/unit/bio/sequence/test_common.rb +174 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -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 +288 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +116 -0
- data/test/unit/bio/test_location.rb +39 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +473 -0
- data/test/unit/bio/test_reference.rb +224 -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 +479 -0
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#
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# = bio/db/genbank/common.rb - Common methods for GenBank style database classes
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#
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# Copyright:: Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: common.rb,v 1.11 2007/04/05 23:35:40 trevor Exp $
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#
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require 'bio/db'
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module Bio
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class NCBIDB
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# == Description
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#
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# This module defines a common framework among GenBank, GenPept, RefSeq, and
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# DDBJ. For more details, see the documentations in each genbank/*.rb files.
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#
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# == References
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#
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# * ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
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# * http://www.ncbi.nlm.nih.gov/collab/FT/index.html
|
24
|
+
#
|
25
|
+
module Common
|
26
|
+
|
27
|
+
DELIMITER = RS = "\n//\n"
|
28
|
+
TAGSIZE = 12
|
29
|
+
|
30
|
+
def initialize(entry)
|
31
|
+
super(entry, TAGSIZE)
|
32
|
+
end
|
33
|
+
|
34
|
+
# LOCUS -- Locus class must be defined in child classes.
|
35
|
+
def locus
|
36
|
+
# must be overrided in each subclass
|
37
|
+
end
|
38
|
+
|
39
|
+
# DEFINITION -- Returns contents of the DEFINITION record as a String.
|
40
|
+
def definition
|
41
|
+
field_fetch('DEFINITION')
|
42
|
+
end
|
43
|
+
|
44
|
+
|
45
|
+
# ACCESSION -- Returns contents of the ACCESSION record as an Array.
|
46
|
+
def accessions
|
47
|
+
accession.split(/\s+/)
|
48
|
+
end
|
49
|
+
|
50
|
+
|
51
|
+
# VERSION -- Returns contents of the VERSION record as an Array of Strings.
|
52
|
+
def versions
|
53
|
+
@data['VERSION'] ||= fetch('VERSION').split(/\s+/)
|
54
|
+
end
|
55
|
+
|
56
|
+
# Returns the first part of the VERSION record as "ACCESSION.VERSION" String.
|
57
|
+
def acc_version
|
58
|
+
versions.first.to_s
|
59
|
+
end
|
60
|
+
|
61
|
+
# Returns the ACCESSION part of the acc_version.
|
62
|
+
def accession
|
63
|
+
acc_version.split(/\./).first.to_s
|
64
|
+
end
|
65
|
+
|
66
|
+
# Returns the VERSION part of the acc_version as a Fixnum
|
67
|
+
def version
|
68
|
+
acc_version.split(/\./).last.to_i
|
69
|
+
end
|
70
|
+
|
71
|
+
# Returns the second part of the VERSION record as a "GI:#######" String.
|
72
|
+
def gi
|
73
|
+
versions.last
|
74
|
+
end
|
75
|
+
|
76
|
+
|
77
|
+
# NID -- Returns contents of the NID record as a String.
|
78
|
+
def nid
|
79
|
+
field_fetch('NID')
|
80
|
+
end
|
81
|
+
|
82
|
+
|
83
|
+
# KEYWORDS -- Returns contents of the KEYWORDS record as an Array of Strings.
|
84
|
+
def keywords
|
85
|
+
@data['KEYWORDS'] ||= fetch('KEYWORDS').chomp('.').split(/; /)
|
86
|
+
end
|
87
|
+
|
88
|
+
|
89
|
+
# SEGMENT -- Returns contents of the SEGMENT record as a "m/n" form String.
|
90
|
+
def segment
|
91
|
+
@data['SEGMENT'] ||= fetch('SEGMENT').scan(/\d+/).join("/")
