bio 1.0.0 → 1.1.0

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Files changed (340) hide show
  1. data/bin/bioruby +14 -122
  2. data/bin/br_biofetch.rb +2 -2
  3. data/bin/br_bioflat.rb +2 -2
  4. data/bin/br_biogetseq.rb +2 -2
  5. data/bin/br_pmfetch.rb +3 -3
  6. data/doc/Changes-0.7.rd +77 -0
  7. data/doc/KEGG_API.rd +523 -232
  8. data/doc/KEGG_API.rd.ja +529 -207
  9. data/doc/Tutorial.rd +48 -11
  10. data/lib/bio.rb +59 -6
  11. data/lib/bio/alignment.rb +713 -103
  12. data/lib/bio/appl/bl2seq/report.rb +2 -18
  13. data/lib/bio/appl/blast.rb +108 -91
  14. data/lib/bio/appl/blast/format0.rb +33 -18
  15. data/lib/bio/appl/blast/format8.rb +6 -20
  16. data/lib/bio/appl/blast/report.rb +293 -429
  17. data/lib/bio/appl/blast/rexml.rb +8 -22
  18. data/lib/bio/appl/blast/wublast.rb +21 -12
  19. data/lib/bio/appl/blast/xmlparser.rb +180 -183
  20. data/lib/bio/appl/blat/report.rb +127 -30
  21. data/lib/bio/appl/clustalw.rb +87 -59
  22. data/lib/bio/appl/clustalw/report.rb +20 -22
  23. data/lib/bio/appl/emboss.rb +113 -20
  24. data/lib/bio/appl/fasta.rb +173 -198
  25. data/lib/bio/appl/fasta/format10.rb +244 -347
  26. data/lib/bio/appl/gcg/msf.rb +212 -0
  27. data/lib/bio/appl/gcg/seq.rb +195 -0
  28. data/lib/bio/appl/genscan/report.rb +5 -23
  29. data/lib/bio/appl/hmmer.rb +8 -45
  30. data/lib/bio/appl/hmmer/report.rb +2 -20
  31. data/lib/bio/appl/iprscan/report.rb +374 -0
  32. data/lib/bio/appl/mafft.rb +87 -50
  33. data/lib/bio/appl/mafft/report.rb +151 -44
  34. data/lib/bio/appl/muscle.rb +52 -0
  35. data/lib/bio/appl/phylip/alignment.rb +129 -0
  36. data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
  37. data/lib/bio/appl/probcons.rb +41 -0
  38. data/lib/bio/appl/psort.rb +89 -96
  39. data/lib/bio/appl/psort/report.rb +6 -22
  40. data/lib/bio/appl/pts1.rb +263 -0
  41. data/lib/bio/appl/sim4.rb +26 -36
  42. data/lib/bio/appl/sim4/report.rb +2 -18
  43. data/lib/bio/appl/sosui/report.rb +5 -20
  44. data/lib/bio/appl/spidey/report.rb +2 -2
  45. data/lib/bio/appl/targetp/report.rb +4 -20
  46. data/lib/bio/appl/tcoffee.rb +55 -0
  47. data/lib/bio/appl/tmhmm/report.rb +4 -20
  48. data/lib/bio/command.rb +235 -64
  49. data/lib/bio/data/aa.rb +21 -26
  50. data/lib/bio/data/codontable.rb +2 -20
  51. data/lib/bio/data/na.rb +19 -4
  52. data/lib/bio/db.rb +27 -12
  53. data/lib/bio/db/aaindex.rb +2 -20
  54. data/lib/bio/db/embl/common.rb +4 -21
  55. data/lib/bio/db/embl/embl.rb +33 -85
  56. data/lib/bio/db/embl/sptr.rb +612 -302
  57. data/lib/bio/db/embl/swissprot.rb +10 -29
  58. data/lib/bio/db/embl/trembl.rb +10 -29
  59. data/lib/bio/db/embl/uniprot.rb +10 -29
  60. data/lib/bio/db/fantom.rb +15 -20
  61. data/lib/bio/db/fasta.rb +3 -3
  62. data/lib/bio/db/genbank/common.rb +37 -46
  63. data/lib/bio/db/genbank/ddbj.rb +6 -18
  64. data/lib/bio/db/genbank/genbank.rb +47 -186
  65. data/lib/bio/db/genbank/genpept.rb +4 -17
  66. data/lib/bio/db/genbank/refseq.rb +4 -17
  67. data/lib/bio/db/gff.rb +103 -35
  68. data/lib/bio/db/go.rb +4 -20
  69. data/lib/bio/db/kegg/brite.rb +26 -36
  70. data/lib/bio/db/kegg/compound.rb +81 -85
  71. data/lib/bio/db/kegg/drug.rb +98 -0
  72. data/lib/bio/db/kegg/enzyme.rb +133 -110
  73. data/lib/bio/db/kegg/expression.rb +2 -20
  74. data/lib/bio/db/kegg/genes.rb +208 -238
  75. data/lib/bio/db/kegg/genome.rb +164 -285
  76. data/lib/bio/db/kegg/glycan.rb +114 -157
  77. data/lib/bio/db/kegg/keggtab.rb +242 -303
  78. data/lib/bio/db/kegg/kgml.rb +117 -160
  79. data/lib/bio/db/kegg/orthology.rb +112 -0
  80. data/lib/bio/db/kegg/reaction.rb +54 -69
  81. data/lib/bio/db/kegg/taxonomy.rb +331 -0
  82. data/lib/bio/db/lasergene.rb +209 -0
  83. data/lib/bio/db/litdb.rb +3 -27
  84. data/lib/bio/db/medline.rb +228 -249
  85. data/lib/bio/db/nbrf.rb +3 -3
  86. data/lib/bio/db/newick.rb +510 -0
  87. data/lib/bio/db/nexus.rb +1854 -0
  88. data/lib/bio/db/pdb.rb +5 -17
  89. data/lib/bio/db/pdb/atom.rb +2 -18
  90. data/lib/bio/db/pdb/chain.rb +2 -18
  91. data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
  92. data/lib/bio/db/pdb/model.rb +2 -18
  93. data/lib/bio/db/pdb/pdb.rb +73 -34
  94. data/lib/bio/db/pdb/residue.rb +4 -20
  95. data/lib/bio/db/pdb/utils.rb +2 -18
  96. data/lib/bio/db/prosite.rb +403 -422
  97. data/lib/bio/db/rebase.rb +84 -40
  98. data/lib/bio/db/soft.rb +404 -0
  99. data/lib/bio/db/transfac.rb +5 -17
  100. data/lib/bio/feature.rb +106 -52
  101. data/lib/bio/io/das.rb +32 -42
  102. data/lib/bio/io/dbget.rb +2 -20
  103. data/lib/bio/io/ddbjxml.rb +77 -138
  104. data/lib/bio/io/ebisoap.rb +158 -0
  105. data/lib/bio/io/ensembl.rb +229 -0
  106. data/lib/bio/io/fastacmd.rb +89 -82
  107. data/lib/bio/io/fetch.rb +163 -96
  108. data/lib/bio/io/flatfile.rb +170 -73
  109. data/lib/bio/io/flatfile/bdb.rb +3 -16
  110. data/lib/bio/io/flatfile/index.rb +2 -2
  111. data/lib/bio/io/flatfile/indexer.rb +3 -2
  112. data/lib/bio/io/higet.rb +12 -31
  113. data/lib/bio/io/keggapi.rb +210 -269
  114. data/lib/bio/io/ncbisoap.rb +155 -0
  115. data/lib/bio/io/pubmed.rb +169 -147
  116. data/lib/bio/io/registry.rb +4 -20
  117. data/lib/bio/io/soapwsdl.rb +43 -38
  118. data/lib/bio/io/sql.rb +242 -305
  119. data/lib/bio/location.rb +407 -285
  120. data/lib/bio/map.rb +410 -0
  121. data/lib/bio/pathway.rb +558 -695
  122. data/lib/bio/reference.rb +272 -75
  123. data/lib/bio/sequence.rb +255 -13
  124. data/lib/bio/sequence/aa.rb +71 -10
  125. data/lib/bio/sequence/common.rb +187 -33
  126. data/lib/bio/sequence/compat.rb +59 -4
  127. data/lib/bio/sequence/format.rb +54 -7
  128. data/lib/bio/sequence/generic.rb +3 -3
  129. data/lib/bio/sequence/na.rb +328 -26
  130. data/lib/bio/shell.rb +11 -4
  131. data/lib/bio/shell/core.rb +221 -160
  132. data/lib/bio/shell/demo.rb +18 -15
  133. data/lib/bio/shell/interface.rb +14 -12
  134. data/lib/bio/shell/irb.rb +95 -0
  135. data/lib/bio/shell/object.rb +45 -26
  136. data/lib/bio/shell/plugin/blast.rb +42 -0
  137. data/lib/bio/shell/plugin/codon.rb +22 -14
  138. data/lib/bio/shell/plugin/das.rb +58 -0
  139. data/lib/bio/shell/plugin/emboss.rb +2 -2
  140. data/lib/bio/shell/plugin/entry.rb +22 -11
  141. data/lib/bio/shell/plugin/flatfile.rb +2 -2
  142. data/lib/bio/shell/plugin/keggapi.rb +13 -6
  143. data/lib/bio/shell/plugin/midi.rb +4 -4
  144. data/lib/bio/shell/plugin/obda.rb +2 -2
  145. data/lib/bio/shell/plugin/psort.rb +56 -0
  146. data/lib/bio/shell/plugin/seq.rb +35 -8
  147. data/lib/bio/shell/plugin/soap.rb +87 -0
  148. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
  149. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
  150. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
  151. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
  152. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
  153. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
  154. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
  155. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
  156. data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
  157. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
  158. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
  159. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
  160. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
  161. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
  162. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
  163. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
  164. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
  165. data/lib/bio/shell/script.rb +25 -0
  166. data/lib/bio/shell/setup.rb +109 -0
  167. data/lib/bio/shell/web.rb +70 -58
  168. data/lib/bio/tree.rb +850 -0
  169. data/lib/bio/util/color_scheme.rb +84 -107
  170. data/lib/bio/util/color_scheme/buried.rb +5 -24
  171. data/lib/bio/util/color_scheme/helix.rb +5 -24
  172. data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
  173. data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
  174. data/lib/bio/util/color_scheme/strand.rb +5 -24
  175. data/lib/bio/util/color_scheme/taylor.rb +5 -24
  176. data/lib/bio/util/color_scheme/turn.rb +5 -24
  177. data/lib/bio/util/color_scheme/zappo.rb +5 -24
  178. data/lib/bio/util/contingency_table.rb +70 -43
  179. data/lib/bio/util/restriction_enzyme.rb +228 -0
  180. data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
  181. data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
  182. data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
  183. data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
  184. data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
  185. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
  186. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
