bio 1.0.0 → 1.1.0
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- data/bin/bioruby +14 -122
- data/bin/br_biofetch.rb +2 -2
- data/bin/br_bioflat.rb +2 -2
- data/bin/br_biogetseq.rb +2 -2
- data/bin/br_pmfetch.rb +3 -3
- data/doc/Changes-0.7.rd +77 -0
- data/doc/KEGG_API.rd +523 -232
- data/doc/KEGG_API.rd.ja +529 -207
- data/doc/Tutorial.rd +48 -11
- data/lib/bio.rb +59 -6
- data/lib/bio/alignment.rb +713 -103
- data/lib/bio/appl/bl2seq/report.rb +2 -18
- data/lib/bio/appl/blast.rb +108 -91
- data/lib/bio/appl/blast/format0.rb +33 -18
- data/lib/bio/appl/blast/format8.rb +6 -20
- data/lib/bio/appl/blast/report.rb +293 -429
- data/lib/bio/appl/blast/rexml.rb +8 -22
- data/lib/bio/appl/blast/wublast.rb +21 -12
- data/lib/bio/appl/blast/xmlparser.rb +180 -183
- data/lib/bio/appl/blat/report.rb +127 -30
- data/lib/bio/appl/clustalw.rb +87 -59
- data/lib/bio/appl/clustalw/report.rb +20 -22
- data/lib/bio/appl/emboss.rb +113 -20
- data/lib/bio/appl/fasta.rb +173 -198
- data/lib/bio/appl/fasta/format10.rb +244 -347
- 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 +5 -23
- data/lib/bio/appl/hmmer.rb +8 -45
- data/lib/bio/appl/hmmer/report.rb +2 -20
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +87 -50
- data/lib/bio/appl/mafft/report.rb +151 -44
- 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 +89 -96
- data/lib/bio/appl/psort/report.rb +6 -22
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +26 -36
- data/lib/bio/appl/sim4/report.rb +2 -18
- data/lib/bio/appl/sosui/report.rb +5 -20
- data/lib/bio/appl/spidey/report.rb +2 -2
- data/lib/bio/appl/targetp/report.rb +4 -20
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +4 -20
- data/lib/bio/command.rb +235 -64
- data/lib/bio/data/aa.rb +21 -26
- data/lib/bio/data/codontable.rb +2 -20
- data/lib/bio/data/na.rb +19 -4
- data/lib/bio/db.rb +27 -12
- data/lib/bio/db/aaindex.rb +2 -20
- data/lib/bio/db/embl/common.rb +4 -21
- data/lib/bio/db/embl/embl.rb +33 -85
- data/lib/bio/db/embl/sptr.rb +612 -302
- data/lib/bio/db/embl/swissprot.rb +10 -29
- data/lib/bio/db/embl/trembl.rb +10 -29
- data/lib/bio/db/embl/uniprot.rb +10 -29
- data/lib/bio/db/fantom.rb +15 -20
- data/lib/bio/db/fasta.rb +3 -3
- data/lib/bio/db/genbank/common.rb +37 -46
- data/lib/bio/db/genbank/ddbj.rb +6 -18
- data/lib/bio/db/genbank/genbank.rb +47 -186
- data/lib/bio/db/genbank/genpept.rb +4 -17
- data/lib/bio/db/genbank/refseq.rb +4 -17
- data/lib/bio/db/gff.rb +103 -35
- data/lib/bio/db/go.rb +4 -20
- data/lib/bio/db/kegg/brite.rb +26 -36
- data/lib/bio/db/kegg/compound.rb +81 -85
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +133 -110
- data/lib/bio/db/kegg/expression.rb +2 -20
- data/lib/bio/db/kegg/genes.rb +208 -238
- data/lib/bio/db/kegg/genome.rb +164 -285
- data/lib/bio/db/kegg/glycan.rb +114 -157
- data/lib/bio/db/kegg/keggtab.rb +242 -303
- data/lib/bio/db/kegg/kgml.rb +117 -160
- data/lib/bio/db/kegg/orthology.rb +112 -0
- data/lib/bio/db/kegg/reaction.rb +54 -69
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +3 -27
- data/lib/bio/db/medline.rb +228 -249
- data/lib/bio/db/nbrf.rb +3 -3
- data/lib/bio/db/newick.rb +510 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +5 -17
- data/lib/bio/db/pdb/atom.rb +2 -18
- data/lib/bio/db/pdb/chain.rb +2 -18
- data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
- data/lib/bio/db/pdb/model.rb +2 -18
- data/lib/bio/db/pdb/pdb.rb +73 -34
- data/lib/bio/db/pdb/residue.rb +4 -20
- data/lib/bio/db/pdb/utils.rb +2 -18
- data/lib/bio/db/prosite.rb +403 -422
- data/lib/bio/db/rebase.rb +84 -40
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +5 -17
- data/lib/bio/feature.rb +106 -52
- data/lib/bio/io/das.rb +32 -42
- data/lib/bio/io/dbget.rb +2 -20
- data/lib/bio/io/ddbjxml.rb +77 -138
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +89 -82
- data/lib/bio/io/fetch.rb +163 -96
- data/lib/bio/io/flatfile.rb +170 -73
- data/lib/bio/io/flatfile/bdb.rb +3 -16
- data/lib/bio/io/flatfile/index.rb +2 -2
- data/lib/bio/io/flatfile/indexer.rb +3 -2
- data/lib/bio/io/higet.rb +12 -31
- data/lib/bio/io/keggapi.rb +210 -269
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +169 -147
- data/lib/bio/io/registry.rb +4 -20
- data/lib/bio/io/soapwsdl.rb +43 -38
- data/lib/bio/io/sql.rb +242 -305
- data/lib/bio/location.rb +407 -285
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +558 -695
- data/lib/bio/reference.rb +272 -75
- data/lib/bio/sequence.rb +255 -13
- data/lib/bio/sequence/aa.rb +71 -10
- data/lib/bio/sequence/common.rb +187 -33
- data/lib/bio/sequence/compat.rb +59 -4
