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
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@@ -1,225 +0,0 @@
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- =begin
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-
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- $Id: BioRuby.rd.ja,v 1.10 2004/08/23 23:41:29 k Exp $
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-
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- Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
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-
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- = BioRuby �ץ���������
8
-
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10
- �����ȥѡ�����������Ϥ���ѥ����������Ϥޤ��͡��ʷ׻����ʤɤ�ɬ�פȤʤ�
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- �͡��ʵ�ǽ�� Ruby ����Ǽ���������ñ�˰�����褦�ˤ���ץ��������ȤǤ���
12
-
13
- ¾����ԥץ��������ȤȤ��Ƥ� BioPerl, BioPython, BioJava �ʤ��͡��ʤ��
14
- ������ޤ��������٤Ǥ���ˤ�Ĺ�� BioPerl ���Ǥ⽼�¤��Ƥ���Ȼפ��ޤ�����
15
- BioPerl ��������Τ�ʣ���ʹ�¤�ǡ��ǡ������󥿡��Ǥ����Ѥ�������ꤵ���
16
- ����褦�˻פ��ޤ��������⤽�� Perl ��ʣ���ʥǡ�����¤�򰷤��ȥ���������
17
- �ɤ��ɤߤŤ餯�ʤ�ޤ������η�̡����ƥʥ󥹤���ɤ��񤷤��ʤ�ޤ���¾
18
- �Υץ��������Ȥˤ⤽�줾������������Ȼפ��ޤ�����������ˤ��Ƥ��ȯ�dz�
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- ȯ�������ʳ��ˤ��뤳�Ȥ�ͤ���С���ʬ�λȤ��䤹�������ɬ�פʵ�ǽ�����
20
- ���ƹԤäƤ⽽ʬ���ɤ��դ���Ȼפ��ޤ���
21
-
22
- BioRuby �Ǥϡ�����ץ�Ƕ��Ϥ� Ruby ����Υ��ɥХ�ơ�������������ʬ����
23
- �䤹�������ɤǥ���ɥ桼����ɬ�פʵ�ǽ��������Ƥ��������Ȼפ��ޤ����ä�
24
- Ruby �Τ����륪�֥������ȤȤ���ȯ�ۤϡ���Τ򰷤���ʪ�ؤˤ���ľ������
25
- �Ϥ�䤹�����󥻥ץȤǤ������ȥ饤�����顼�Ǻ�Ȥ�ʤ������Ǥ��륤�󥿡�
26
- �ץ꥿����� C �� Java ����٤ƥ����åȤʥ�ܤθ���Ԥˤ������ߤ䤹����
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- �פ��ޤ���
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-
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- �ޤ���Ruby �Ǥ� Perl ����ζ��Ϥ�ʸ��������˲ä���Perl �θ�Ť��� OO ��
30
- ��륪�ޥ��ʥ��䡢�ѽФ��� local, my �ʤɤ����פǡ�ʣ���ʥǡ�����¤�⥯
31
- �饹�Ǥ��ä����ɽ���Ǥ��뤿�ᡢ�ܼ�Ū����ʬ����ǰ���ƥ����ǥ��󥰤��뤳
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- �Ȥ��Ǥ��ޤ�������ˤ�ꡢ��ȯ�θ�Ψ��⤯�ʤ뤿�ᡢ¾�Υץ��������Ȥ���
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- �ݤ��Ƥ��ʤ��ΰ�ˤ⤤���᤯����Ȥ�Ǥ�����Ȼפ��ޤ���
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-
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- ����ˡ�Ruby ���Τ����ܤdz�ȯ���줿����Ǥ���Τ˲ä� BioRuby �����ܽ��
36
- �����ץ�� Bio* �ץ��������ȤǤ������Τ��ᡢ�������ܸ������졢��ȯ��
37
- ���ܸ�ǹԤʤ�������KEGG �ʤ������ȼ��Υ����ƥ�ؤ��б��ʤɤ�Ԥʤ��䤹
38
- ������ BioRuby �Υ��åȤǤ��礦��
39
-
40
- BioRuby �Υ����֥����� ((<URL:http://bioruby.org/>)) �ǡ��ǿ��Τ��Τ餻��
41
- ��������������ˡ���᡼��󥰥ꥹ�Ȥʤɤξ���ȡ�¾�Υɥ�����Ȥ䥳���
42
- �Ȥʤɤξ��������ޤ���
43
-
44
- == �Ȥ���
45
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47
-
48
- require 'bio'
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-
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- �Ȥ��Ƥ���������
51
-
52
- ���ƤΥ��饹�� module Bio �β����ɲä���ޤ�����ɬ�פ˱�����
53
-
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- include Bio
55
-
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- �Ȥ��뤳�Ȥǡ�Bio:: ��ʤ��Ƴƥ��饹��Ȥ������Ǥ��ޤ���
57
-
58
- == BioRuby �γ�ά
59
-
60
- bio.rb �� require ����ȡ��ʲ��Υ��饹������ʤɤ��Ȥ���褦�ˤʤ�ޤ���
61
- ���߼�������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
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- |- class Bio::Location bio/location.rb stable
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- |- class Bio::Locations bio/location.rb stable
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- |- class Bio::Feature bio/feature.rb stable
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- |- class Bio::Features bio/feature.rb stable
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- |- class Bio::Reference bio/reference.rb stable
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- |- class Bio::References bio/reference.rb stable
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- |- class Bio::Pathway bio/pathway.rb stable
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- |- class Bio::Relation bio/pathway.rb stable
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- |- class Bio::FlatFile bio/io/flatfile.rb stable
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- |- class Bio::Registry bio/io/registry.rb beta
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- |- class Bio::Fetch bio/io/fetch.rb stable
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- |- class Bio::SQL bio/io/sql.rb beta
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- |- class Bio::DBGET bio/io/dbget.rb stable
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- |- class Bio::PubMed bio/io/pubmed.rb stable
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- |- class Bio::BRDB bio/io/brdb.rb alpha
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- |- class Bio::Fasta bio/appl/fasta.rb stable
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- |- class Bio::Fasta::Report::* bio/appl/fasta/*.rb stable
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- |- class Bio::Blast bio/appl/blast.rb stable
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- |- class Bio::Blast::Report::* bio/appl/blast/*.rb stable
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- |- class Bio::DB bio/db.rb stable