  187. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
  188. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
  189. data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
  190. data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
  191. data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
  192. data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
  193. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
  194. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
  195. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
  196. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
  197. data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
  198. data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
  199. data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
  200. data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
  201. data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
  202. data/lib/bio/util/sirna.rb +4 -22
  203. data/sample/color_scheme_na.rb +4 -12
  204. data/sample/enzymes.rb +78 -0
  205. data/sample/goslim.rb +5 -13
  206. data/sample/psortplot_html.rb +4 -12
  207. data/test/data/blast/2.2.15.blastp.m7 +876 -0
  208. data/test/data/embl/AB090716.embl.rel89 +63 -0
  209. data/test/data/fasta/example1.txt +75 -0
  210. data/test/data/fasta/example2.txt +21 -0
  211. data/test/data/iprscan/merged.raw +32 -0
  212. data/test/data/iprscan/merged.txt +74 -0
  213. data/test/data/soft/GDS100_partial.soft +92 -0
  214. data/test/data/soft/GSE3457_family_partial.soft +874 -0
  215. data/test/functional/bio/io/test_ensembl.rb +103 -0
  216. data/test/functional/bio/io/test_soapwsdl.rb +5 -17
  217. data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
  218. data/test/unit/bio/appl/blast/test_report.rb +3 -16
  219. data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
  220. data/test/unit/bio/appl/genscan/test_report.rb +3 -16
  221. data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
  222. data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
  223. data/test/unit/bio/appl/mafft/test_report.rb +63 -0
  224. data/test/unit/bio/appl/sosui/test_report.rb +3 -16
  225. data/test/unit/bio/appl/targetp/test_report.rb +3 -16
  226. data/test/unit/bio/appl/test_blast.rb +3 -16
  227. data/test/unit/bio/appl/test_fasta.rb +4 -16
  228. data/test/unit/bio/appl/test_pts1.rb +140 -0
  229. data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
  230. data/test/unit/bio/data/test_aa.rb +4 -17
  231. data/test/unit/bio/data/test_codontable.rb +3 -16
  232. data/test/unit/bio/data/test_na.rb +3 -3
  233. data/test/unit/bio/db/embl/test_common.rb +3 -16
  234. data/test/unit/bio/db/embl/test_embl.rb +3 -16
  235. data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
  236. data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
  237. data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
  238. data/test/unit/bio/db/kegg/test_genes.rb +3 -16
  239. data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
  240. data/test/unit/bio/db/test_aaindex.rb +2 -2
  241. data/test/unit/bio/db/test_fasta.rb +3 -16
  242. data/test/unit/bio/db/test_gff.rb +3 -16
  243. data/test/unit/bio/db/test_lasergene.rb +95 -0
  244. data/test/unit/bio/db/test_newick.rb +56 -0
  245. data/test/unit/bio/db/test_nexus.rb +360 -0
  246. data/test/unit/bio/db/test_prosite.rb +5 -18
  247. data/test/unit/bio/db/test_rebase.rb +11 -25
  248. data/test/unit/bio/db/test_soft.rb +138 -0
  249. data/test/unit/bio/io/test_ddbjxml.rb +5 -17
  250. data/test/unit/bio/io/test_ensembl.rb +109 -0
  251. data/test/unit/bio/io/test_fastacmd.rb +3 -16
  252. data/test/unit/bio/io/test_flatfile.rb +237 -0
  253. data/test/unit/bio/io/test_soapwsdl.rb +4 -17
  254. data/test/unit/bio/sequence/test_aa.rb +3 -3
  255. data/test/unit/bio/sequence/test_common.rb +3 -16
  256. data/test/unit/bio/sequence/test_compat.rb +3 -16
  257. data/test/unit/bio/sequence/test_na.rb +29 -3
  258. data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
  259. data/test/unit/bio/test_alignment.rb +16 -27
  260. data/test/unit/bio/test_command.rb +242 -25
  261. data/test/unit/bio/test_db.rb +3 -16
  262. data/test/unit/bio/test_feature.rb +4 -16
  263. data/test/unit/bio/test_location.rb +4 -16
  264. data/test/unit/bio/test_map.rb +230 -0
  265. data/test/unit/bio/test_pathway.rb +4 -16
  266. data/test/unit/bio/test_reference.rb +2 -2
  267. data/test/unit/bio/test_sequence.rb +7 -19
  268. data/test/unit/bio/test_shell.rb +3 -16
  269. data/test/unit/bio/test_tree.rb +593 -0
  270. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
  271. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
  272. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
  273. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +100 -0
  274. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
  275. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
  276. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
  277. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
  278. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
  279. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
  280. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
  281. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
  282. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
  283. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
  284. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
  285. data/test/unit/bio/util/test_color_scheme.rb +6 -18
  286. data/test/unit/bio/util/test_contingency_table.rb +6 -18
  287. data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
  288. data/test/unit/bio/util/test_sirna.rb +3 -16
  289. metadata +228 -169
  290. data/doc/BioRuby.rd.ja +0 -225
  291. data/doc/Design.rd.ja +0 -341
  292. data/doc/TODO.rd.ja +0 -138
  293. data/lib/bio/appl/fasta/format6.rb +0 -37
  294. data/lib/bio/db/kegg/cell.rb +0 -88
  295. data/lib/bio/db/kegg/ko.rb +0 -178
  296. data/lib/bio/shell/rails/Rakefile +0 -10
  297. data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
  298. data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
  299. data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
  300. data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
  301. data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
  302. data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
  303. data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
  304. data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
  305. data/lib/bio/shell/rails/config/boot.rb +0 -19
  306. data/lib/bio/shell/rails/config/database.yml +0 -85
  307. data/lib/bio/shell/rails/config/environment.rb +0 -53
  308. data/lib/bio/shell/rails/config/environments/development.rb +0 -19
  309. data/lib/bio/shell/rails/config/environments/production.rb +0 -19
  310. data/lib/bio/shell/rails/config/environments/test.rb +0 -19
  311. data/lib/bio/shell/rails/config/routes.rb +0 -19
  312. data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
  313. data/lib/bio/shell/rails/public/404.html +0 -8
  314. data/lib/bio/shell/rails/public/500.html +0 -8
  315. data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
  316. data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
  317. data/lib/bio/shell/rails/public/dispatch.rb +0 -10
  318. data/lib/bio/shell/rails/public/favicon.ico +0 -0
  319. data/lib/bio/shell/rails/public/images/rails.png +0 -0
  320. data/lib/bio/shell/rails/public/index.html +0 -277
  321. data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
  322. data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
  323. data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
  324. data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
  325. data/lib/bio/shell/rails/public/robots.txt +0 -1
  326. data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
  327. data/lib/bio/shell/rails/script/about +0 -3
  328. data/lib/bio/shell/rails/script/breakpointer +0 -3
  329. data/lib/bio/shell/rails/script/console +0 -3
  330. data/lib/bio/shell/rails/script/destroy +0 -3
  331. data/lib/bio/shell/rails/script/generate +0 -3
  332. data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
  333. data/lib/bio/shell/rails/script/performance/profiler +0 -3
  334. data/lib/bio/shell/rails/script/plugin +0 -3
  335. data/lib/bio/shell/rails/script/process/reaper +0 -3
  336. data/lib/bio/shell/rails/script/process/spawner +0 -3
  337. data/lib/bio/shell/rails/script/process/spinner +0 -3
  338. data/lib/bio/shell/rails/script/runner +0 -3
  339. data/lib/bio/shell/rails/script/server +0 -42
  340. data/lib/bio/shell/rails/test/test_helper.rb +0 -28
@@ -1,6 +1,6 @@
1
1
  =begin
2
2
 