|
92
|
+
end
|
93
|
+
|
94
|
+
|
95
|
+
# SOURCE -- Returns contents of the SOURCE record as a Hash.
|
96
|
+
def source
|
97
|
+
unless @data['SOURCE']
|
98
|
+
name, org = get('SOURCE').split('ORGANISM')
|
99
|
+
org ||= ""
|
100
|
+
if org[/\S+;/]
|
101
|
+
organism = $`
|
102
|
+
taxonomy = $& + $'
|
103
|
+
elsif org[/\S+\./] # rs:NC_001741
|
104
|
+
organism = $`
|
105
|
+
taxonomy = $& + $'
|
106
|
+
else
|
107
|
+
organism = org
|
108
|
+
taxonomy = ''
|
109
|
+
end
|
110
|
+
@data['SOURCE'] = {
|
111
|
+
'common_name' => truncate(tag_cut(name)),
|
112
|
+
'organism' => truncate(organism),
|
113
|
+
'taxonomy' => truncate(taxonomy),
|
114
|
+
}
|
115
|
+
@data['SOURCE'].default = ''
|
116
|
+
end
|
117
|
+
@data['SOURCE']
|
118
|
+
end
|
119
|
+
|
120
|
+
def common_name
|
121
|
+
source['common_name']
|
122
|
+
end
|
123
|
+
alias vernacular_name common_name
|
124
|
+
|
125
|
+
def organism
|
126
|
+
source['organism']
|
127
|
+
end
|
128
|
+
|
129
|
+
def taxonomy
|
130
|
+
source['taxonomy']
|
131
|
+
end
|
132
|
+
|
133
|
+
|
134
|
+
# REFERENCE -- Returns contents of the REFERENCE records as an Array of
|
135
|
+
# Bio::Reference objects.
|
136
|
+
def references
|
137
|
+
unless @data['REFERENCE']
|
138
|
+
ary = []
|
139
|
+
toptag2array(get('REFERENCE')).each do |ref|
|
140
|
+
hash = Hash.new('')
|
141
|
+
subtag2array(ref).each do |field|
|
142
|
+
case tag_get(field)
|
143
|
+
when /AUTHORS/
|
144
|
+
authors = truncate(tag_cut(field))
|
145
|
+
authors = authors.split(/, /)
|
146
|
+
authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
|
147
|
+
authors = authors.flatten.map { |a| a.sub(/,/, ', ') }
|
148
|
+
hash['authors'] = authors
|
149
|
+
when /TITLE/
|
150
|
+
hash['title'] = truncate(tag_cut(field)) + '.'
|
151
|
+
when /JOURNAL/
|
152
|
+
journal = truncate(tag_cut(field))
|
153
|
+
if journal =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
|
154
|
+
hash['journal'] = $1
|
155
|
+
hash['volume'] = $2
|
156
|
+
hash['issue'] = $3
|
157
|
+
hash['pages'] = $4
|
158
|
+
hash['year'] = $5
|
159
|
+
else
|
160
|
+
hash['journal'] = journal
|
161
|
+
end
|
162
|
+
when /MEDLINE/
|
163
|
+
hash['medline'] = truncate(tag_cut(field))
|
164
|
+
when /PUBMED/
|
165
|
+
hash['pubmed'] = truncate(tag_cut(field))
|
166
|
+
end
|
167
|
+
end
|
168
|
+
ary.push(Reference.new(hash))
|
169
|
+
end
|
170
|
+
@data['REFERENCE'] = References.new(ary)
|
171
|
+
end
|
172
|
+
if block_given?
|
173
|
+
@data['REFERENCE'].each do |r|
|
174
|
+
yield r
|
175
|
+
end
|
176
|
+
else
|
177
|
+
@data['REFERENCE']
|
178
|
+
end
|
179
|
+
end
|
180
|
+
|
181
|
+
|
182
|
+
# COMMENT -- Returns contents of the COMMENT record as a String.
|
183
|
+
def comment
|
184
|
+
field_fetch('COMMENT')
|
185
|
+
end
|
186
|
+
|
187
|
+
|
188
|
+
# FEATURES -- Returns contents of the FEATURES record as a Bio::Features
|
189
|
+
# object.
|
190
|
+
def features
|
191
|
+
unless @data['FEATURES']
|
192
|
+
ary = []