- data/lib/bio/sequence/format.rb +54 -7
- data/lib/bio/sequence/generic.rb +3 -3
- data/lib/bio/sequence/na.rb +328 -26
- data/lib/bio/shell.rb +11 -4
- data/lib/bio/shell/core.rb +221 -160
- data/lib/bio/shell/demo.rb +18 -15
- data/lib/bio/shell/interface.rb +14 -12
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +45 -26
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +22 -14
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +2 -2
- data/lib/bio/shell/plugin/entry.rb +22 -11
- data/lib/bio/shell/plugin/flatfile.rb +2 -2
- data/lib/bio/shell/plugin/keggapi.rb +13 -6
- data/lib/bio/shell/plugin/midi.rb +4 -4
- data/lib/bio/shell/plugin/obda.rb +2 -2
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +35 -8
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
- data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +70 -58
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +84 -107
- data/lib/bio/util/color_scheme/buried.rb +5 -24
- data/lib/bio/util/color_scheme/helix.rb +5 -24
- data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
- data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
- data/lib/bio/util/color_scheme/strand.rb +5 -24
- data/lib/bio/util/color_scheme/taylor.rb +5 -24
- data/lib/bio/util/color_scheme/turn.rb +5 -24
- data/lib/bio/util/color_scheme/zappo.rb +5 -24
- data/lib/bio/util/contingency_table.rb +70 -43
- 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 +4 -22
- data/sample/color_scheme_na.rb +4 -12
- data/sample/enzymes.rb +78 -0
- data/sample/goslim.rb +5 -13
- data/sample/psortplot_html.rb +4 -12
- data/test/data/blast/2.2.15.blastp.m7 +876 -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/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/functional/bio/io/test_ensembl.rb +103 -0
- data/test/functional/bio/io/test_soapwsdl.rb +5 -17
- data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
- data/test/unit/bio/appl/blast/test_report.rb +3 -16
- data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
- data/test/unit/bio/appl/genscan/test_report.rb +3 -16
- data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
- 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 +3 -16
- data/test/unit/bio/appl/targetp/test_report.rb +3 -16
- data/test/unit/bio/appl/test_blast.rb +3 -16
- data/test/unit/bio/appl/test_fasta.rb +4 -16
- data/test/unit/bio/appl/test_pts1.rb +140 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
- data/test/unit/bio/data/test_aa.rb +4 -17
- data/test/unit/bio/data/test_codontable.rb +3 -16
- data/test/unit/bio/data/test_na.rb +3 -3
- data/test/unit/bio/db/embl/test_common.rb +3 -16
- data/test/unit/bio/db/embl/test_embl.rb +3 -16
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
- data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
- data/test/unit/bio/db/kegg/test_genes.rb +3 -16
- data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
- data/test/unit/bio/db/test_aaindex.rb +2 -2
- data/test/unit/bio/db/test_fasta.rb +3 -16
- data/test/unit/bio/db/test_gff.rb +3 -16
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +56 -0
- data/test/unit/bio/db/test_nexus.rb +360 -0
- data/test/unit/bio/db/test_prosite.rb +5 -18
- data/test/unit/bio/db/test_rebase.rb +11 -25
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/io/test_ddbjxml.rb +5 -17
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +3 -16
- data/test/unit/bio/io/test_flatfile.rb +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +4 -17
- data/test/unit/bio/sequence/test_aa.rb +3 -3
- data/test/unit/bio/sequence/test_common.rb +3 -16
- data/test/unit/bio/sequence/test_compat.rb +3 -16
- data/test/unit/bio/sequence/test_na.rb +29 -3
- data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
- data/test/unit/bio/test_alignment.rb +16 -27
- data/test/unit/bio/test_command.rb +242 -25
- data/test/unit/bio/test_db.rb +3 -16
- data/test/unit/bio/test_feature.rb +4 -16
- data/test/unit/bio/test_location.rb +4 -16
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +4 -16
- data/test/unit/bio/test_reference.rb +2 -2
- data/test/unit/bio/test_sequence.rb +7 -19
- data/test/unit/bio/test_shell.rb +3 -16
- 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 +100 -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 +6 -18
- data/test/unit/bio/util/test_contingency_table.rb +6 -18
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +3 -16
- metadata +228 -169
- data/doc/BioRuby.rd.ja +0 -225
- data/doc/Design.rd.ja +0 -341
- data/doc/TODO.rd.ja +0 -138
- data/lib/bio/appl/fasta/format6.rb +0 -37
- data/lib/bio/db/kegg/cell.rb +0 -88