3
- $Id: KEGG_API.rd.ja,v 1.8 2006/02/23 04:51:23 k Exp $
3
+ $Id: KEGG_API.rd.ja,v 1.11 2006/12/27 13:40:45 k Exp $
4
4
 
5
5
  Copyright (C) 2003-2006 Toshiaki Katayama <k@bioruby.org>
6
6
 
@@ -19,6 +19,7 @@ KEGG API
19
19
  * ((<KEGG API �λȤ���>))
20
20
  * ((<Ruby �ξ��>))
21
21
  * ((<Perl �ξ��>))
22
+ * ((<Perl ��������>))
22
23
  * ((<Python �ξ��>))
23
24
  * ((<Java �ξ��>))
24
25
  * ((<KEGG API ��ե����>))
@@ -30,76 +31,96 @@ KEGG API
30
31
  * ((<Definition ��>)), ((<ArrayOfDefinition ��>))
31
32
  * ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
32
33
  * ((<PathwayElement ��>)), ((<ArrayOfPathwayElement ��>))
34
+ * ((<PathwayElementRelation ��>)), ((<ArrayOfPathwayElementRelation ��>))
35
+ * ((<Subtype ��>)), ((<ArrayOfSubtype ��>))
36
+ * ((<StructureAlignment ��>)), ((<ArrayOfStructureAlignment ��>))
33
37
  * ((<�᥽�åɰ���>))
34
38
  * ((<�᥿����>))
35
- * ((<list_databases>)),
36
- ((<list_organisms>)),
37
- ((<list_pathways>))
39
+ * ((<list_databases>))
40
+ * ((<list_organisms>))
41
+ * ((<list_pathways>))
38
42
  * ((<DBGET>))
39
- * ((<binfo>)),
40
- ((<bfind>)),
41
- ((<bget>)),
42
- ((<btit>)),
43
- ((<bconv>))
43
+ * ((<binfo>))
44
+ * ((<bfind>))
45
+ * ((<bget>))
46
+ * ((<btit>))
47
+ * ((<bconv>))
44
48
  * ((<LinkDB>))
45
- * ((<get_linkdb_by_entry>))
46
- * ((<get_genes_by_enzyme>)),
47
- ((<get_enzymes_by_gene>))
48
- * ((<get_enzymes_by_compound>)),
49
- ((<get_enzymes_by_glycan>)),
50
- ((<get_enzymes_by_reaction>)),
51
- ((<get_compounds_by_enzyme>)),
52
- ((<get_compounds_by_reaction>)),
53
- ((<get_glycans_by_enzyme>)),
54
- ((<get_glycans_by_reaction>)),
55
- ((<get_reactions_by_enzyme>)),
56
- ((<get_reactions_by_compound>)),
57
- ((<get_reactions_by_glycan>))
49
+ * ((<�ǡ����١����֤Υ��>))
50
+ * ((<get_linkdb_by_entry>))
51
+ * ((<get_linkdb_between_databases>))
52
+ * ((<�����Ҥȹ����ֹ�δط�>))
53
+ * ((<get_genes_by_enzyme>))
54
+ * ((<get_enzymes_by_gene>))
55
+ * ((<���ǡ�����ʪ���ꥢ�������δط�>))
56
+ * ((<get_enzymes_by_compound>))
57
+ * ((<get_enzymes_by_glycan>))
58
+ * ((<get_enzymes_by_reaction>))
59
+ * ((<get_compounds_by_enzyme>))
60
+ * ((<get_compounds_by_reaction>))
61
+ * ((<get_glycans_by_enzyme>))
62
+ * ((<get_glycans_by_reaction>))
63
+ * ((<get_reactions_by_enzyme>))
64
+ * ((<get_reactions_by_compound>))
65
+ * ((<get_reactions_by_glycan>))
58
66
  * ((<SSDB>))
59
- * ((<get_best_best_neighbors_by_gene>)),
60
- ((<get_best_neighbors_by_gene>)),
61
- ((<get_reverse_best_neighbors_by_gene>)),
62
- ((<get_paralogs_by_gene>))
63
- # * ((<get_neighbors_by_gene>)),
64
- # ((<get_similarity_between_genes>))
67
+ * ((<get_best_best_neighbors_by_gene>))
68
+ * ((<get_best_neighbors_by_gene>))
69
+ * ((<get_reverse_best_neighbors_by_gene>))
70
+ * ((<get_paralogs_by_gene>))
65
71
  * ((<Motif>))
66
- * ((<get_motifs_by_gene>)),
67
- ((<get_genes_by_motifs>))
68
- * ((<KO, OC, PC>))
69
- * ((<get_ko_by_gene>)),
70
- ((<get_ko_by_ko_class>)),
71
- ((<get_genes_by_ko_class>)),
72
- ((<get_genes_by_ko>)),
73
- ((<get_oc_members_by_gene>)),
74
- ((<get_pc_members_by_gene>))
75
- # ((<get_ko_members>)),
72
+ * ((<get_motifs_by_gene>))
73
+ * ((<get_genes_by_motifs>))
74
+ * ((<KO>))
75
+ * ((<get_ko_by_gene>))
76
+ * ((<get_ko_by_ko_class>))
77
+ * ((<get_genes_by_ko_class>))
78
+ * ((<get_genes_by_ko>))
76
79
  * ((<PATHWAY>))
77
- * ((<mark_pathway_by_objects>)),
78
- ((<color_pathway_by_objects>)),
79
- ((<color_pathway_by_elements>)),
80
- ((<get_html_of_marked_pathway_by_objects>)),
81
- ((<get_html_of_colored_pathway_by_objects>)),
82
- ((<get_html_of_colored_pathway_by_elements>))
83
- * ((<get_elements_by_pathway>)),
84
- ((<get_genes_by_pathway>)),
85
- ((<get_enzymes_by_pathway>)),
86
- ((<get_compounds_by_pathway>)),
87
- ((<get_glycans_by_pathway>)),
88
- ((<get_reactions_by_pathway>)),
89
- ((<get_kos_by_pathway>))
90
- * ((<get_pathways_by_genes>)),
91
- ((<get_pathways_by_enzymes>)),
92
- ((<get_pathways_by_compounds>)),
93
- ((<get_pathways_by_glycans>)),
94
- ((<get_pathways_by_reactions>)),
95
- ((<get_pathways_by_kos>))
96
- * ((<get_linked_pathways>))
80
+ * ((<�ѥ��������ؤο��Ť�>))
81
+ * ((<mark_pathway_by_objects>))
82
+ * ((<color_pathway_by_objects>))
83
+ * ((<color_pathway_by_elements>))
84
+ * ((<get_html_of_marked_pathway_by_objects>))
85
+ * ((<get_html_of_colored_pathway_by_objects>))
86
+ * ((<get_html_of_colored_pathway_by_elements>))
87
+ * ((<�ѥ���������Υ��֥������ȴ֤δط�>))
88
+ * ((<get_element_relations_by_pathway>))
89
+ * ((<�ѥ���������Υ��֥������ȸ���>))
90
+ * ((<get_elements_by_pathway>))
91
+ * ((<get_genes_by_pathway>))
92
+ * ((<get_enzymes_by_pathway>))
93
+ * ((<get_compounds_by_pathway>))
94
+ * ((<get_glycans_by_pathway>))
95
+ * ((<get_reactions_by_pathway>))
96
+ * ((<get_kos_by_pathway>))
97
+ * ((<���֥������Ȥ���ѥ�����������>))
98
+ * ((<get_pathways_by_genes>))
99
+ * ((<get_pathways_by_enzymes>))
100
+ * ((<get_pathways_by_compounds>))
101
+ * ((<get_pathways_by_glycans>))
102
+ * ((<get_pathways_by_reactions>))
103
+ * ((<get_pathways_by_kos>))
104
+ * ((<�ѥ��������֤δط�>))
105
+ * ((<get_linked_pathways>))
97
106
  * ((<GENES>))
98
107
  * ((<get_genes_by_organism>))
99
108
  * ((<GENOME>))
100
109
  * ((<get_number_of_genes_by_organism>))
101
110
  * ((<LIGAND>))
102
111
  * ((<convert_mol_to_kcf>))
112
+ * ((<search_compounds_by_name>))
113
+ * ((<search_drugs_by_name>))
114
+ * ((<search_glycans_by_name>))
115
+ * ((<search_compounds_by_composition>))
116
+ * ((<search_drugs_by_composition>))
117
+ * ((<search_glycans_by_composition>))
118
+ * ((<search_compounds_by_mass>))
119
+ * ((<search_drugs_by_mass>))
120
+ * ((<search_glycans_by_mass>))
121
+ * ((<search_compounds_by_subcomp>))
122
+ * ((<search_drugs_by_subcomp>))
123
+ * ((<search_glycans_by_kcam>))
103
124
 
104
125
  == ����ȥ����������
105
126
 
@@ -162,13 +183,13 @@ XML
162
183
  require 'soap/wsdlDriver'
163
184
 
164
185
  wsdl = "http://soap.genome.jp/KEGG.wsdl"
165
- serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
186
+ serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
166
187
  serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
167
188
 
168
- start = 1
169
- max_results = 5
189
+ offset = 1
190
+ limit = 5
170
191
 
171
- top5 = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
192
+ top5 = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
172
193
  top5.each do |hit|
173
194
  print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
174
195
  end
@@ -185,7 +206,7 @@ XML
185
206
 
186
207
  ���ޤ�ư���ʤ����ϡ�
187
208
 
188
- serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
209
+ serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
189
210
  serv.wiredump_dev = STDERR # �����ιԤ��­��
190
211
  serv.generate_explicit_type = true
191
212
 
@@ -193,28 +214,30 @@ XML
193
214
  �����ФȤΤ���꤬ɸ�२�顼�˽��Ϥ���ޤ���
194
215
 
195
216
  KEGG API v3.0 ���顢�����Ф���ô��ڤ������꥿���ॢ���Ȥ��ɤ���Ū�ǡ�
196
- ���̤η�̤��֤��᥽�åɤˤ� start, max_results ������Ƴ�����졢���٤�
197
- �������̤ο������¤����褦�ˤʤ�ޤ��������Τ��ᡢ�����Υ᥽��
198
- �ɤ����Ƥη�̤����뤿��ˤϥ롼�פ��Ѥ���ɬ�פ�����ޤ���
217
+ ���̤η�̤��֤��᥽�åɤˤ� offset, limit ������Ƴ�����졢���٤�
218
+ �������̤ο������¤����褦�ˤʤ�ޤ�����KEGG API v3.0��v5.0 �Ǥ�
219
+ ���줾�� start, max_results �ȸƤФ�Ƥ��ޤ�������KEGG API v6.0 ��
220
+ offset, limit ��̾���ѹ����ޤ����ˡ����Τ��ᡢ�����Υ᥽�åɤ�
221
+ ���Ƥη�̤����뤿��ˤϥ롼�פ��Ѥ���ɬ�פ�����ޤ���
199
222
 
200
223
  #!/usr/bin/env ruby
201
224
 
202
225
  require 'soap/wsdlDriver'
203
226
 
204
227
  wsdl = "http://soap.genome.jp/KEGG.wsdl"
205
- serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
228
+ serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
206
229
  serv.generate_explicit_type = true
207
230
 
208
- start = 1
209
- max_results = 100
231
+ offset = 1
232
+ limit = 100
210
233
 
211
234
  loop do
212
- results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
235
+ results = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
213
236
  break unless results # ��̤��֤äƤ��ʤ���н�λ
214
237
  results.each do |hit|
215
238
  print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
216
239
  end
217
- start += max_results
240
+ offset += limit
218
241
  end
219
242
 
220
243
  WSDL ���Ѥ��Ƥ��뤿�ᡢ��������Ǥ� Ruby �ξ��Ͻ�ʬ�˴�ñ�˽񤱤�
@@ -299,7 +322,8 @@ sw_score
299
322
 
300
323
  Perl �Ǥϡ��ʲ��Υ饤�֥����ɲå��󥹥ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
301
324
 
302
- * ((<SOAP::Lite|URL://soaplite.com/>))
325
+ * ((<SOAP::Lite|URL://www.soaplite.com/>)) (Ver. 0.60 ��ư���ǧ)
326
+ * �������� 0.60 ��꿷�����С������ǤϤ����Ĥ��Υ᥽�åɤ��Ȥ��ʤ��褦�Ǥ�
303
327
  * ((<MIME-Base64|URL:http://search.cpan.org/author/GAAS/MIME-Base64/>))
304
328
  * ((<libwww-perl|URL:http://search.cpan.org/author/GAAS/libwww-perl/>))
305
329
  * ((<URI|URL:http://search.cpan.org/author/GAAS/URI/>))
@@ -314,10 +338,10 @@ Perl
314
338
 
315
339
  $serv = SOAP::Lite -> service($wsdl);
316
340
 
317
- $start = 1;
318
- $max_results = 5;
341
+ $offset = 1;
342
+ $limit = 5;
319
343
 
320
- $top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $start, $max_results);
344
+ $top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $offset, $limit);
321
345
 
322
346
  foreach $hit (@{$top5}) {
323
347
  print "$hit->{genes_id1}\t$hit->{genes_id2}\t$hit->{sw_score}\n";
@@ -362,6 +386,74 @@ SOAP::Lite
362
386
 