|
193
|
+
in_quote = false
|
194
|
+
get('FEATURES').each_line do |line|
|
195
|
+
next if line =~ /^FEATURES/
|
196
|
+
|
197
|
+
# feature type (source, CDS, ...)
|
198
|
+
head = line[0,20].to_s.strip
|
199
|
+
|
200
|
+
# feature value (position or /qualifier=)
|
201
|
+
body = line[20,60].to_s.chomp
|
202
|
+
|
203
|
+
# sub-array [ feature type, position, /q="data", ... ]
|
204
|
+
if line =~ /^ {5}\S/
|
205
|
+
ary.push([ head, body ])
|
206
|
+
|
207
|
+
# feature qualifier start (/q="data..., /q="data...", /q=data, /q)
|
208
|
+
elsif body =~ /^ \// and not in_quote # gb:IRO125195
|
209
|
+
ary.last.push(body)
|
210
|
+
|
211
|
+
# flag for open quote (/q="data...)
|
212
|
+
if body =~ /="/ and body !~ /"$/
|
213
|
+
in_quote = true
|
214
|
+
end
|
215
|
+
|
216
|
+
# feature qualifier continued (...data..., ...data...")
|
217
|
+
else
|
218
|
+
ary.last.last << body
|
219
|
+
|
220
|
+
# flag for closing quote (/q="data... lines ...")
|
221
|
+
if body =~ /"$/
|
222
|
+
in_quote = false
|
223
|
+
end
|
224
|
+
end
|
225
|
+
end
|
226
|
+
|
227
|
+
ary.collect! do |subary|
|
228
|
+
parse_qualifiers(subary)
|
229
|
+
end
|
230
|
+
|
231
|
+
@data['FEATURES'] = Features.new(ary)
|
232
|
+
end
|
233
|
+
if block_given?
|
234
|
+
@data['FEATURES'].each do |f|
|
235
|
+
yield f
|
236
|
+
end
|
237
|
+
else
|
238
|
+
@data['FEATURES']
|
239
|
+
end
|
240
|
+
end
|
241
|
+
|
242
|
+
|
243
|
+
# ORIGIN -- Returns contents of the ORIGIN record as a String.
|
244
|
+
def origin
|
245
|
+
unless @data['ORIGIN']
|
246
|
+
ori, seqstr = get('ORIGIN').split("\n", 2)
|
247
|
+
seqstr ||= ""
|
248
|
+
@data['ORIGIN'] = truncate(tag_cut(ori))
|
249
|
+
@data['SEQUENCE'] = seqstr.tr("0-9 \t\n\r\/", '')
|
250
|
+
end
|
251
|
+
@data['ORIGIN']
|
252
|
+
end
|
253
|
+
|
254
|
+
|
255
|
+
### private methods
|
256
|
+
|
257
|
+
private
|
258
|
+
|
259
|
+
def parse_qualifiers(ary)
|
260
|
+
feature = Feature.new
|
261
|
+
|
262
|
+
feature.feature = ary.shift
|
263
|
+
feature.position = ary.shift.gsub(/\s/, '')
|
264
|
+
|
265
|
+
ary.each do |f|
|
266
|
+
if f =~ %r{/([^=]+)=?"?([^"]*)"?}
|
267
|
+
qualifier, value = $1, $2
|
268
|
+
|
269
|
+
case qualifier
|
270
|
+
when 'translation'
|
271
|
+
value = Sequence::AA.new(value)
|
272
|
+
when 'codon_start'
|
273
|
+
value = value.to_i
|
274
|
+
else
|
275
|
+
value = true if value.empty?
|
276
|
+
end
|
277
|
+
|
278
|
+
feature.append(Feature::Qualifier.new(qualifier, value))
|
279
|
+
end
|
280
|
+
end
|
281
|
+
|
282
|
+
return feature
|
283
|
+
end
|
284
|
+
|
285
|
+
end # Common
|
286
|
+
|
287
|
+
end # GenBank
|
288
|
+
end # Bio
|
289
|
+
|
290
|
+
|
@@ -0,0 +1,22 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/genbank/ddbj.rb - DDBJ database class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: ddbj.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'bio/db/genbank/genbank'
|
11
|
+
|
12
|
+
module Bio
|
13
|
+
|
14
|
+
class DDBJ < GenBank
|
15
|
+
|
16
|
+
autoload :XML, 'bio/io/ddbjxml'
|
17
|
+
|
18
|
+
# Nothing to do (DDBJ database format is completely same as GenBank)
|
19
|
+
|
20
|
+
end # DDBJ
|
21
|
+
|
22
|
+
end # Bio
|
@@ -0,0 +1,215 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/genbank/genbank.rb - GenBank database class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: genbank.rb,v 0.40 2007/04/05 23:35:40 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'bio/db'
|
11
|
+
require 'bio/db/genbank/common'