- data/lib/bio/db/kegg/ko.rb +0 -178
- data/lib/bio/shell/rails/Rakefile +0 -10
- data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
- data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
- data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
- data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
- data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
- data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
- data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
- data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
- data/lib/bio/shell/rails/config/boot.rb +0 -19
- data/lib/bio/shell/rails/config/database.yml +0 -85
- data/lib/bio/shell/rails/config/environment.rb +0 -53
- data/lib/bio/shell/rails/config/environments/development.rb +0 -19
- data/lib/bio/shell/rails/config/environments/production.rb +0 -19
- data/lib/bio/shell/rails/config/environments/test.rb +0 -19
- data/lib/bio/shell/rails/config/routes.rb +0 -19
- data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
- data/lib/bio/shell/rails/public/404.html +0 -8
- data/lib/bio/shell/rails/public/500.html +0 -8
- data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
- data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
- data/lib/bio/shell/rails/public/dispatch.rb +0 -10
- data/lib/bio/shell/rails/public/favicon.ico +0 -0
- data/lib/bio/shell/rails/public/images/rails.png +0 -0
- data/lib/bio/shell/rails/public/index.html +0 -277
- data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
- data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
- data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
- data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
- data/lib/bio/shell/rails/public/robots.txt +0 -1
- data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
- data/lib/bio/shell/rails/script/about +0 -3
- data/lib/bio/shell/rails/script/breakpointer +0 -3
- data/lib/bio/shell/rails/script/console +0 -3
- data/lib/bio/shell/rails/script/destroy +0 -3
- data/lib/bio/shell/rails/script/generate +0 -3
- data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
- data/lib/bio/shell/rails/script/performance/profiler +0 -3
- data/lib/bio/shell/rails/script/plugin +0 -3
- data/lib/bio/shell/rails/script/process/reaper +0 -3
- data/lib/bio/shell/rails/script/process/spawner +0 -3
- data/lib/bio/shell/rails/script/process/spinner +0 -3
- data/lib/bio/shell/rails/script/runner +0 -3
- data/lib/bio/shell/rails/script/server +0 -42
- data/lib/bio/shell/rails/test/test_helper.rb +0 -28
data/doc/BioRuby.rd.ja
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$Id: BioRuby.rd.ja,v 1.10 2004/08/23 23:41:29 k Exp $
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Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
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= BioRuby �ץ���������
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BioRuby �ϡ�Bioinformatics ��ɬ�פȤ���롢�ǡ����١����θ������ǡ�����
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�����ȥѡ�����������Ϥ���ѥ����������Ϥޤ��͡��ʷ����ʤɤ�ɬ�פȤʤ�
|
11
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-
�͡��ʵ�ǽ�� Ruby ����Ǽ���������ñ�˰�����褦�ˤ���ץ��������ȤǤ���
|
12
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-
|
13
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-
¾����ԥץ��������ȤȤ��Ƥ� BioPerl, BioPython, BioJava �ʤ��͡��ʤ��
|
14
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-
������ޤ��������٤Ǥ���ˤ�Ĺ�� BioPerl ���Ǥ⽼�¤��Ƥ���Ȼפ��ޤ�����
|
15
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-
BioPerl ��������Τ�ʣ���ʹ�¤�ǡ��ǡ��������Ǥ����Ѥ�������ꤵ���
|
16
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-
����褦�˻פ��ޤ��������⤽�� Perl ��ʣ���ʥǡ�����¤���ȥ���������
|
17
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-
�ɤ��ɤߤŤ餯�ʤ�ޤ������η�̡����ƥʥ���ɤ����ʤ�ޤ���¾
|
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-
�Υץ��������Ȥˤ⤽�줾������������Ȼפ��ޤ�����������ˤ��Ƥ��ȯ�dz�
|
19
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-
ȯ�������ʳ��ˤ��뤳�Ȥ�ͤ���С���ʬ�λȤ��䤹�������ɬ�פʵ�ǽ�����
|
20
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-
���ƹԤäƤ⽽ʬ���ɤ��դ���Ȼפ��ޤ���
|
21
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-
|
22
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-
BioRuby �Ǥϡ�����ץ�Ƕ��Ϥ� Ruby ����Υ��ɥХ�ơ�������������ʬ����
|
23
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-
�䤹�������ɤǥ���ɥ桼����ɬ�פʵ�ǽ��������Ƥ��������Ȼפ��ޤ����ä�
|
24
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-
Ruby �Τ����륪�֥������ȤȤ���ȯ�ۤϡ���Τ���ʪ�ؤˤ���ľ������
|
25