363
387
  �Τ褦�ˤʤ�ޤ���
364
388
 
389
+ === Perl ��������
390
+
391
+ KEGG API �ˤ�ʸ�������ͤ����������˼��᥽�åɤ������Ĥ�����ޤ�����
392
+ ���Ѥ��� SOAP::Lite �ΥС������˱����ơ�ɬ���ʲ��Τɤ��餫���н褬ɬ�פǤ���
393
+
394
+ ==== SOAP::Lite v0.60 �ޤ�
395
+
396
+ Perl ������ (array) ���֥������Ȥ�����Ȥ��� KEGG API ���Ϥ����ϡ�
397
+ ɬ���ʲ��Τ褦�� SOAP ���֥������Ȥ�����Ū���Ѵ�����ɬ�פ�����ޤ���
398
+
399
+ SOAP::Data->type(array => [value1, value2, ... ])
400
+
401
+ ==== SOAP::Lite v0.61 �ʹ�
402
+
403
+ SOAP::Lite v0.68 �ޤǤϥХ�������ޤ��Τ� v0.69 �ʹߤ����Ѥ򤪴��ᤷ�ޤ���
404
+
405
+ Perl ��ʸ���� (string) ����� (int) ������ (array) ���֥������Ȥ�
406
+ ArrayOfstring �� ArrayOfint ���� SOAP ���֥������Ȥ��Ѵ�����
407
+ ���֥롼����������ɲä���ɬ�פ�����ޤ���
408
+
409
+ sub SOAP::Serializer::as_ArrayOfstring{
410
+ my ($self, $value, $name, $type, $attr) = @_;
411
+
412
+ return [$name, {'xsi:type' => 'array', %$attr}, $value];
413
+ }
414
+
415
+ sub SOAP::Serializer::as_ArrayOfint{
416
+ my ($self, $value, $name, $type, $attr) = @_;
417
+ return [$name, {'xsi:type' => 'array', %$attr}, $value];
418
+ }
419
+
420
+ �ޤ���������ץ���ˤ��������񤤤Ƥ������Ȥǡ�
421
+
422
+ $genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]);
423
+
424
+ �ǤϤʤ�
425
+
426
+ $genes = ["eco:b1002", "eco:b2388"];
427
+
428
+ �Τ褦�˾�ά���ƽ񤯤��Ȥ��Ǥ���褦�ˤʤ�ޤ��ʾ�ά���ʤ��Ƥ⹽���ޤ���ˡ�
429
+
430
+ ==== �ƥ��ȥץ������
431
+
432
+ SOAP::Lite v0.69 �� ArrayOfstring ���Ѵ������ޤ�Ư���Ƥ��뤫�ɤ�����
433
+ �ʲ��Υץ������ǥƥ��ȤǤ��ޤ��������� URL ��ɽ�������� OK �Ǥ���
434
+
435
+ #!/usr/bin/env perl
436
+
437
+ use SOAP::Lite +trace => [qw(debug)];
438
+
439
+ print "SOAP::Lite = ", $SOAP::Lite::VERSION, "\n";
440
+
441
+ my $serv = SOAP::Lite -> service("http://soap.genome.jp/KEGG.wsdl");
442
+
443
+ my $result = $serv->mark_pathway_by_objects("map:eco00010", $genes);
444
+ print $result, "\n";
445
+
446
+ # sub routines implicitly used in the above code
447
+
448
+ sub SOAP::Serializer::as_ArrayOfstring{
449
+ my ($self, $value, $name, $type, $attr) = @_;
450
+ return [$name, {'xsi:type' => 'array', %$attr}, $value];
451
+ }
452
+
453
+ sub SOAP::Serializer::as_ArrayOfint{
454
+ my ($self, $value, $name, $type, $attr) = @_;
455
+ return [$name, {'xsi:type' => 'array', %$attr}, $value];
456
+ }
365
457
 
366
458
  === Python �ξ��
367
459
 
@@ -385,7 +477,6 @@ Python
385
477
  results = serv.get_genes_by_pathway('path:eco00020')
386
478
  print results
387
479
 
388
-
389
480
  === Java �ξ��
390
481
 
391
482
  Java �Ǥ� Apache Axis �饤�֥��� axis-1.2alpha ��꿷�����С������
@@ -485,7 +576,6 @@ tcsh
485
576
 
486
577
  * ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/>))
487
578
 
488
-
489
579
  == KEGG API ��ե����
490
580
 
491
581
  �ʲ��Ǥϡ�KEGG API ��Ȥ��Τ�ɬ�פʾ�������ƤΥ᥽�åɤ���⤷�ޤ���
@@ -517,7 +607,7 @@ URL
517
607
  * entry_id �� db_name �ȥ���ȥ�̾�� ':' �Ƿ�礷�����ƤΥǡ����١����֤�
518
608
  ��ˡ����� ID �Ǥ������Ȥ��� embl:J00231 �� EMBL �Υ���ȥ� J00231 ��
519
609
  �ؤ��ޤ���entry_id �ϡ��ʲ��� genes_id, enzyme_id, compound_id,
520
- glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
610
+ drug_id, glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
521
611
 
522
612
  * genes_id �� keggorg �Ȱ�����̾�� ':' �Ƿ�礷�� KEGG �ΰ����� ID �Ǥ���
523
613
  eco:b0001 ����IJ�ݤΰ����� b0001 ��ؤ��ޤ���
@@ -528,6 +618,9 @@ URL
528
618
  * compound_id �� cpd: ��Ĥ�������ʪ�� ID �Ǥ���cpd:C00158 �ϲ���ʪ�ֹ�
529
619
  C00158 �β���ʪ�Ǥ��륯�������ؤ��ޤ���
530
620
 
621
+ * drug_id �� dr: ��Ĥ�������ʪ�� ID �Ǥ���dr:D00201 �ϥɥ�å��ֹ�
622
+ D00201 �Υɥ�å��Ǥ���ƥȥ饵��������ؤ��ޤ���
623
+
531
624
  * glycan_id �� gl: ��Ĥ�������ʪ�� ID �Ǥ���gl:G00050 �������ֹ�
532
625
  G00050 �������Ǥ��� Paragloboside ��ؤ��ޤ���
533
626
 
@@ -555,9 +648,9 @@ URL
555
648
 
556
649
  * ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
557
650
 
558
- * start, max_results �ϰ��٤��֤äƤ����̤ο�����ꤹ�륪�ץ����ǡ�
559
- start ���ܤ��� max_results �Ĥη�̤�������ޤ������Ƥη�̤�����ˤ�
560
- start = start + max_results �Ȥ��ƶ��������֤äƤ���ޤǷ����֤�
651
+ * offset, limit �ϰ��٤��֤äƤ����̤ο�����ꤹ�륪�ץ����ǡ�
652
+ offset ���ܤ��� limit �Ĥη�̤�������ޤ������Ƥη�̤�����ˤ�
653
+ offset = offset + limit �Ȥ��ƶ��������֤äƤ���ޤǷ����֤�
561
654
  �᥽�åɤ�ƤӤޤ���
562
655
 
563
656
  * fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ�ʸ����������
@@ -566,6 +659,9 @@ URL
566
659
  * fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ��طʤ�
567
660
  ������ꤹ������Ǥ���
568
661
 
662
+ ��Ϣ URL��
663
+ * ((<URL:http://www.genome.jp/kegg/kegg3.html>))
664
+
569
665
  === ����ͤΥǡ�����
570
666
 
571
667
  KEGG API �Υ᥽�åɤ�ʸ����ʤ�ñ����ͤ��֤���Τ����Ǥʤ���ʣ���ʥǡ���
@@ -640,6 +736,8 @@ SSDB
640
736
 
641
737
  + PathwayElement ��
642
738
 
739
+ �ѥ����������������Ƥ���ġ���Ȣ��ݤʤɤΥ��֥������Ȥ�ɽ���ǡ������Ǥ���
740
+
643
741
  element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
644
742
  type ���֥������Ȥμ��� ("gene", "enzyme" �ʤ�) (string)
645
743
  names ���֥������ȤˤĤ���줿̾���Υꥹ�� (ArrayOfstring)
@@ -649,6 +747,46 @@ SSDB
649
747
 
650
748
  ʣ���� PathwayElement ���ǡ�����ޤ�����Ǥ���
651
749
 
750
+ + PathwayElementRelation ��
751
+
752
+ PathwayElement �֤δط���ɽ���ǡ������Ǥ���
753
+
754
+ element_id1 �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
755
+ element_id2 �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
756
+ type �ط��μ��� ("ECrel", "maplink" �ʤ�) (string)
757
+ subtypes �ط��˴ؤ�륪�֥������Ȥ����� (ArrayOfSubtype)
758
+
759
+ + ArrayOfPathwayElementRelation ��
760
+
761
+ ʣ���� PathwayElementRelation ���ǡ�����ޤ�����Ǥ���
762
+
763
+ ++ Subtype ��
764
+
765
+ PathwayElementRelation ������ǻȤ�������Ǥǡ�PathwayElement �֤�
766
+ �ط��Ť��륪�֥������ȡʲ���ʪ�ʤɡˤ�ɽ���ǡ������Ǥ���
767
+
768
+ element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
769
+ relation �ط��μ��� ("compound", "inhibition" �ʤ�) (string)
770
+ type �ط��ε��� ("+p", "--|" �ʤ�) (string)
771
+
772
+ ++ ArrayOfSubtype ��
773
+
774
+ ʣ���� PathwayElementRelation ���ǡ�����ޤ�����Ǥ���
775
+
776
+ + StructureAlignment ��
777
+
778
+ �桼���λ��ꤷ�����ع�¤�ȥǡ����١�����ι�¤����Ӥ�������
779
+ ���饤����ȤΥ��������б�����Ρ��ɡʸ��ǡˤΥꥹ�Ȥ�ɽ��
780
+ �ǡ������Ǥ���
781
+
782
+ target_id ��¤����оݤΥ���ȥ� ID (string)
783
+ score ��¤��ӤΥ����� (float)
784
+ query_nodes ���Ϲ�¤��ǥ��饤����Ȥ��줿�Ρ����ֹ� (ArrayOfint)
785
+ target_nodes �оݹ�¤����б�����Ρ����ֹ� (ArrayOfint)
786
+
787
+ + ArrayOfStructureAlignment ��
788
+
789
+ ʣ���� StructureAlignment ���ǡ�����ޤ�����Ǥ���
652
790
 
653
791
  === �᥽�åɰ���
654
792
 
@@ -660,7 +798,6 @@ KEGG API
660
798
  �ʲ�����Ǥϡ������ʤɤ� Ruby �����ɽ������äƽ񤫤�Ƥ��ޤ������ºݤ�
661
799
  �������ä˥ꥹ�Ȥ��Ϥ����ʤɡˤϻ��Ѥ������ˤ�äưۤʤ��ǽ��������ޤ���
662
800
 
663
-
664
801
  ==== �᥿����
665
802
 
666
803
  �ǿ��Υǡ����١�������ʤɤ��֤�����Υ᥽�åɤǤ���
@@ -672,6 +809,10 @@ KEGG
672
809
  ���͡�
673
810
  ArrayOfDefinition (db, definition)
674
811
 
812
+ ��Ϣ URL��
813
+ * ((<URL:http://www.genome.jp/dbget/>))
814
+ * ((<URL:http://www.genome.jp/about_genomenet/service.html>)) (section 2.2)
815
+
675
816
  --- list_organisms
676
817
 
677
818
  ���� KEGG �˴ޤޤ�Ƥ�����ʪ�� (org) �Υꥹ�Ȥ��֤��ޤ���
@@ -679,7 +820,11 @@ KEGG
679
820
  ���͡�
680
821
  ArrayOfDefinition (org, definition)
681
822
 
682
- --- list_pathways(org)
823
+ ��Ϣ URL��
824
+ * ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
825
+ * ((<URL:http://www.genome.jp/dbget-bin/get_htext?Organisms+-n>))
826
+
827
+ --- list_pathways(string:org)
683
828
 
684
829
  ���� KEGG �˴ޤޤ�Ƥ�����ꤷ����ʪ�Υѥ��������Υꥹ�Ȥ��֤��ޤ���������
685
830
  'map' �Ȥ���ʸ�����Ϳ����ȥ�ե���󥹥ѥ��������Υꥹ�Ȥ��֤��ޤ���
@@ -687,15 +832,19 @@ KEGG
687
832
  ���͡�
688
833
  ArrayOfDefinition (pathway_id, definition)
689
834
 
835
+ ��Ϣ URL��
836
+ * ((<URL:http://www.genome.jp/kegg/pathway.html>))
690
837
 
691
838
  ==== DBGET
692
839
 
693
840
  DBGET �����ƥ���Ф���᥽�åɤΰ����Ǥ���DBGET �ˤĤ��ƾܤ����ϰʲ���
694
841
  �ڡ����򻲾Ȥ��Ƥ���������
695
842
 
