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
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