|
12
|
+
|
13
|
+
module Bio
|
14
|
+
|
15
|
+
# == Description
|
16
|
+
#
|
17
|
+
# Parses a GenBank formatted database entry
|
18
|
+
#
|
19
|
+
# == Example
|
20
|
+
#
|
21
|
+
# # entry is a string containing only one entry contents
|
22
|
+
# gb = Bio::GenBank.new(entry)
|
23
|
+
#
|
24
|
+
class GenBank < NCBIDB
|
25
|
+
|
26
|
+
include Bio::NCBIDB::Common
|
27
|
+
|
28
|
+
# Parses the LOCUS line and returns contents of the LOCUS record
|
29
|
+
# as a Bio::GenBank::Locus object. Locus object is created automatically
|
30
|
+
# when Bio::GenBank#locus, entry_id etc. methods are called.
|
31
|
+
class Locus
|
32
|
+
def initialize(locus_line)
|
33
|
+
if locus_line.empty?
|
34
|
+
# do nothing (just for empty or incomplete entry string)
|
35
|
+
elsif locus_line.length > 75 # after Rel 126.0
|
36
|
+
@entry_id = locus_line[12..27].strip
|
37
|
+
@length = locus_line[29..39].to_i
|
38
|
+
@strand = locus_line[44..46].strip
|
39
|
+
@natype = locus_line[47..52].strip
|
40
|
+
@circular = locus_line[55..62].strip
|
41
|
+
@division = locus_line[63..66].strip
|
42
|
+
@date = locus_line[68..78].strip
|
43
|
+
else
|
44
|
+
@entry_id = locus_line[12..21].strip
|
45
|
+
@length = locus_line[22..29].to_i
|
46
|
+
@strand = locus_line[33..35].strip
|
47
|
+
@natype = locus_line[36..39].strip
|
48
|
+
@circular = locus_line[42..51].strip
|
49
|
+
@division = locus_line[52..54].strip
|
50
|
+
@date = locus_line[62..72].strip
|
51
|
+
end
|
52
|
+
end
|
53
|
+
attr_accessor :entry_id, :length, :strand, :natype, :circular,
|
54
|
+
:division, :date
|
55
|
+
end
|
56
|
+
|
57
|
+
# Accessor methods for the contents of the LOCUS record.
|
58
|
+
|
59
|
+
def locus
|
60
|
+
@data['LOCUS'] ||= Locus.new(get('LOCUS'))
|
61
|
+
end
|
62
|
+
|
63
|
+
def entry_id; locus.entry_id; end
|
64
|
+
def length; locus.length; end
|
65
|
+
def circular; locus.circular; end
|
66
|
+
def division; locus.division; end
|
67
|
+
def date; locus.date; end
|
68
|
+
|
69
|
+
def strand; locus.strand; end
|
70
|
+
def natype; locus.natype; end
|
71
|
+
|
72
|
+
|
73
|
+
# FEATURES -- Iterate only for the 'CDS' portion of the Bio::Features.
|
74
|
+
def each_cds
|
75
|
+
features.each do |feature|
|
76
|
+
if feature.feature == 'CDS'
|
77
|
+
yield(feature)
|
78
|
+
end
|
79
|
+
end
|
80
|
+
end
|
81
|
+
|
82
|
+
# FEATURES -- Iterate only for the 'gene' portion of the Bio::Features.
|
83
|
+
def each_gene
|
84
|
+
features.each do |feature|
|
85
|
+
if feature.feature == 'gene'
|
86
|
+
yield(feature)
|
87
|
+
end
|
88
|
+
end
|
89
|
+
end
|
90
|
+
|
91
|
+
|
92
|
+
# BASE COUNT (this field is obsoleted after GenBank release 138.0) --
|
93
|
+
# Returns the BASE COUNT as a Hash. When the base is specified, returns
|
94
|
+
# count of the base as a Fixnum. The base can be one of 'a', 't', 'g',
|
95
|
+
# 'c', and 'o' (others).
|
96
|
+
def basecount(base = nil)
|
97
|
+
unless @data['BASE COUNT']
|
98
|
+
hash = Hash.new(0)
|
99
|
+
get('BASE COUNT').scan(/(\d+) (\w)/).each do |c, b|
|
100
|
+
hash[b] = c.to_i
|
101
|
+
end
|
102
|
+
@data['BASE COUNT'] = hash
|
103
|
+
end
|
104
|
+
|
105
|
+
if base
|
106
|
+
base.downcase!