843
+ ��Ϣ URL��
696
844
  * ((<URL:http://www.genome.jp/dbget/dbget_manual.html>))
845
+ * ((<URL:http://www.genome.jp/dbget-bin/binfo>))
697
846
 
698
- --- binfo(string)
847
+ --- binfo(string:db)
699
848
 
700
849
  ���ꤷ���ǡ����١����Υ���ȥ���乹�����ʤɾܤ����ǿ�������֤��ޤ���
701
850
  'all' ���Ϥ������Ѳ�ǽ�����ƤΥǡ����١����ξ�����֤��ޤ���
@@ -710,7 +859,7 @@ binfo
710
859
  # ���ƤΥǡ����١����κǿ�����
711
860
  binfo('all')
712
861
 
713
- --- bfind(string)
862
+ --- bfind(string:str)
714
863
 
715
864
  DBGET �� bfind ���ޥ�ɤؤΥ�åѡ��Ǥ���������ɤˤ�ꥨ��ȥ��
716
865
  �������뤳�Ȥ��Ǥ��ޤ������٤�Ϳ�����륭����ɤο��� 100 �İʲ���
@@ -724,7 +873,7 @@ DBGET
724
873
  bfind("gb E-cadherin human")
725
874
 
726
875
 
727
- --- bget(string)
876
+ --- bget(string:str)
728
877
 
729
878
  ���ꤷ�� entry_id �Υ���ȥ���֤��ޤ���GENES �ΰ����ҥ���ȥ��Ϥ��ᡢ
730
879
  ���Υ�ͥåȤ� DBGET �����ƥ���󶡤���Ƥ����͡��ʥǡ����١���
@@ -743,7 +892,7 @@ DBGET
743
892
  # FASTA �ե����ޥåȤα�����������
744
893
  bget("-f -n n eco:b0002 hin:tRNA-Cys-1")
745
894
 
746
- --- btit(string)
895
+ --- btit(string:str)
747
896
 
748
897
  DBGET �� btit ���ޥ�ɤؤΥ�åѡ��Ǥ������ꤷ������ȥ�� ID ���б���
749
898
  ��ǥե��˥������֤��ޤ������٤�Ϳ�����륨��ȥ�ο��� 100 �İʲ���
@@ -756,11 +905,25 @@ DBGET
756
905
  # ����飴�Ĥΰ����ҤΥǥե��˥����򸡺�
757
906
  btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
758
907
 
759
- --- bconv(string)
908
+ --- bconv(string:str)
760
909
 
761
- �����ǡ����١����� ID �� KEGG �� ID ���Ѵ����ޤ����б����Ƥ��볰���ǡ���
762
- �١����� NCBI Gene ID, NCBI GI, GenBank ID, UniProt ID �Ǥ���
910
+ �����ǡ����١����� ID �� KEGG �� ID ���Ѵ����ޤ���
763
911
  ��̤ϡ���������䤤��碌 ID ���Ѵ� ID �Υ����ڤ�ʸ����Ȥ����֤���ޤ���
912
+ ���ߡ��ʲ��γ����ǡ����١������б����Ƥ��ޤ���
913
+
914
+ �����ǡ����١��� �ǡ����١���̾�� prefix
915
+ ---------------- -----------------------
916
+ NCBI GI ncbi-gi:
917
+ NCBI GeneID ncbi-geneid:
918
+ GenBank genbank:
919
+ UniGene unigene:
920
+ UniProt uniprot:
921
+ OMIM omim:
922
+
923
+ ���Ȥ��� UniProt ID �ϡ����Ǥ� KEGG GENES �˵��ܤ���Ƥ��� UniProt
924
+ �ؤΥ�󥯤�¾��EBI �� Genome Reviews �˵��ܤ���Ƥ��� UniProt ID
925
+ �ȥ����������� ID ���б����Ѥ��ơ�NCBI �ȶ��̤Υ����������� ID ��
926
+ KEGG GENES ���б�ɽ���Ȥ��Ѵ�����Ƥ��ޤ���
764
927
 
765
928
  ���͡�
766
929
  string
@@ -769,9 +932,14 @@ DBGET
769
932
  # NCBI GI �� Gene ID �� KEGG genes_id ���Ѵ�
770
933
  serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
771
934
 
935
+ ��Ϣ URL��
936
+ * ((<URL:http://www.genome.jp/kegg/genes.html>)) (Gene name conversion)
937
+
772
938
  ==== LinkDB
773
939
 
774
- --- get_linkdb_by_entry(entry_id, db, start, max_results)
940
+ + �ǡ����١����֤Υ��
941
+
942
+ --- get_linkdb_by_entry(string:entry_id, string:db, int:offset, int:limit)
775
943
 
776
944
  ���ꤷ�� entry_id ����ľ�ܤޤ��ϴ���Ū�˥�󥯤���Ƥ��륨��ȥ�η�ϩ��
777
945
  db �ǻ��ꤷ���ǡ����١����ˤ��ɤ��ޤǸ������ޤ���
@@ -784,9 +952,35 @@ db
784
952
  get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
785
953
  get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
786
954
 
955
+ ��Ϣ URL��
956
+ * ((<URL:http://www.genome.jp/dbget-bin/www_linkdb>)) (Single entry to database)
957
+
958
+ --- get_linkdb_between_databases(string:from_db, string:to_db, int:offset, int:limit)
959
+
960
+ ���ꤷ�����ĤΥǡ����١����ǡ�����ȥ�֤Υ�󥯤����Ƹ������ޤ���
961
+
962
+ ���͡�
963
+ ArrayOfLinkDBRelation
964
+
965
+ �㡧
966
+ # ��IJ�ݤ� KEGG GENES �� KEGG PATHWAY �δ֤Υ�󥯤����Ƹ���
967
+ get_linkdb_between_databases("eco", "pathway", 1, 100)
968
+
969
+ # Ruby �Ǽ���������󥯤����ɽ��������
970
+ links = get_linkdb_between_databases("eco", "pathway", 1, 100)
971
+ links.each do |link|
972
+ puts link.entry_id1 # => "eco:b0084"
973
+ puts link.entry_id2 # => "path:map00550"
974
+ puts link.type # => "indirect"
975
+ puts link.path # => "eco->ec->path"
976
+ end
977
+
978
+ ��Ϣ URL��
979
+ * ((<URL:http://www.genome.jp/dbget-bin/www_linkdb>)) (Database to database)
980
+
787
981
  + �����Ҥȹ����ֹ�δط�
788
982
 
789
- --- get_genes_by_enzyme(enzyme_id, org)
983
+ --- get_genes_by_enzyme(string:enzyme_id, string:org)
790
984
 
791
985
  �о���ʪ��ˤ����ơ����ꤷ�������ֹ����İ����ҤΥꥹ�Ȥ��֤��ޤ���
792
986
 
@@ -797,7 +991,7 @@ db
797
991
  # �����ֹ� 1.1.1.1 �������IJ�ݤΰ����ҤΥꥹ��
798
992
  get_genes_by_enzyme('ec:1.1.1.1', 'eco')
799
993
 
800
- --- get_enzymes_by_gene(genes_id)
994
+ --- get_enzymes_by_gene(string:genes_id)
801
995
 
802
996
  ���ꤷ�������Ҥ��б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
803
997
 
@@ -808,10 +1002,9 @@ db
808
1002
  # ��IJ�ݰ����� 'eco:b0002' �ι����ֹ�Υꥹ��
809
1003
  get_enzymes_by_gene(eco:b0002)
810
1004
 
811
-
812
1005
  + ���ǡ�����ʪ���ꥢ�������δط�
813
1006
 
814
- --- get_enzymes_by_compound(compound_id)
1007
+ --- get_enzymes_by_compound(string:compound_id)
815
1008
 
816
1009
  ���ꤷ������ʪ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
817
1010
 
@@ -822,7 +1015,7 @@ db
822
1015
  # ����ʪ 'cpd:C00345' ����դ˴ؤ����ǤΥꥹ��
823
1016
  get_enzymes_by_compound('cpd:C00345')
824
1017
 
825
- --- get_enzymes_by_glycan(compound_id)
1018
+ --- get_enzymes_by_glycan(string:compound_id)
826
1019
 
827
1020
  ���ꤷ���������б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
828
1021
 
@@ -833,7 +1026,7 @@ db
833
1026
  # ���� 'gl:G00001' ����դ˴ؤ����ǤΥꥹ��
834
1027
  get_enzymes_by_glycan('gl:G00001')
835
1028
 
836
- --- get_enzymes_by_reaction(reaction_id)
1029
+ --- get_enzymes_by_reaction(string:reaction_id)
837
1030
 
838
1031
  ���ꤷ���ꥢ��������ֹ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
839
1032
 
@@ -844,7 +1037,7 @@ db
844
1037
  # �ꥢ��������ֹ� R00100 ����Ĺ��ǤΥꥹ��
845
1038
  get_enzymes_by_reaction('rn:R00100')
846
1039
 
847
- --- get_compounds_by_enzyme(enzyme_id)
1040
+ --- get_compounds_by_enzyme(string:enzyme_id)
848
1041
 
849
1042
  ���ꤷ�������ֹ���б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
850
1043
 
@@ -855,7 +1048,7 @@ db
855
1048
  # �����ֹ� 'ec:2.7.1.12' ����դ˴ؤ�벽��ʪ�Υꥹ��
856
1049
  get_compounds_by_enzyme('ec:2.7.1.12')
857
1050
 
858
- --- get_compounds_by_reaction(reaction_id)
1051
+ --- get_compounds_by_reaction(string:reaction_id)
859
1052
 
860
1053
  ���ꤷ���ꥢ���������б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
861
1054
 
@@ -866,7 +1059,7 @@ db
866
1059
  # �ꥢ��������ֹ� 'rn:R00100' ��ȿ���˴ؤ�벽��ʪ�Υꥹ��
867
1060
  get_compounds_by_reaction('rn:R00100')
868
1061
 
869
- --- get_glycans_by_enzyme(enzyme_id)
1062
+ --- get_glycans_by_enzyme(string:enzyme_id)
870
1063
 
871
1064
  ���ꤷ�������ֹ���б����������Υꥹ�Ȥ��֤��ޤ���
872
1065
 
@@ -877,7 +1070,7 @@ db
877
1070
  # �����ֹ� 'ec:2.4.1.141' ����դ˴ؤ�������Υꥹ��
878
1071
  get_glycans_by_enzyme('ec:2.4.1.141')
879
1072
 
880
- --- get_glycans_by_reaction(reaction_id)
1073
+ --- get_glycans_by_reaction(string:reaction_id)
881
1074
 
882
1075
  ���ꤷ���ꥢ���������б����������Υꥹ�Ȥ��֤��ޤ���
883
1076
 
@@ -888,7 +1081,7 @@ db
888
1081
  # �ꥢ��������ֹ� 'rn:R06164' ��ȿ���˴ؤ�������Υꥹ��
889
1082
  get_glycans_by_reaction('rn:R06164')
890
1083
 