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-
�Ϥ�䤹�����ץȤǤ������ȥ饤�����顼�Ǻ�Ȥ�ʤ������Ǥ��륤��
|
26
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-
�ץ����� C �� Java ����٤ƥ����åȤʥ�ܤθ���Ԥˤ������ߤ䤹����
|
27
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-
�פ��ޤ���
|
28
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-
|
29
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-
�ޤ���Ruby �Ǥ� Perl ����ζ��Ϥ�ʸ��������˲ä���Perl �θ�Ť��� OO ��
|
30
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-
��륪�ޥ��ʥ��䡢�ѽФ��� local, my �ʤɤ����פǡ�ʣ���ʥǡ�����¤�⥯
|
31
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�饹�Ǥ��ä����ɽ���Ǥ��뤿�ᡢ�ܼ�Ū����ʬ����ǰ���ƥ����ǥ����뤳
|
32
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-
�Ȥ��Ǥ��ޤ�������ˤ�ꡢ��ȯ�θ�Ψ��⤯�ʤ뤿�ᡢ¾�Υץ��������Ȥ���
|
33
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-
�ݤ��Ƥ��ʤ��ΰ�ˤ⤤�������Ȥ�Ǥ�����Ȼפ��ޤ���
|
34
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-
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����ˡ�Ruby ���Τ����ܤdz�ȯ���줿����Ǥ���Τ˲ä� BioRuby �����ܽ��
|
36
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-
�����ץ�� Bio* �ץ��������ȤǤ������Τ��ᡢ�������ܸ������졢��ȯ��
|
37
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-
���ܸ�ǹԤʤ�������KEGG �ʤ������ȼ��Υ����ƥ�ؤ��б��ʤɤ�Ԥʤ��䤹
|
38
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-
������ BioRuby �Υ��åȤǤ��礦��
|
39
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-
|
40
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-
BioRuby �Υ����֥����� ((<URL:http://bioruby.org/>)) �ǡ��ǿ��Τ��Τ餻��
|
41
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-
��������������ˡ�����ꥹ�Ȥʤɤξ���ȡ�¾�Υɥ�����Ȥ䥳���
|
42
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-
�Ȥʤɤξ��������ޤ���
|
43
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-
|
44
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-
== �Ȥ���
|
45
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-
|
46
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-
BioRuby ��Ȥ�������ץȤ����
|
47
|
-
|
48
|
-
require 'bio'
|
49
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-
|
50
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-
�Ȥ��Ƥ���������
|
51
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-
|
52
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-
���ƤΥ��饹�� module Bio �β����ɲä���ޤ�����ɬ�פ˱�����
|
53
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-
|
54
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-
include Bio
|
55
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-
|
56
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-
�Ȥ��뤳�Ȥǡ�Bio:: ��ʤ��Ƴƥ��饹��Ȥ������Ǥ��ޤ���
|
57
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-
|
58
|
-
== BioRuby �γ�ά
|
59
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-
|
60
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-
bio.rb �� require ����ȡ��ʲ��Υ��饹������ʤɤ��Ȥ���褦�ˤʤ�ޤ���
|
61
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-
����������Ƥ����ʵ�ǽ�ϡ�
|
62
|
-
|
63
|
-
* ���ߥλ�������������Ρ������䥦����ɥ��������ʤɤ�ޤ���
|
64
|
-
���ץ饤���ʤɤ�ɽ�� GenBank ������ location �ե����ޥåȤν���
|
65
|
-
* BLAST/FASTA �ʤɤ��Ѥ�����Ʊ������
|
66
|
-
* ���Υ�ͥå� ((<URL:http://www.genome.jp>)) �θ����ȥǡ�������
|
67
|
-
* GenBank �� KEGG �ʤ��͡��ʥǡ����١����κ٤����ѡ���
|
68
|
-
* PubMed/MEDLINE �ʤɤΰ���ʸ���ǡ����μ���������
|
69
|
-
* �ѥ����������Ϥ�ɬ�פʥ���դȣ���ط������
|
70
|
-
|
71
|
-
�ʤɤǤ����ܤ���������ˡ�ˤĤ��Ƥϡ��ġ��Υ��饹�˴ؤ���ɥ�����Ȥ䡢
|
72
|
-
���塼�ȥꥢ��Ȥ��Ʋ�������
|
73
|
-
|
74
|
-
¾�ˡ��ޤ�̤����Ǥ��� C ����ˤ�롢���饹����� Smith-Waterman ��
|
75
|
-
�르�ꥺ��μ����ʤɤ�Ԥʤ��Ƥ��ޤ���
|
76
|
-
|
77
|
-
=== ���饹����
|
78
|
-
|
79
|
-
class Object �ե����� ��٥�
|
80
|
-
|- class String
|
81
|
-
| `- class Bio::Sequence bio/sequence.rb stable
|
82
|
-
| |- class Bio::Sequence::AA bio/sequence.rb stable
|
83
|
-
| `- class Bio::Sequence::NA bio/sequence.rb stable
|
84
|
-
|- class Bio::Location bio/location.rb stable
|
85
|
-
|- class Bio::Locations bio/location.rb stable
|
86
|
-
|- class Bio::Feature bio/feature.rb stable
|
87
|
-
|- class Bio::Features bio/feature.rb stable
|
88
|
-
|- class Bio::Reference bio/reference.rb stable
|
89
|
-
|- class Bio::References bio/reference.rb stable
|
90
|
-
|- class Bio::Pathway bio/pathway.rb stable
|
91
|
-
|- class Bio::Relation bio/pathway.rb stable
|
92
|
-
|- class Bio::FlatFile bio/io/flatfile.rb stable
|
93
|
-
|- class Bio::Registry bio/io/registry.rb beta
|
94
|
-
|- class Bio::Fetch bio/io/fetch.rb stable
|
95
|
-
|- class Bio::SQL bio/io/sql.rb beta
|
96
|
-
|- class Bio::DBGET bio/io/dbget.rb stable
|
97
|
-