|
107
|
+
@data['BASE COUNT'][base]
|
108
|
+
else
|
109
|
+
@data['BASE COUNT']
|
110
|
+
end
|
111
|
+
end
|
112
|
+
|
113
|
+
# ORIGIN -- Returns DNA sequence in the ORIGIN record as a
|
114
|
+
# Bio::Sequence::NA object.
|
115
|
+
def seq
|
116
|
+
unless @data['SEQUENCE']
|
117
|
+
origin
|
118
|
+
end
|
119
|
+
Bio::Sequence::NA.new(@data['SEQUENCE'])
|
120
|
+
end
|
121
|
+
alias naseq seq
|
122
|
+
alias nalen length
|
123
|
+
|
124
|
+
def seq_len
|
125
|
+
seq.length
|
126
|
+
end
|
127
|
+
|
128
|
+
end # GenBank
|
129
|
+
end # Bio
|
130
|
+
|
131
|
+
|
132
|
+
|
133
|
+
if __FILE__ == $0
|
134
|
+
|
135
|
+
begin
|
136
|
+
require 'pp'
|
137
|
+
alias p pp
|
138
|
+
rescue LoadError
|
139
|
+
end
|
140
|
+
|
141
|
+
puts "### GenBank"
|
142
|
+
if ARGV.size > 0
|
143
|
+
gb = Bio::GenBank.new(ARGF.read)
|
144
|
+
else
|
145
|
+
require 'bio/io/fetch'
|
146
|
+
gb = Bio::GenBank.new(Bio::Fetch.query('gb', 'LPATOVGNS'))
|
147
|
+
end
|
148
|
+
|
149
|
+
puts "## LOCUS"
|
150
|
+
puts "# GenBank.locus"
|
151
|
+
p gb.locus
|
152
|
+
puts "# GenBank.entry_id"
|
153
|
+
p gb.entry_id
|
154
|
+
puts "# GenBank.nalen"
|
155
|
+
p gb.nalen
|
156
|
+
puts "# GenBank.strand"
|
157
|
+
p gb.strand
|
158
|
+
puts "# GenBank.natype"
|
159
|
+
p gb.natype
|
160
|
+
puts "# GenBank.circular"
|
161
|
+
p gb.circular
|
162
|
+
puts "# GenBank.division"
|
163
|
+
p gb.division
|
164
|
+
puts "# GenBank.date"
|
165
|
+
p gb.date
|
166
|
+
|
167
|
+
puts "## DEFINITION"
|
168
|
+
p gb.definition
|
169
|
+
|
170
|
+
puts "## ACCESSION"
|
171
|
+
p gb.accession
|
172
|
+
|
173
|
+
puts "## VERSION"
|
174
|
+
p gb.versions
|
175
|
+
p gb.version
|
176
|
+
p gb.gi
|
177
|
+
|
178
|
+
puts "## NID"
|
179
|
+
p gb.nid
|
180
|
+
|
181
|
+
puts "## KEYWORDS"
|
182
|
+
p gb.keywords
|
183
|
+
|
184
|
+
puts "## SEGMENT"
|
185
|
+
p gb.segment
|
186
|
+
|
187
|
+
puts "## SOURCE"
|
188
|
+
p gb.source
|
189
|
+
p gb.common_name
|
190
|
+
p gb.vernacular_name
|
191
|
+
p gb.organism
|
192
|
+
p gb.taxonomy
|
193
|
+
|
194
|
+
puts "## REFERENCE"
|
195
|
+
p gb.references
|
196
|
+
|
197
|
+
puts "## COMMENT"
|
198
|
+
p gb.comment
|
199
|
+
|
200
|
+
puts "## FEATURES"
|
201
|
+
p gb.features
|
202
|
+
|
203
|
+
puts "## BASE COUNT"
|
204
|
+
p gb.basecount
|
205
|
+
p gb.basecount('a')
|
206
|
+
p gb.basecount('A')
|
207
|
+
|
208
|
+
puts "## ORIGIN"
|
209
|
+
p gb.origin
|
210
|
+
p gb.naseq
|
211
|
+
|
212
|
+
end
|
213
|
+
|
214
|
+
|
215
|
+
|