891
- --- get_reactions_by_enzyme(enzyme_id)
1084
+ --- get_reactions_by_enzyme(string:enzyme_id)
892
1085
 
893
1086
  ���ꤷ�������ֹ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
894
1087
 
@@ -899,7 +1092,7 @@ db
899
1092
  # �����ֹ� 'ec:2.7.1.12' ��ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
900
1093
  get_reactions_by_enzyme('ec:2.7.1.12')
901
1094
 
902
- --- get_reactions_by_compound(compound_id)
1095
+ --- get_reactions_by_compound(string:compound_id)
903
1096
 
904
1097
  ���ꤷ������ʪ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
905
1098
 
@@ -910,7 +1103,7 @@ db
910
1103
  # ����ʪ 'cpd:C00199' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
911
1104
  get_reactions_by_compound('cpd:C00199')
912
1105
 
913
- --- get_reactions_by_glycan(glycan_id)
1106
+ --- get_reactions_by_glycan(string:glycan_id)
914
1107
 
915
1108
  ���ꤷ���������б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
916
1109
 
@@ -921,7 +1114,6 @@ db
921
1114
  # ���� 'gl:G00001' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
922
1115
  get_reactions_by_glycan('gl:G00001')
923
1116
 
924
-
925
1117
  ==== SSDB
926
1118
 
927
1119
  SSDB �ǡ����١������Ф���᥽�åɤΰ����Ǥ���SSDB �� KEGG/GENES �˴ޤޤ��
@@ -937,22 +1129,8 @@ SSDB
937
1129
 
938
1130
  * ((<URL:http://www.genome.jp/kegg/ssdb/>))
939
1131
 
940
- #--- get_neighbors_by_gene(genes_id, org, start, max_results)
941
- #
942
- #���ꤷ�� genes_id �ΰ����Ҥ˥ۥ�������Τ����������Ҥ���ꤷ����ʪ����
943
- #�������ޤ����ޤ� org �� 'all' ����ꤹ�������ʪ�狼�鸡�����ޤ���
944
- #
945
- #���͡�
946
- # ArrayOfSSDBRelation
947
- #
948
- #�㡧
949
- # # ��IJ�ݤΰ����� b0002 ����Ʊ���Τ�������Ҥ����Ƹ������ơ���̤Σ���
950
- # # ���飱�����ܤޤǤ��֤��ޤ�
951
- # get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
952
- # # ���Σ����Ĥ� start = start + max_results �Ȥ��Ƽ��ޤ�
953
- # get_neighbors_by_gene('eco:b0002', 'all' 11, 10)
954
1132
 
955
- --- get_best_best_neighbors_by_gene(genes_id, start, max_results)
1133
+ --- get_best_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
956
1134
 
957
1135
  ������ȥ������åȤ� best-best �δط��ˤ�������Ҥ����򸡺����ޤ���
958
1136
 
@@ -964,7 +1142,7 @@ SSDB
964
1142
  get_best_best_neighbors_by_gene('eco:b0002', 1, 10)
965
1143
  get_best_best_neighbors_by_gene('eco:b0002', 11, 10)
966
1144
 
967
- --- get_best_neighbors_by_gene(genes_id, start, max_results)
1145
+ --- get_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
968
1146
 
969
1147
  �����꤫�鸫�ƥ٥��ȥҥåȤδط��ˤ�������Ҥ����򸡺����ޤ���
970
1148
 
@@ -976,7 +1154,7 @@ SSDB
976
1154
  get_best_neighbors_by_gene('eco:b0002', 1, 10)
977
1155
  get_best_neighbors_by_gene('eco:b0002', 11, 10)
978
1156
 
979
- --- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
1157
+ --- get_reverse_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
980
1158
 
981
1159
  �������å�¦����ʪ�狼�鸫�ƥ����꤬�٥��ȥҥåȤȤʤ�����Ҥ򸡺����ޤ���
982
1160
 
@@ -988,7 +1166,7 @@ SSDB
988
1166
  get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10)
989
1167
  get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10)
990
1168
 
991
- --- get_paralogs_by_gene(genes_id, start, max_results)
1169
+ --- get_paralogs_by_gene(string:genes_id, int:offset, int:limit)
992
1170
 
993
1171
  �������Ʊ����ʪ����ǥѥ���������Ҥ򸡺����ޤ���
994
1172
 
@@ -1000,21 +1178,10 @@ SSDB
1000
1178
  get_paralogs_by_gene('eco:b0002', 1, 10)
1001
1179
  get_paralogs_by_gene('eco:b0002', 11, 10)
1002
1180
 
1003
- #--- get_similarity_between_genes(genes_id1, genes_id2)
1004
- #
1005
- #���ꤷ�����Ĥΰ����Ҵ֤� Smith-Waterman ��������ޤ�ǡ������֤��ޤ���
1006
- #
1007
- #���͡�
1008
- # SSDBRelation
1009
- #
1010
- #�㡧
1011
- # # ��IJ�ݤ� b0002 �����Ҥ� b3940 �����Ҵ֤Υ������䥢�饤�����ΰ������
1012
- # get_similarity_between_genes('eco:b0002', 'eco:b3940')
1013
-
1014
1181
 
1015
1182
  ==== Motif
1016
1183
 
1017
- --- get_motifs_by_gene(genes_id, db)
1184
+ --- get_motifs_by_gene(string:genes_id, string:db)
1018
1185
 
1019
1186
  ���ꤷ�������Ҥ�¸�ߤ��������դΥꥹ�Ȥ��֤��ޤ���������եǡ����١���
1020
1187
  �Υꥹ�Ȥˤϡ�Pfam (pfam), TIGRFAM (tfam), PROSITE pattern (pspt), PROSITE
@@ -1027,7 +1194,7 @@ profile (pspf)
1027
1194
  # ��IJ�ݤΰ����� b0002 ����Pfam������դΥꥹ��
1028
1195
  get_motifs_by_gene('eco:b0002', 'pfam')
1029
1196
 
1030
- --- get_genes_by_motifs(motif_id_list, start, max_results)
1197
+ --- get_genes_by_motifs([string]:motif_id_list, int:offset, int:limit)
1031
1198
 
1032
1199
  ���ꤷ��������դ����ƻ��İ����Ҥ򸡺����ޤ���
1033
1200
 
@@ -1040,14 +1207,13 @@ profile (pspf)
1040
1207
  get_genes_by_motifs(list, 1, 10)
1041
1208
  get_genes_by_motifs(list, 11, 10)
1042
1209
 
1043
-
1044
- ==== KO, OC, PC
1210
+ ==== KO
1045
1211
 
1046
1212
  KO (KEGG orthology), OC (KEGG ortholog cluster), PC (KEGG paralog cluster) ��
1047
1213
  ��������뤿��Υ᥽�åɤǤ���KO �ϥ���졼����󤵤줿���������������ҷ���
1048
1214
  OC �� PC �ϵ���Ū�˥��饹����󥰤��줿��Ʊ���Τ�������ҷ��Υǡ����١����Ǥ���
1049
1215
 
1050
- --- get_ko_by_gene(genes_id)
1216
+ --- get_ko_by_gene(string:genes_id)
1051
1217
 
1052
1218
  ���ꤷ�������Ҥ˥������󤵤�Ƥ��� KO �Υ���ȥ��ֹ�������֤��ޤ���
1053
1219
 
@@ -1058,18 +1224,8 @@ OC
1058
1224
  # eco:b0002 �����Ҥ˥������󤵤�Ƥ��� KO �Υꥹ��
1059
1225
  get_ko_by_gene('eco:b0002')
1060
1226
 
1061
- #--- get_ko_members(ko_id)
1062
- #
1063
- #���ꤷ�� ko_id �� KO ����ȥ�˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
1064
- #
1065
- #���͡�
1066
- # ArrayOfstring (genes_id)
1067
- #
1068
- #�㡧
1069
- # # KO �ֹ� K02208 �Υ������󤵤�Ƥ�������ҤΥꥹ��
1070
- # get_ko_by_gene('ko:K02598')
1071
1227
 
1072
- --- get_ko_by_ko_class(ko_class_id)
1228
+ --- get_ko_by_ko_class(string:ko_class_id)
1073
1229
 
1074
1230
  ���ꤷ�� ko_class_id �˴ޤޤ�� ko_id �Υꥹ�Ȥ��֤��ޤ���
1075
1231
 
@@ -1080,7 +1236,7 @@ OC
1080
1236
  # KO class '01196' �˴ޤޤ�� KO �Υꥹ��
1081
1237
  get_ko_by_ko_class('01196')
1082
1238
 
1083
- --- get_genes_by_ko_class(ko_class_id, org, start, max_results)
1239
+ --- get_genes_by_ko_class(string:ko_class_id, string:org, int:offset, int:limit)
1084
1240
 
1085
1241
  ���ꤷ����ʪ��� ko_class_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
1086
1242
 
@@ -1091,7 +1247,7 @@ OC
1091
1247
  # KO ���饹 '00930' �˴ޤޤ��ҥȰ����ҤΥꥹ��
1092
1248
  get_genes_by_ko_class('00903', 'hsa' , 1, 100)
1093
1249
 
1094
- --- get_genes_by_ko(ko_id, org)
1250
+ --- get_genes_by_ko(string:ko_id, string:org)
1095
1251
 
1096
1252
  ���ꤷ����ʪ��� ko_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
1097
1253
  ��ʪ�拾���ɤ� all ����ꤹ�������ʪ��ΰ����Ҥ��֤��ޤ���
@@ -1106,29 +1262,6 @@ OC
1106
1262
  # KO �ֹ� 'K00010' �˴ޤޤ������ʪ��ΰ����ҥꥹ��
1107
1263
  get_genes_by_ko('ko:K00010', 'all')
1108
1264
 
1109
- --- get_oc_members_by_gene(genes_id, start, max_results)
1110
-
1111
- ���ꤷ�������Ҥ�Ʊ�� OC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
1112
-
1113
- ���͡�
1114
- ArrayOfstring (genes_id)
1115
-
1116
- �㡧
1117
- # eco:b0002 �����Ҥ�Ʊ���������������饹�����˴ޤޤ������ҤΥꥹ��
1118
- get_oc_members_by_gene('eco:b0002', 1, 10)
1119
- get_oc_members_by_gene('eco:b0002', 11, 10)
1120
-
1121
- --- get_pc_members_by_gene(genes_id, start, max_results)
1122
-
1123
- ���ꤷ�������Ҥ�Ʊ�� PC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
1124
-
1125
- ���͡�
1126
- ArrayOfstring (genes_id)
1127
-
1128
- �㡧
1129
- # eco:b0002 �����Ҥ�Ʊ���ѥ�������饹�����˴ޤޤ������ҤΥꥹ��
1130
- get_pc_members_by_gene('eco:b0002', 1, 10)
1131
- get_pc_members_by_gene('eco:b0002', 11, 10)
1132
1265
 