|- class Bio::PubMed bio/io/pubmed.rb stable
|
98
|
-
|- class Bio::BRDB bio/io/brdb.rb alpha
|
99
|
-
|- class Bio::Fasta bio/appl/fasta.rb stable
|
100
|
-
|- class Bio::Fasta::Report::* bio/appl/fasta/*.rb stable
|
101
|
-
|- class Bio::Blast bio/appl/blast.rb stable
|
102
|
-
|- class Bio::Blast::Report::* bio/appl/blast/*.rb stable
|
103
|
-
|- class Bio::DB bio/db.rb stable
|
104
|
-
| |- class Bio::FastaFormat bio/db/fasta.rb stable
|
105
|
-
| |- class Bio::NCBIDB bio/db.rb stable
|
106
|
-
| | |- class Bio::GenBank bio/db/genbank/genbank.rb stable
|
107
|
-
| | | |- class Bio::GenPept bio/db/genbank/genpept.rb stable
|
108
|
-
| | | |- class Bio::RefSeq bio/db/genbank/refseq.rb stable
|
109
|
-
| | | `- class Bio::DDBJ bio/db/genbank/ddbj.rb stable
|
110
|
-
| | |- class Bio::MEDLINE bio/db/medline.rb stable
|
111
|
-
| | |- class Bio::LITDB bio/db/litdb.rb stable
|
112
|
-
| | `- class Bio::KEGGDB bio/db.rb beta
|
113
|
-
| | |- class Bio::AAindex bio/db/aaindex.rb beta
|
114
|
-
| | | |- class Bio::AAindex1 bio/db/aaindex.rb beta
|
115
|
-
| | | `- class Bio::AAindex2 bio/db/aaindex.rb beta
|
116
|
-
| | |- class Bio::KEGG::GENES bio/db/kegg/genes.rb stable
|
117
|
-
| | |- class Bio::KEGG::GENOME bio/db/kegg/genome.rb stable
|
118
|
-
| | |- class Bio::KEGG::BRITE bio/db/kegg/brite.rb alpha
|
119
|
-
| | |- class Bio::KEGG::CELL bio/db/kegg/cell.rb beta
|
120
|
-
| | |- class Bio::KEGG::ENZYME bio/db/kegg/enzyme.rb alpha
|
121
|
-
| | `- class Bio::KEGG::COMPOUND bio/db/kegg/compound.rb alpha
|
122
|
-
| `- class Bio::EMBLDB bio/db.rb stable
|
123
|
-
| |- class Bio::EMBL bio/db/embl/embl.rb beta
|
124
|
-
| |- class Bio::SPTR bio/db/embl/sptr.rb beta
|
125
|
-
| | |- class Bio::SwissProt bio/db/embl/swissprot.rb beta
|
126
|
-
| | `- class Bio::TrEMBL bio/db/embl/swissprot.rb beta
|
127
|
-
| |- class Bio::PROSITE bio/db/prosite.rb beta
|
128
|
-
| `- class Bio::TRANSFAC bio/db/transfac.rb beta
|
129
|
-
| |- class Bio::TFMATRIX bio/db/transfac.rb beta
|
130
|
-
| |- class Bio::TFSITE bio/db/transfac.rb beta
|
131
|
-
| |- class Bio::TFFACTOR bio/db/transfac.rb beta
|
132
|
-
| |- class Bio::TFCELL bio/db/transfac.rb beta
|
133
|
-
| |- class Bio::TFCLASS bio/db/transfac.rb beta
|
134
|
-
| `- class Bio::TFGENE bio/db/transfac.rb beta
|
135
|
-
|- class Bio::KEGG::DBname bio/db/kegg/keggtab.rb beta
|
136
|
-
|- class Bio::KEGG::Keggtab bio/db/kegg/keggtab.rb beta
|
137
|
-
|- class Bio::KEGG::Microarray bio/db/kegg/microarray.rb alpha
|
138
|
-
`- class Bio::KEGG::Microarrays bio/db/kegg/microarray.rb alpha
|
139
|
-
|
140
|
-
=== ɸ�९�饹�ؤΥ�å��ɲ�
|
141
|
-
|
142
|
-
class Matrix bio/matrix.rb alpha
|
143
|
-
class Vector bio/matrix.rb alpha
|
144
|
-
class String bio/extend.rb beta
|
145
|
-
class Array bio/extend.rb beta
|
146
|
-
|
147
|
-
=== �����̾�����֤γ���
|
148
|
-
|
149
|
-
module Bio �ե����� ������
|
150
|
-
|- AAindex bio/db/aaindex.rb class
|
151
|
-
|- AAindex1 bio/db/aaindex.rb class
|
152
|
-
|- AAindex2 bio/db/aaindex.rb class
|
153
|
-
|- AminoAcid bio/data/aa.rb constant
|
154
|
-
|- AminoAcid_weight bio/data/aa.rb constant
|
155
|
-
|- BIORUBY_VERSION bio.rb constant
|
156
|
-
|- Blast bio/appl/blast.rb class
|
157
|
-
| `- Report::* bio/appl/blast/*.rb class
|
158
|
-
|- BRDB bio/io/brdb.rb class
|
159
|
-
|- CodonTable bio/data/codontable.rb constant
|
160
|
-
|- DB bio/db.rb class
|
161
|
-
|- DBGET bio/io/dbget.rb class
|
162
|
-
|- DDBJ bio/db/genbank/ddbj.rb class
|
163
|
-
|- EMBL_COMMON bio/db/embl.rb module
|
164
|
-
|- EMBL bio/db/embl/embl.rb class
|
165
|
-
|- EMBLDB bio/db.rb class
|
166
|
-
|- Fasta bio/appl/fasta.rb class
|
167
|
-
| `- Report::* bio/appl/fasta/*.rb class
|
168
|
-
|- FastaFormat bio/db/fasta.rb class
|
169
|
-
|- FastaNumericFormat bio/db/fasta.rb class
|
170
|
-
|- Fetch bio/io/fetch.rb class
|
171
|
-
|- FlatFile bio/io/flatfile.rb class
|
172
|
-
|- GENBANK_COMMON bio/db/genbank.rb module
|
173
|
-
|- GenBank bio/db/genbank/genbank.rb class
|
174
|
-
|- GenPept bio/db/genbank/genpept.rb class
|
175
|
-
|- KEGG bio/db/kegg/ class
|
176
|
-
| |- BRITE bio/db/kegg/brite.rb class
|
177
|
-
| |- CELL bio/db/kegg/cell.rb class
|
178
|
-
| |- COMPOUND bio/db/kegg/compound.rb class
|
179
|
-
| |- ENZYME bio/db/kegg/enzyme.rb class
|
180
|
-
| |- GENES bio/db/kegg/genes.rb class
|
181
|
-
| |- GENOME bio/db/kegg/genome.rb class
|
182
|
-
| |- Keggtab bio/db/kegg/keggtab.rb class
|
183
|
-
| |- DBname bio/db/kegg/keggtab.rb class
|
184
|
-
| |- Microarray bio/db/kegg/microarray.rb class
|
185
|
-
| `- Microarrays bio/db/kegg/microarray.rb class