1133
1266
 
1134
1267
  ==== PATHWAY
@@ -1140,7 +1273,10 @@ PATHWAY
1140
1273
 
1141
1274
  + �ѥ��������ؤο��Ť�
1142
1275
 
1143
- --- mark_pathway_by_objects(pathway_id, object_id_list)
1276
+ ��Ϣ URL��
1277
+ * ((<URL:http://www.genome.jp/kegg/tool/color_pathway.html>))
1278
+
1279
+ --- mark_pathway_by_objects(string:pathway_id, [string]:object_id_list)
1144
1280
 
1145
1281
  ���ꤷ����ʪ��ǡ�Ϳ����줿�ѥ��������ޥåפ�Ϳ����줿���֥�������
1146
1282
  �ʰ����ҡ�����ʪ�������ֹ�ˤ��б������Ȥ˿���Ĥ���������������
@@ -1155,7 +1291,7 @@ PATHWAY
1155
1291
  obj_list = ['eco:b0002', 'cpd:C00263']
1156
1292
  mark_pathway_by_objects('path:eco00260', obj_list)
1157
1293
 
1158
- --- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
1294
+ --- color_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
1159
1295
 
1160
1296
  ���ꤷ���ѥ���������Ϳ����줿���֥������ȡʰ����ҡ�����ʪ�����ǡˤ��Ф���
1161
1297
  ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list �ǻ��ꤷ������
@@ -1174,7 +1310,7 @@ bg_color_list
1174
1310
  bg_list = ['#ff0000', 'yellow']
1175
1311
  color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
1176
1312
 
1177
- --- color_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
1313
+ --- color_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
1178
1314
 
1179
1315
  ���ꤷ�� element_id ���б�����ѥ���������Υ��֥������ȡ�Ĺ������ݤʤɡ�
1180
1316
  ���Ф���ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list ��
@@ -1213,7 +1349,7 @@ KGML
1213
1349
  bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
1214
1350
  color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
1215
1351
 
1216
- --- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
1352
+ --- get_html_of_marked_pathway_by_objects(string:pathway_id, [string]:object_id_list)
1217
1353
 
1218
1354
  ����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
1219
1355
  �С������� 'mark_pathway_by_objects' �᥽�åɤǤ���
@@ -1228,7 +1364,7 @@ KGML
1228
1364
  obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
1229
1365
  get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
1230
1366
 
1231
- --- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
1367
+ --- get_html_of_colored_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
1232
1368
 
1233
1369
  ����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
1234
1370
  �С������� 'color_pathway_by_objects' �᥽�åɤǤ���
@@ -1245,7 +1381,7 @@ KGML
1245
1381
  bg_list = ['#ff0000', 'yellow', 'orange']
1246
1382
  get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
1247
1383
 
1248
- --- get_html_of_colored_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
1384
+ --- get_html_of_colored_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
1249
1385
 
1250
1386
  ����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
1251
1387
  �С������� 'color_pathway_by_elements' �᥽�åɤǤ���
@@ -1265,9 +1401,38 @@ KGML
1265
1401
  bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
1266
1402
  color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
1267
1403
 
1404
+ + �ѥ���������Υ��֥������ȴ֤δط�
1405
+
1406
+ --- get_element_relations_by_pathway(string:pathway_id)
1407
+
1408
+ ���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������Ǥδ֤δط����֤��ޤ���
1409
+ �ѥ��������������ˤ��������Ƥ���ط���ɽ����KGML �ˤ�����
1410
+ <relation> �������������ʥ���աˤ�������뤳�Ȥ��Ǥ��ޤ���
1411
+ ���� get_elements_by_pathway �᥽�åɤ⻲�ȡ�
1412
+
1413
+ ���͡�
1414
+ ArrayOfPathwayElementRelation
1415
+
1416
+ �㡧
1417
+ # ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��� PathwayElement �֤�
1418
+ # �ط��Ǥ��� PathwayElementRelation �Υꥹ�Ȥ�������롣
1419
+ relations = get_element_relations_by_pathway('path:bsu00010')
1420
+
1421
+ # ���������ꥹ�Ȥ���Ȥ�ɽ�����롣
1422
+ relations.each do |rel|
1423
+ puts rel.element_id1
1424
+ puts rel.element_id2
1425
+ puts rel.type
1426
+ rel.subtypes.each do |sub|
1427
+ puts sub.element_id
1428
+ puts sub.relation
1429
+ puts sub.type
1430
+ end
1431
+ end
1432
+
1268
1433
  + �ѥ���������Υ��֥������ȸ���
1269
1434
 
1270
- --- get_elements_by_pathway(pathway_id)
1435
+ --- get_elements_by_pathway(string:pathway_id)
1271
1436
 
1272
1437
  ���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������ǤΥꥹ�Ȥ��֤��ޤ���
1273
1438
  ����ˡ�ˤĤ��Ƥ� color_pathway_by_elements �᥽�åɤ򻲾Ȥ��Ƥ���������
@@ -1292,7 +1457,7 @@ KGML
1292
1457
  end
1293
1458
  end
1294
1459
 
1295
- --- get_genes_by_pathway(pathway_id)
1460
+ --- get_genes_by_pathway(string:pathway_id)
1296
1461
 
1297
1462
  ���ꤷ���ѥ���������˺ܤäƤ�������ҤΥꥹ�Ȥ��֤��ޤ�����ʪ��̾��
1298
1463
  pathway_id �˴ޤޤ�� keggorg �ǻ��ꤷ�ޤ���
@@ -1304,7 +1469,7 @@ pathway_id
1304
1469
  # ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ҤΥꥹ��
1305
1470
  get_genes_by_pathway('path:eco00020')
1306
1471
 
1307
- --- get_enzymes_by_pathway(pathway_id)
1472
+ --- get_enzymes_by_pathway(string:pathway_id)
1308
1473
 
1309
1474
  ���ꤷ���ѥ��������˺ܤäƤ�������ֹ�Υꥹ�Ȥ��֤��ޤ���
1310
1475
 
@@ -1315,7 +1480,7 @@ pathway_id
1315
1480
  # ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ֹ�Υꥹ��
1316
1481
  get_enzymes_by_pathway('path:eco00020')
1317
1482
 
1318
- --- get_compounds_by_pathway(pathway_id)
1483
+ --- get_compounds_by_pathway(string:pathway_id)
1319
1484
 
1320
1485
  ���ꤷ���ѥ��������˺ܤäƤ��벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
1321
1486
 
@@ -1326,7 +1491,7 @@ pathway_id
1326
1491
  # ��IJ�ݤΥѥ������� 00020 �˺ܤäƤ��벽��ʪ�Υꥹ��
1327
1492
  get_compounds_by_pathway('path:eco00020')
1328
1493
 
1329
- --- get_glycans_by_pathway(pathway_id)
1494
+ --- get_glycans_by_pathway(string:pathway_id)
1330
1495
 
1331
1496
  ���ꤷ���ѥ��������˺ܤäƤ��������Υꥹ�Ȥ��֤��ޤ���
1332
1497
 
@@ -1337,7 +1502,7 @@ pathway_id
1337
1502
  # ��IJ�ݤΥѥ������� 00510 �˺ܤäƤ��������Υꥹ��
1338
1503
  get_glycans_by_pathway('path:eco00510')
1339
1504
 
1340
- --- get_reactions_by_pathway(pathway_id)
1505
+ --- get_reactions_by_pathway(string:pathway_id)
1341
1506
 
1342
1507
  ���ꤷ���ѥ��������˺ܤäƤ���ꥢ��������ֹ�Υꥹ�Ȥ��֤��ޤ���
1343
1508
 
@@ -1348,7 +1513,7 @@ pathway_id
1348
1513
  # ��IJ�ݤΥѥ������� 00260 �֤˺ܤäƤ���ꥢ�������Υꥹ��
1349
1514
  get_reactions_by_pathway('path:eco00260')
1350
1515
 
1351
- --- get_kos_by_pathway(pathway_id)
1516
+ --- get_kos_by_pathway(string:pathway_id)
1352
1517
 
1353
1518
  ���ꤷ���ѥ��������˺ܤäƤ��� KO �ֹ�Υꥹ�Ȥ��֤��ޤ���
1354
1519
 
@@ -1359,11 +1524,12 @@ pathway_id
1359
1524
  # �ҥȤΥѥ������� 00010 �˺ܤäƤ��� KO �ֹ�Υꥹ��
1360
1525
  get_kos_by_pathway('path:hsa00010')
1361
1526
 
1362
-
1363
-
1364
1527
  + ���֥������Ȥ���ѥ�����������
1365
1528
 
1366
- --- get_pathways_by_genes(genes_id_list)
1529
+ ��Ϣ URL��
1530
+ * ((<URL:http://www.genome.jp/kegg/tool/search_pathway.html>))
1531
+
1532
+ --- get_pathways_by_genes([string]:genes_id_list)
1367
1533
 
1368
1534
  ���ꤷ�������Ҥ����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1369
1535
 
@@ -1374,7 +1540,7 @@ pathway_id
1374
1540
  # ��IJ�ݤΰ����� b0077 �� b0078 ��ξ���ܤäƤ���ѥ��������Υꥹ��
1375
1541
  get_pathways_by_genes(['eco:b0077', 'eco:b0078'])
1376
1542
 
1377
- --- get_pathways_by_enzymes(enzyme_id_list)
1543
+ --- get_pathways_by_enzymes([string]:enzyme_id_list)
1378
1544
 
1379
1545
  ���ꤷ�������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1380
1546
 
@@ -1385,7 +1551,7 @@ pathway_id
1385
1551
  # �����ֹ� 1.3.99.1 �ι��Ǥ��ܤäƤ���ѥ��������Υꥹ��
1386
1552
  get_pathways_by_enzymes(['ec:1.3.99.1'])
1387
1553
 
1388
- --- get_pathways_by_compounds(compound_id_list)
1554
+ --- get_pathways_by_compounds([string]:compound_id_list)
1389
1555
 
1390
1556
  ���ꤷ������ʪ�����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1391
1557
 
@@ -1396,7 +1562,7 @@ pathway_id
1396
1562
  # ����ʪ C00033 �� C00158 ��ξ���ܤäƤ���ѥ��������Υꥹ��
1397
1563
  get_pathways_by_compounds(['cpd:C00033', 'cpd:C00158'])
1398
1564
 
1399
- --- get_pathways_by_glycans(compound_id_list)
1565
+ --- get_pathways_by_glycans([string]:compound_id_list)
1400
1566
 
1401
1567
  ���ꤷ�����������ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1402
1568
 
@@ -1407,7 +1573,7 @@ pathway_id
1407
1573
  # ���� G00009 �� G00011 ��ξ���ܤäƤ���ѥ��������Υꥹ��
1408
1574
  get_pathways_by_glycans(['gl:G00009', 'gl:G00011'])
1409
1575
 
1410
- --- get_pathways_by_reactions(reaction_id_list)
1576
+ --- get_pathways_by_reactions([string]:reaction_id_list)
1411
1577
 
1412
1578
  ���ꤷ���ꥢ��������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1413
1579
 
@@ -1419,7 +1585,7 @@ pathway_id
1419
1585
  # ȿ����ޤ�ѥ��������Υꥹ��
1420
1586
  get_pathways_by_reactions(['rn:R00959', 'rn:R02740', 'rn:R00960', 'rn:R01786'])
1421
1587
 
1422
- --- get_pathways_by_kos(ko_id_list, org)
1588
+ --- get_pathways_by_kos([string]:ko_id_list, string:org)
1423
1589
 
1424
1590
  ���ꤷ����ʪ�� KO �ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
1425
1591
 
@@ -1433,10 +1599,9 @@ pathway_id
1433
1599
  # KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�����ʪ��Υѥ��������Υꥹ��
1434
1600
  get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'all')
1435
1601
 
1436
-
1437
1602
  + �ѥ��������֤δط�
1438
1603
 
1439
- --- get_linked_pathways(pathway_id)
1604
+ --- get_linked_pathways(string:pathway_id)
1440
1605
 
1441
1606
  ���ꤷ���ѥ��������ֹ�Υѥ������������󥯤���Ƥ���ѥ���������
1442
1607
  �ꥹ�Ȥ��֤��ޤ���
@@ -1448,7 +1613,6 @@ pathway_id
1448
1613
  # �ѥ������� path:eco00620 �����󥯤���Ƥ���ѥ��������Υꥹ��
1449
1614
  get_linked_pathways('path:eco00620')
1450
1615
 
1451
-
1452
1616
  ==== GENES
1453
1617
 
1454
1618
  GENES �ǡ����١������Ф���᥽�åɤΰ����Ǥ���GENES �ǡ����١����ˤĤ���
@@ -1456,9 +1620,9 @@ GENES
1456
1620
 
1457
1621
  * ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))
1458
1622
 
1459
- --- get_genes_by_organism(org, start, max_results)
1623
+ --- get_genes_by_organism(string:org, int:offset, int:limit)
1460
1624
 
1461
- ���ꤷ����ʪ����� GENES ����ȥ�Τ�����start ���ܤ��� max_results ʬ��
1625
+ ���ꤷ����ʪ����� GENES ����ȥ�Τ�����offset ���ܤ��� limit ʬ��
1462
1626
  ��̤��֤��ޤ���
1463
1627
 
1464
1628
  ���͡�
@@ -1469,7 +1633,6 @@ GENES
1469
1633
  get_genes_by_organism('hin', 1, 100)
1470
1634
  get_genes_by_organism('hin', 101, 100)
1471
1635
 
1472
-
1473
1636
  ==== GENOME
1474
1637
 
1475
1638
  GENOME �ǡ����١������Ф���᥽�åɤΰ����Ǥ���GENOME �ǡ����١����ˤĤ���
@@ -1477,7 +1640,7 @@ GENOME
1477
1640
 
1478
1641
  * ((<URL:http://www.genome.jp/kegg/kegg2.html#genome>))
1479
1642
 
1480
- --- get_number_of_genes_by_organism(org)
1643
+ --- get_number_of_genes_by_organism(string:org)
1481
1644
 
1482
1645
  ���ꤷ����ʪ�郎���İ����ҿ����֤��ޤ���
1483
1646
 
@@ -1488,25 +1651,184 @@ GENOME
1488
1651
  # ��IJ�ݤ����İ����Ҥο�
1489
1652
  get_number_of_genes_by_organism('eco')
1490
1653
 
1491
-
1492
1654
  ==== LIGAND
1493
1655
 
1494
1656
  LIGAND �ǡ����١������Ф���᥽�åɤΰ����Ǥ���
1495
1657
 
1496
- --- convert_mol_to_kcf(mol_text)
1658
+ ��Ϣ URL��
1659
+ * ((<URL:http://www.genome.jp/kegg/ligand.html>))
1660
+
1661
+ --- convert_mol_to_kcf(string:mol)
1497
1662
 
1498
1663
  MOL �ե����ޥåȤΥ���ȥ�� KCF �ե����ޥåȤ��Ѵ����ޤ���
1499
1664
 
1500
1665
  ���͡�
1501
- String
1666
+ string
1502
1667
 
1503
1668
  �㡧
1504
1669
  convert_mol_to_kcf(mol_str)
1505
1670
 
1671
+ --- search_compounds_by_name(string:name)
1672
+
1673
+ ����ʪ��̾���Ǹ������ޤ���
1674
+
1675
+ ���͡�
1676
+ ArrayOfstring (compound_id)
1677
+
1678
+ �㡧
1679
+ search_compounds_by_name("shikimic acid")
1680
+
1681
+ --- search_drugs_by_name(string:name)
1682
+
1683
+ �ɥ�å���̾���Ǹ������ޤ���
1684
+
1685
+ ���͡�
1686
+ ArrayOfstring (drug_id)
1687
+
1688
+ �㡧
1689
+ search_drugs_by_name("tetracyclin")
1690
+
1691
+ --- search_glycans_by_name(string:name)
1692
+
1693
+ ������̾���Ǹ������ޤ���
1694
+
1695
+ ���͡�
1696
+ ArrayOfstring
1697
+
1698
+ �㡧
1699
+ search_glycans_by_name("Paragloboside")
1700
+
1701
+ --- search_compounds_by_composition(string:composition)
1702
+
1703
+ ����ʪ�������Ǹ������ޤ���
1704
+ �����ϸ��ǤȸĿ���Ĥʤ���ʸ����ǻ��ꤷ�ޤ���
1705
+ ���Ǥν��֤�̵�ط��Ǥ���
1706
+
1707
+ ���͡�
1708
+ ArrayOfstring (compound_id)
1709
+
1710
+ �㡧
1711
+ search_compounds_by_composition("C7H10O5")
1712
+
1713
+ --- search_drugs_by_composition(string:composition)
1714
+
1715
+ �ɥ�å��������Ǹ������ޤ���
1716
+ �����ϸ��ǤȸĿ���Ĥʤ���ʸ����ǻ��ꤷ�ޤ���
1717
+ ���Ǥν��֤�̵�ط��Ǥ���
1718
+
1719
+ ���͡�
1720
+ ArrayOfstring (drug_id)
1721
+
1722
+ �㡧
1723
+ search_drugs_by_composition("HCl")
1724
+
1725
+ --- search_glycans_by_composition(string:composition)
1726
+
1727
+ �����������Ǹ������ޤ���
1728
+ �����ϥ��å��dz�ä����ȸĿ��򥹥ڡ����Ƕ��ڤä�ʸ����ǻ��ꤷ�ޤ���
1729
+ ���ν��֤ϼ�ͳ�Ǥ���
1730
+
1731
+ ���͡�
1732
+ ArrayOfstring
1733
+
1734
+ �㡧
1735
+ search_glycans_by_composition("(Man)4 (GalNAc)1")
1736
+
1737
+ --- search_compounds_by_mass(float:mass, float:range)
1738
+
1739
+ ����ʪ��ʬ���̤Ǹ������ޤ���
1740
+ mass ���濴�Ȥ��� ��range �νŤ��β���ʪ����������ޤ���
1741
+
1742
+ ���͡�
1743
+ ArrayOfstring (compound_id)
1744
+
1745
+ �㡧
1746
+ search_compounds_by_mass(174.05, 0.1)
1747
+
1748
+ --- search_drugs_by_mass(float:mass, float:range)
1749
+
1750
+ �ɥ�å���ʬ���̤Ǹ������ޤ���
1751
+ mass ���濴�Ȥ��� ��range �νŤ��Υɥ�å�����������ޤ���
1752
+
1753
+ ���͡�
1754
+ ArrayOfstring (drug_id)
1755
+
1756
+ �㡧
1757
+ search_drugs_by_mass(150, 1.0)
1758
+
1759
+ --- search_glycans_by_mass(float:mass, float:range)
1760
+
1761
+ ������ʬ���̤Ǹ������ޤ���
1762
+ mass ���濴�Ȥ��� ��range �νŤ�����������������ޤ���
1763
+
1764
+ ���͡�
1765
+ ArrayOfstring
1766
+
1767
+ �㡧
1768
+ search_glycans_by_mass(1200, 0.5)
1769
+
1770
+ --- search_compounds_by_subcomp(string:mol, int:offset, int:limit)
1771
+
1772
+ ������ʬ��¤����IJ���ʪ�� subcomp �ץ�������ȤäƸ������ޤ���
1773
+
1774
+ ���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
1775
+ ���饤����Ȥ��줿����ʪ�ι�¤�� bget ���ޥ�ɤ� "-f m"
1776
+ ���ץ�����Ĥ��� MOL �ե����ޥåȤǼ��������б����ǧ���ޤ���
1777
+
1778
+ ���͡�
1779
+ ArrayOfStructureAlignment
1780
+
1781
+ �㡧
1782
+ mol = bget("-f m cpd:C00111")
1783
+ search_compounds_by_subcomp(mol, 1, 5)
1784
+
1785
+ ��Ϣ URL��
1786
+ * ((<URL:http://www.genome.jp/ligand-bin/search_compound>))
1787
+
1788
+ --- search_drugs_by_subcomp(string:mol, int:offset, int:limit)
1789
+
1790
+ ������ʬ��¤����ĥɥ�å��� subcomp �ץ�������ȤäƸ������ޤ���
1791
+
1792
+ ���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
1793
+ ���饤����Ȥ��줿�ɥ�å��ι�¤�� bget ���ޥ�ɤ� "-f m"
1794
+ ���ץ�����Ĥ��� MOL �ե����ޥåȤǼ��������б����ǧ���ޤ���
1795
+
1796
+ ���͡�
1797
+ ArrayOfStructureAlignment
1798
+
1799
+ �㡧
1800
+ mol = bget("-f m dr:D00201")
1801
+ search_drugs_by_subcomp(mol, 1, 5)
1802
+
1803
+ ��Ϣ URL��
1804
+ * ((<URL:http://www.genome.jp/ligand-bin/search_compound>))
1805
+
1806
+ --- search_glycans_by_kcam(string:kcf, string:program, string:option, int:offset, int:limit)
1807
+
1808
+ ������ʬ��¤����������� KCaM �ץ�������ȤäƸ������ޤ���
1809
+
1810
+ ������ program �ˤ� approximate �ޥå���Ԥ� "gapped" �ޤ���
1811
+ exact �ޥå���Ԥ� "ungapped" ����ꤷ�ޤ����ޤ� option �ˤ�
1812
+ "global" �ޤ��� "local" ����ꤷ�ޤ���
1813
+
1814
+ ���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
1815
+ ���饤����Ȥ��줿�����ι�¤�� bget ���ޥ�ɤ� "-f k"
1816
+ ���ץ�����Ĥ��� KCF �ե����ޥåȤǼ��������б����ǧ���ޤ���
1817
+
1818
+ ���͡�
1819
+ ArrayOfStructureAlignment
1820
+
1821
+ �㡧
1822
+ kcf = bget("-f k gl:G12922")
1823
+ search_glycans_by_kcam(kcf, "gapped", "local", 1, 5)
1824
+
1825
+ ��Ϣ URL��
1826
+ * ((<URL:http://www.genome.jp/ligand-bin/search_glycan.cgi>))
1827
+ * ((<URL:http://www.genome.jp/ligand/kcam/>))
1506
1828
 
1507
1829
  == Notes
1508
1830
 
1509
- Last updated: Feb 17, 2006
1831
+ Last updated: December 27, 2006
1510
1832
 
1511
1833
  =end
1512
1834