|
186
|
-
|- KEGGDB bio/db.rb class
|
187
|
-
|- KEGGORG bio/data/keggorg.rb constant
|
188
|
-
|- LITDB bio/db/litdb.rb class
|
189
|
-
|- Location bio/location.rb class
|
190
|
-
|- Locations bio/location.rb class
|
191
|
-
|- MEDLINE bio/db/medline.rb class
|
192
|
-
|- NCBIDB bio/db.rb class
|
193
|
-
|- NucleicAcid bio/data/na.rb constant
|
194
|
-
|- NucleicAcid_weight bio/data/na.rb constant
|
195
|
-
|- Pathway bio/pathway.rb class
|
196
|
-
|- PROSITE bio/db/prosite.rb class
|
197
|
-
|- PubMed bio/io/pubmed.rb class
|
198
|
-
|- Reference bio/reference.rb class
|
199
|
-
|- RefSeq bio/db/genbank/refseq.rb class
|
200
|
-
|- Registry bio/db/registry.rb class
|
201
|
-
|- Relation bio/pathway.rb class
|
202
|
-
|- Seq bio/sequence.rb class
|
203
|
-
| |- AA bio/sequence.rb class
|
204
|
-
| `- NA bio/sequence.rb class
|
205
|
-
|- Sequence bio/sequence.rb class
|
206
|
-
| |- AA bio/sequence.rb class
|
207
|
-
| `- NA bio/sequence.rb class
|
208
|
-
|- SwissProt bio/db/embl/swissprot.rb class
|
209
|
-
|- SPTR bio/db/embl/sptr.rb class
|
210
|
-
|- SQL bio/io/sql.rb class
|
211
|
-
|- TFCELL bio/db/transfac.rb class
|
212
|
-
|- TFCLASS bio/db/transfac.rb class
|
213
|
-
|- TFFACTOR bio/db/transfac.rb class
|
214
|
-
|- TFGENE bio/db/transfac.rb class
|
215
|
-
|- TFMATRIX bio/db/transfac.rb class
|
216
|
-
|- TFSITE bio/db/transfac.rb class
|
217
|
-
|- TRANSFAC bio/db/transfac.rb class
|
218
|
-
`- TrEMBL bio/db/embl/trembl.rb class
|
219
|
-
|
220
|
-
=== �ե����볬��
|
221
|
-
|
222
|
-
BioRuby �Υե����빽���ˤĤ��Ƥ� Design.rd.ja �Ȥ��Ƥ���������
|
223
|
-
|
224
|
-
=end
|
225
|
-
|
data/doc/Design.rd.ja
DELETED
@@ -1,341 +0,0 @@
|
|
1
|
-
=begin
|
2
|
-
|
3
|
-
$Id: Design.rd.ja,v 1.7 2002/07/02 01:40:24 k Exp $
|
4
|
-
|
5
|
-
Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
6
|
-
|
7
|
-
= BioRuby �γ�ȯ���ˤȥǥ�����
|
8
|
-
|
9
|
-
�������⥸�塼����ɲä������ CVS �ΰʲ��Υ�ݥ��ȥ�ˡ����Ƥ˽��ä�
|
10
|
-
Ŭ�ڤ� commit ���ޤ������ꥹ�Ȥʤɤ� contribute ���줿�����ɤ�
|
11
|
-
�ܿͤ� committer �ˤʤäƤ�餦���������åդ� commit ���ޤ���
|
12
|
-
|
13
|
-
bioruby/
|
14
|
-
|-- README �Ϥ����
|
15
|
-
|-- install.rb ���ȡ���
|
16
|
-
|-- COPYING
|
17
|
-
|-- COPYING.LIB
|
18
|
-
|-- bin/ ���ץꥱ�������
|
19
|
-
|-- lib/ Ruby �ǽ줿�饤�֥��
|
20
|
-
| `-- bio/ ����ʤɴ���Ū�ʥ��饹
|
21
|
-
| |-- data/ ��ʪ��Ū������ʤɥǡ������Τ��
|
22
|
-
| |-- db/ �Ƽ�ǡ����١����ѡ���
|
23
|
-
| |-- io/ �ǡ�����������
|
24
|
-
| `-- appl/ �������ץ�ν���
|
25
|
-
|-- doc/ �ɥ������
|
26
|
-
|-- ext/ C �ǽ줿�饤�֥��
|
27
|
-
`-- sample/ ����ץ륳����
|
28
|
-
|
29
|
-
== Ruby ��ʬ�ˤĤ��ƤΥǥ������bioruby/lib/bio/ �ʲ���
|
30
|
-
|
31
|
-
����ޤǤ˹Ԥʤ�줿�����Υǥ����ץȤȡ���������ˤʤɤˤĤ��Ƥ�
|
32
|
-
�Ȥ�Ƥ����ޤ���
|
33
|
-
|
34
|
-
BioRuby �������饹�� module Bio �ǰϤळ�Ȥǡ�̾�����֤��ڤ�ʬ������ˤ�
|
35
|
-
�ޤ���
|
36
|
-
|
37
|
-
=== lib/bio/ �ǡ�����¤��
|
38
|
-
|
39
|
-
����䥢�ߥλ�������ʸ���������Ҥ� location �� feature������դʤ�
|
40
|
-
����ݥǡ�����¤�����饹�� lib/bio/ ľ�������֤��Ƥ��ޤ��������ϳ�
|
41
|
-
�ǡ����١������ѡ����ʤɤ����ľ�ܸƤФ�ޤ���
|
42
|
-
|
43
|
-
¾�ˡ����饤���ȥ��饹�ʤɤμ�����ɬ�פ����Τ�ޤ��ޤ�����ʪ��η�
|
44
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-
��ʬ���ɽ�� Taxonomy ���饹�� GeneOntology �ʤɤΥ��饹�⤢�����������
|
45
|
-
�Τ�ޤ���
|
46
|
-
|
47
|
-
=== lib/bio/db/ �ǡ����١������ѡ�����
|
48
|
-
|
49
|
-
�Ȥ����δ�ñ�� vs ������ʣ�������������ᤵ vs ����νŤ����ʤɥХ��
|
50
|
-
�������ɬ�������ɤ��Ȥϸ����ʤ����⤢��ޤ�����lib/bio/db.rb �Ǥϰʲ�
|
51
|
-
�Τ褦���ȼ��Υ����ǥ��ʤ��Ǥ�Ʊ�ͤʻ�ߤ��ʤ���Ƥ������ɤ�����Ĵ�٤Ƥ�
|
52
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-
�ޤ���ˤ���Ѥ��Ƥ��ޤ����������ѡ������ɲä�����⻲�ͤˤ��Ʋ�������
|
53
|
-
|
54
|
-
����ȥ� ���줾��Υǡ����١����ˤ����룱�ĤΥǡ���ñ��
|
55
|
-
��) GenBank �ʤ� LOCUS ���� // �ޤǤ����Ƥι�
|
56
|
-
�ǥ�ߥ� ����ȥ�ȥ���ȥ����ڤ�ʸ����
|
57
|
-
��) GenBank �ʤ� // �����ι�
|
58
|
-
���� ����ȥ�κ�ü�������ʤɤ˵������ȥåץ�٥�μ��̻�
|
59
|
-
��) GenBank �ʤ� DEFINITION �� FEATURES �ʤ�
|
60
|
-
�ե������ ������˰�̣�Τ���ñ�̤�ʤ�ʣ���Ԥ���ʤ�֥��å�
|
61
|
-
��) GenBank �ʤ� SOURCE �˴ޤޤ�� taxonomy �ޤǤι������ʤ�
|
62
|
-
|
63
|
-
BioRuby �Υǡ����١������ѡ����ϡ�������ȥ�ʬ��ʸ����� .new ���Ϥ�����
|
64
|
-
�ѡ���������̤��ݻ����륤�����֤��ǥ�����ˤʤäƤ��ޤ����ƥǡ�
|
65
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-
���١������饨��ȥ�ñ�̤Υǡ�����������ˡ�ϡ��긵�Υե�åȥե�������
|
66
|
-
����硢�ͥåȱۤ��� DBGET �� BioFetch ������硢NCBI �����äƤ�����硢
|
67
|
-
�ʤɻȤ����ˤ�ä��͡��Ǥ������ɤ����饨��ȥ�������� (io) �˴ؤ�餺��
|
68
|
-
�ѡ����ϥ���ȥ��ѡ��������������ǰ�Ǥ��ޤ���
|
69
|
-
|
70
|
-
�ǽ�Ū�ˤ����ƤΥǡ����Ϥ��餫����ѡ������� tab �ڤ�Υǡ������ڤ��ߡ�
|
71
|
-
MySQL �ʤɤ��ͤù���Ǥ��ޤäƥѡ�����ɬ�פ��ʤ��褦�������ˤ������Ǥ���
|
72
|
-
BioPerl �� BioPerl-DB �˻��Ƥ���Ȼפ��ޤ�����BioRuby ɸ��� DataBase ��
|
73
|
-
�������Ȥ� BioRuby-DB (class BRDB) �Ȥ��Ƴ�ȯ��ʤ�Ƥ��ޤ���BioRuby ��
|
74
|
-
���������Ȥ� BioHackathon �� BOSC �˻��ä��� OBDA �� BioSQL �ʤɤ˽��
|
75
|
-
��褦�ˤʤ�ޤ����Τǡ�������ȼ��ǡ����١�����ɬ�פ���ʬ�ϸ��äƤ�����
|
76
|
-
�⤷��ޤ���
|
77
|
-
|
78
|
-
* OBDA : Open Bio Sequence Database Access
|
79
|
-
* ((<URL:http://obda.open-bio.org/>))
|
80
|
-
* ((<URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=obf-common>))
|
81
|
-
* BOSC : Bioinformatics Open Source Conference
|
82
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-
* ((<URL:http://bosc.open-bio.org/>))
|
83
|
-
|
84
|
-
+ �ǡ����١�����¤����ݲ�
|
85
|
-
|
86
|
-
lib/bio/db/ �ʲ��Υ⥸�塼��ϡ�lib/bio/db.rb �� require �������ʤ��Ȥ�
|
87
|
-
DB ���饹��Ѿ����ޤ�������ˡ������Ĥ��Υǡ����١���������ι�¤�����
|
88
|
-
�Ƥ��뤿�ᡢ�Ȥꤢ���� NCBI ����KEGG ��ޤ�ˡ�EMBL ����ʬ���ơ��ѡ�����
|
89
|
-
�ݤ˶��̤ǻȤ����åɤ�ͭ���褦�Ȥ��Ƥ��ޤ������������ºݤˤϤ����
|
90
|
-
�η��������ƤϤޤ�ʤ��ǡ����١�����¿���Τǡ�DB ������Ѿ�������⤢
|
91
|
-
��Ǥ��礦��
|
92
|
-
|
93
|
-
+ �ե�����ɤ��Ф��붦�̤� API �����
|
94
|
-
|
95
|
-
�͡��ʥǡ����١����Ǥ褯���̤��Ƹ����褦�ʥե�����ɤ��Ф��Ƥϡ�db.rb
|
96
|
-
��ˤ���ɥ�����ȤǼ�����붦�̤Υ�å�̾��Ȥäơ��ǡ����������
|
97
|
-
��褦�ˤ��ޤ���
|
98
|
-
|
99
|
-
���Τ褦�ˡ��ե�����ɤ��Ф��붦�̤Υ�å�̾�����ƥǡ����١����Υѡ���
|
100
|
-
��Ŭ�ڤ˼�������Ƥ���С��ǡ����١�����˥�åɤ�Ф���ɬ�פ�����ޤ���
|
101
|
-
�㤨�С��ǡ����١������ۤʤäƤ�֥���ȥ�������ե�����ɡ����Τ����
|
102
|
-
��åɤ� definition �������ȿ�¬���䤹���ʤ�ޤ���
|
103
|
-
|
104
|
-
+ ɬ�פʻ��ޤǥѡ������٤餻���on-demand parsing��
|
105
|
-
|
106
|
-
GenBank �ʤ�ʣ���ʹ�¤�Υǡ����١�����ѡ�������ݤˤ⥹�롼�ץåȤ��ɤ�
|
107
|
-
���뤿�ᡢ�ǽ�ϥե����������ڤ�ʬ����������������Ԥʤ�������Υե���
|
108
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-
�����Υǡ������᤹���åɤ��ƤФ줿�������ºݤ˥ե��������Υǡ�
|
109
|
-
����٤����ѡ������������Ԥʤ��ޤ���������λ��ѡ��������Τϡ�ɬ
|
110
|
-
�פʥե�����ɤ����Ǥ���
|
111
|
-
|
112
|
-
+ ���٥ѡ���������̤ϥ���å��夷�Ƥ���
|
113
|
-
|
114
|
-
�嵭�� on-demand parsing �ǥѡ���������̤ϡ����֥���������˥���å���
|
115
|
-
���Ƥ����Τǡ������ܰʹߤΥ�åɥ�����Ǥ��ݻ����Ƥ���ѡ����ѤߤΥǡ�
|
116
|
-
�����֤��ޤ�������ˤ��Ť��ѡ������֤��褦�ʥ����С��إåɤ�̵����
|
117
|
-
�Ƥ��ޤ���
|
118
|
-
|
119
|
-
=== lib/bio/data/ ������ǡ�����
|
120
|
-
|
121
|
-
lib/bio/data/ �ʲ��ˡ������Ĥ��Υǡ����ʥ��ߥλ���̾����KEGG �Ǥ���ʪ��
|
122
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-
̾�����ɥ�ɽ�ʤɡˤ�����Ȥ����֤���Ƥ��ޤ���
|
123
|
-
|
124
|
-
Bio::AminoAcid �� ���ߥλ���̾����ɽ���ϥå��塢�ʤ�
|
125
|
-
|
126
|
-
�����ϡ�ɬ�פʥ��饹�˥���������åɤ�������Ƥ��ɤ��Ǥ��礦��
|
127
|
-
|
128
|
-
=== lib/bio/io/ �����ե�������IO ��
|
129
|
-
|
130
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-
lib/bio/io/ �ʲ��ˤϡ��ե�åȥե����������ȥ�ñ�̤��ɤ߹��९�饹��
|
131
|
-
���Υ�ͥåȤ���ǡ���������Ԥʤ� DBGET ���饹�� NCBI �� PubMed �ˤ��
|
132
|
-
MEDLINE �ǡ���������Ԥʤ� PubMed ���饹��OBDA �˽�� BioRegistry,
|
133
|
-
BioFetch, BioSQL �ʤɤˤ��ǡ���������Ԥ����饹�ʤɤ�����ޤ���
|
134
|
-
|
135
|
-
* flatfile.rb �ʼ����ѡ�
|
136
|
-
|
137
|
-
# ��������Υե������ GenBank �ե����ޥåȤȤ��Ƴ���
|
138
|
-
flatfile = Bio::FlatFile.open(Bio::GenBank, "genbank/gbest40.seq")
|
139
|
-
|
140
|
-
# �ޤ��ϥե�����ϰ�����Ϳ����
|
141
|
-
Bio::FlatFile.new(Bio::GenBank, ARGF)
|
142
|
-
|
143
|
-
# �ޤ��� IO ��Ϳ����
|
144
|
-
Bio::FlatFile.new(Bio::GenBank, IO.popen("gzip -dc nc1101.flat.gz"))
|
145
|
-
|
146
|
-
# �ǽ�Υ���ȥ�� GenBank ���֥������Ȥ�
|
147
|
-
gb = flatfile.next_entry
|
148
|
-
|
149
|
-
# ����ȥꤴ�Ȥ� Bio::GenBank ���֥������Ȥ�����
|
150
|
-
flatfile.each do |gb|
|
151
|
-
puts gb.definition
|
152
|
-
end
|
153
|
-
|
154
|
-
=== lib/bio/appl/ �ġ����
|
155
|
-
|
156
|
-
FASTA(SSEARCH), [PSI-]BLAST, HMMER, CLUSTALW �ʤɤγ������ץ��Ȥä���
|
157
|
-
����Ԥ��ޤ�����������ʼ¹ԡ�http �ʤɤˤ���⡼�ȼ¹ԡ���̤Υե���
|
158
|
-
�ޥåȤʤɤ�ռ������ˡ���̤��ѡ��������Ǽ���줿 Report ���֥������Ȥ�
|
159
|
-
�ɤ��֤�褦�ʴ����ˤ��Ƥ����ޤ���
|
160
|
-
|
161
|
-
* query �Ȥʤ륪�֥������Ȥˡ����ץ��¹Ԥ����åɤ������ɬ�פʰ���
|
162
|
-
��Ϳ�����
|
163
|
-
|
164
|
-
factory = Bio::Fasta.remote('fasta', 'genes')
|
165
|
-
fa_res = f.fasta(factory) # f �� Bio::FastaFormat ���֥�������
|
166
|
-
fa_res = seq.fasta(factory) # seq �� Bio::Sequence::AA ���֥������Ȥʤ�
|
167
|
-
|
168
|
-
* ���������������ե����ȥ�ˡ������С�query��target �ʤɤ����ꤷ�ơ�����
|
169
|
-
���¹Ԥ����åɤ�Ƥ�
|
170
|
-
|
171
|
-
factory = Bio::Fasta.local(prog, target, opt)
|
172
|
-
fa_res = factory.query(seq)
|
173
|
-
|
174
|
-
�ʤɤ����Ĥ��μ�����ˡ���ͤ����ޤ���Bio::Fasta, Bio::Blast �Ǥ�ξ����
|
175
|
-
����ץꤷ�Ƥ��ޤ��ˡ�
|
176
|
-
|
177
|
-
�ե����ȥ���åɤؤΥ��ץ������Ϥ����ϡ�ʣ����ʪ�ϥ���ܥ����
|
178
|
-
���� hash �ˤ��������ɤ����⤷��ޤ��⤷����̾���Ĥ������Ԥ���
|
179
|
-
|
180
|
-
res = a.query(:hoge => fuga, :hoge2 => fuga2)
|
181
|
-
|
182
|
-
����¾�Υ��ץ�Υ����ե�������������ʤ�����ͤ���Ƥ��������Ȼ�
|
183
|
-
���ޤ���
|
184
|
-
|
185
|
-
== �����ǥ���������
|
186
|
-
|
187
|
-
���饹�߷ס���å�����ʤ����̤ˤ����ơ�KISS (keep it simple stupid) ��
|
188
|
-
���ܤǤ������������ʤ�Ǥ⤫��Ǥ� class ��ʬ�Ƥ��ޤ����ɤ��櫓�Ǥ�
|
189
|
-
�ʤ��Ǥ��礦����ǰ�Ȥ��ư�ĤΤޤȤޤ���Ȼפ����Τޤ�ʬ��Ф褯��
|
190
|
-
�ä˻Ȥ��Τ����ʤ����֥������Ȥ���������ɬ�פϤʤ��Ȼפ��ޤ���
|
191
|
-
|
192
|
-
����Ū�ʻ��ˤĤ��Ƥϡ���˲�����;�Ϥ�����Ȼפ��ޤ�����������ˤ��
|
193
|
-
����ץ��ʬ����䤹���ʤ��硢����γ�ȯ�����ࡼ���ˤʤ�Ȼפ�����
|
194
|
-
�ˤϡ��ɤ�ɤ������Ƥ����ޤ����դˡ�¿����Ψ���ɤ��ʤ�Ȥ��Ƥⲿ����
|
195
|
-
�Ƥ��뤫ʬ����ˤ����ʤ��硢ɬ�������⤤�Ȼפ����Ѷ�Ū����ͳ�����Ĥ���
|
196
|
-
�ʤ����Ϻ��Ѥ�碌�뤳�Ȥ⤢��Ȼפ��ޤ���������ˤ��Ƥ⡢�С�����
|
197
|
-
�� 1.0 �ޤǤϲ��̸ߴ��������ˤ����ѹ���Ԥʤ�ͽ��Ǥ���
|
198
|
-
|
199
|
-
��������������ˤ����ܸ�ʤ��� ASCII ��ʸ����ϴޤޤʤ��褦�ˤ��ޤ���
|
200
|
-
|
201
|
-
=== �إå���
|
202
|
-
|
203
|
-
�إå����ˤϡ��ե�����̾�����ס�����ԡ��饤����CVS �� ID ��ޤ�
|
204
|
-
�ʲ�����Ǥ� ID �Ρ��Ÿ������ʤ��褦�����Ѥˤ��Ƥ��ޤ������ºݤ� $ �Ǥ��ˡ�
|
205
|
-
|
206
|
-
#
|
207
|
-
# bio/hoge.rb - biological hoge class
|
208
|
-
#
|
209
|
-
# Copyright (C) 2000, 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
210
|
-
#
|
211
|
-
# This library is free software; you can redistribute it and/or
|
212
|
-
# modify it under the terms of the GNU Lesser General Public
|
213
|
-
# License as published by the Free Software Foundation; either
|
214
|
-
# version 2 of the License, or (at your option) any later version.
|
215
|
-
#
|
216
|
-
# This library is distributed in the hope that it will be useful,
|
217
|
-
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
218
|
-
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
219
|
-
# Lesser General Public License for more details.
|
220
|
-
#
|
221
|
-
# You should have received a copy of the GNU Lesser General Public
|
222
|
-
# License along with this library; if not, write to the Free Software
|
223
|
-
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
224
|
-
#
|
225
|
-
# ��Id:��
|
226
|
-
#
|
227
|
-
|
228
|
-
���ץꥱ�������䥵��ץ륳���ɤ���ϡ�ruby �Υѥ��˰�¸���ʤ���
|
229
|
-
���ˣ����ܤ�
|
230
|
-
|
231
|
-
#!/usr/bin/env ruby
|
232
|
-
|
233
|
-
�Τ褦�˻Ϥ��Τ��ɤ��Ǥ��礦��
|
234
|
-
|
235
|
-
=== ����
|
236
|
-
|
237
|
-
���Τ� module Bio �dz�ꡢɬ�פʥ��饹��������ޤ���������Ǥ� # ��Ȥ�
|
238
|
-
�ƥ����Ȥ�Ĥ���RD ��Ȥä������Ȥϥե�����κǸ�Υɥ����������
|
239
|
-
�ǤϽФƤ��ʤ��褦�ˤ��ޤ����⤷�������륯�饹�� bio/db/ �ʲ��Υǡ����١�
|
240
|
-
���ѡ����Ϥ��ä��顢bio/db.rb �Υɥ�����Ȥ⻲�Ȥ��Ʋ�������
|
241
|
-
|
242
|
-
require 'foo/bar'
|
243
|
-
|
244
|
-
modlue Bio
|
245
|
-
|
246
|
-
class Hoge
|
247
|
-
|
248
|
-
# this method do hogehoge
|
249
|
-
def hoge(fuga)
|
250
|
-
@fuga = fuga # storing data fuga
|
251
|
-
end
|
252
|
-
|
253
|
-
def gege
|
254
|
-
end
|
255
|
-
|
256
|
-
end
|
257
|
-
|
258
|
-
end
|
259
|
-
|
260
|
-
RDoc ��Ȥ��Х��饹���åɤξ�˽줿�����Ȥ��� HTML �ʤɤ�����
|
261
|
-
�Ǥ���褦�Ǥ������� ri �Ѥν��Ϥ�Ǥ���褦�ˤʤäƤ����顢���Ѥ��뤫��
|
262
|
-
����ޤ���
|
263
|
-
|
264
|
-
=== �ƥ��ȥ�������
|
265
|
-
|
266
|
-
�ƥ��ȥ����ɤϥ��饹����ʤ�������ʬ�Τ��Ȥˤ�Ĥ��뤳�Ȥˤ��ޤ����ƥ���
|
267
|
-
�����ɤν����Ϥ��줫�鸡Ƥ���Ƥ���ɬ�פ�����ޤ������Ȥꤢ�����ʲ��Τ�
|
268
|
-
���ʹ�ʸ�ǥƥ��ȥ����ɤ�Ϥߤޤ���
|
269
|
-
|
270
|
-
if __FILE__ == $0
|
271
|
-
# test code here
|
272
|
-
end
|
273
|
-
|
274
|
-
���Τ��ޤ��ʤ��Τ褦�ʹ�ʸ�ϡ��ե����� hoge.rb �����ޥ�ɥ饤��
|
275
|
-
|
276
|
-
% ruby hoge.rb
|
277
|
-
|
278
|
-
�ʤɤȥ�����ץȤȤ��Ƶ�ư���줿���˼¹Ԥ���ޤ������饤�֥��Ȥ���
|
279
|
-
|
280
|
-
require 'hoge'
|
281
|
-
|
282
|
-
�Τ褦�˥����ɤ��줿���ˤϼ¹Ԥ���ʤ��褦�ˤ��뤿��ξ����Ǥ���
|
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�ƥ��Ȥ���ˡ�ϡ�Test::Unit �� ruby ��ɸ��饤�֥��Ȥ���ź�դ����褦
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�ˤʤ�к��Ѥ��Ƥ⤤���Ȼפ��ޤ���������ޤǤϿ���������Ȼפ��ޤ�����
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���Ȥ˳����ե������ͥåȥ���ʤɤ�ɬ�פʾ��ɤ����뤫�Ȥ������ȡ�
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������ư���ǧ�Ȥ��ƥƥ��Ȥ�¹Ԥ�����ˡ�ʤɤ⸡Ƥ����ɬ�פ�����ޤ���
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=== �ɥ��������
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����ޤǡ��ƥ��饹�ˤĤ��Ƥϡ����ޤ�ɥ�����Ȳ�����Ƥ��ޤ���Ǥ�������
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����ϥƥ��ȥ����ɤΤ��ȡ��ե�����κǸ����� RD �ǥ�åɤʤɤΥɥ����
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��Ȥ��ɲä��뤳�Ȥˤ��Ƥ����ޤ���
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=begin
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= Bio::Hoge
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Hoge ���饹�γ���������
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--- Bio::Hoge.new(fuga)
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���饹��åɤ�������
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--- Bio::Hoge#to_a
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��åɤ�������
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== Bio::Hoge::Fuga
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�������饹 Hoge::Fuga �γ�������
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--- Bio::Hoge::Fuga.new(fuga)
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���饹��åɤ�������
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--- Bio::Hoge::Fuga#to_a
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��åɤ�������
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=end
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��������
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* ����������ˤ� ASCII �ʳ���ʸ��������ʤ����ˤΤ��ᡢ���ܸ�Υɥ����
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��Ȥϡ�������ʬ�ǤϤʤ��̥ե�����˵��Ҥ���doc/ �ǥ��쥯�ȥ�ʲ�����
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���ʤɤ��ޤ������κݡ���ĥ�Ҥ� .ja ���դ��ơ��ե�����̾��������ܸ��
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ʬ����褦�ˤ��ޤ���
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* ���ҤΤ褦�ˡ�������������������Ǥ� RD �ˤ��ɥ�����Ȥ϶ػߤ��ޤ���
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��ͳ�Ͻ��˥����ɤ��ɤߤŤ餯�ʤ뤫��Ǥ������������ # ��Ȥä�ɬ��
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�ʥ����Ȥ��ɲä�����ϴ��ޤ��ޤ���(���ҤΤ褦�� RDoc ���ˤ��뤫��
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����ޤ���)
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== ��ȯ�˻��ä���ˤ�
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BioRuby �Υ����֥����� ((<URL:http://bioruby.org>)) �ơ�����
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���Ȥ˻��ä��뤫�������å� <staff@bioruby.org> ��Ϣ�����Ƥ���������
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=end
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