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- | |- class Bio::FastaFormat bio/db/fasta.rb stable
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- | |- class Bio::NCBIDB bio/db.rb stable
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- | | |- class Bio::GenBank bio/db/genbank/genbank.rb stable
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- | | | |- class Bio::GenPept bio/db/genbank/genpept.rb stable
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- | | | |- class Bio::RefSeq bio/db/genbank/refseq.rb stable
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- | | | `- class Bio::DDBJ bio/db/genbank/ddbj.rb stable
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- | | |- class Bio::MEDLINE bio/db/medline.rb stable
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- | | |- class Bio::LITDB bio/db/litdb.rb stable
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- | | `- class Bio::KEGGDB bio/db.rb beta
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- | | |- class Bio::AAindex bio/db/aaindex.rb beta
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- | | | |- class Bio::AAindex1 bio/db/aaindex.rb beta
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- | | | `- class Bio::AAindex2 bio/db/aaindex.rb beta
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- | | |- class Bio::KEGG::GENES bio/db/kegg/genes.rb stable
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- | | |- class Bio::KEGG::GENOME bio/db/kegg/genome.rb stable
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- | | |- class Bio::KEGG::BRITE bio/db/kegg/brite.rb alpha
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- | | |- 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
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- | `- 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
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- | |- class Bio::PROSITE bio/db/prosite.rb beta
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- | `- class Bio::TRANSFAC bio/db/transfac.rb beta
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- | |- class Bio::TFMATRIX bio/db/transfac.rb beta
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- | |- class Bio::TFSITE bio/db/transfac.rb beta
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- | |- class Bio::TFFACTOR bio/db/transfac.rb beta
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- | |- class Bio::TFCELL bio/db/transfac.rb beta
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- | |- class Bio::TFCLASS bio/db/transfac.rb beta
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- | `- 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
-
@@ -1,341 +0,0 @@
1
- =begin
2
-
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- $Id: Design.rd.ja,v 1.7 2002/07/02 01:40:24 k Exp $
4
-
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- Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
6
-
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- = BioRuby �γ�ȯ���ˤȥǥ�����
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-
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- Ŭ�ڤ� commit ���ޤ����᡼��󥰥ꥹ�Ȥʤɤ� contribute ���줿�����ɤ�
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-
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- |-- README �Ϥ����
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- |-- COPYING
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- |-- COPYING.LIB
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- |-- bin/ ���ץꥱ�������
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- |-- lib/ Ruby �ǽ񤫤줿�饤�֥��
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- | `-- bio/ ����ʤɴ���Ū�ʥ��饹
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- | |-- data/ ��ʪ��Ū������ʤɥǡ������Τ��
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-
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- == Ruby ��ʬ�ˤĤ��ƤΥǥ������bioruby/lib/bio/ �ʲ���
30
-
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- ����ޤǤ˹Ԥʤ�줿�����Υǥ����󥳥󥻥ץȤȡ���������ˤʤɤˤĤ��Ƥ�
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- ����ݥǡ�����¤�򰷤����饹�� lib/bio/ ľ�������֤��Ƥ��ޤ��������ϳ�
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45
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46
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- �Ȥ����δ�ñ�� vs ������ʣ�������������ᤵ vs ����νŤ����ʤɥХ��
50
- �������ɬ�������ɤ��Ȥϸ����ʤ����⤢��ޤ�����lib/bio/db.rb �Ǥϰʲ�
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- ����ȥ� ���줾��Υǡ����١����ˤ����룱�ĤΥǡ���ñ��
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62
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- 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
- * ((<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
- �����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
- ̾�����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
- 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���
283
-
284
- �ƥ��Ȥ���ˡ�ϡ�Test::Unit �� ruby ��ɸ��饤�֥��Ȥ���ź�դ����褦
285
- �ˤʤ�к��Ѥ��Ƥ⤤���Ȼפ��ޤ���������ޤǤϿ���������Ȼפ��ޤ�����
286
- ���Ȥ˳����ե������ͥåȥ���ʤɤ�ɬ�פʾ��ɤ����뤫�Ȥ������󥹥ȡ�
287
- ������ư���ǧ�Ȥ��ƥƥ��Ȥ�¹Ԥ�����ˡ�ʤɤ⸡Ƥ����ɬ�פ�����ޤ���
288
-
289
- === �ɥ��������
290
-
291
- ����ޤǡ��ƥ��饹�ˤĤ��Ƥϡ����ޤ�ɥ�����Ȳ�����Ƥ��ޤ���Ǥ�������
292
- ����ϥƥ��ȥ����ɤΤ��ȡ��ե�����κǸ����� RD �ǥ᥽�åɤʤɤΥɥ����
293
- ��Ȥ��ɲä��뤳�Ȥˤ��Ƥ����ޤ���
294
-
295
- =begin
296
-
297
- = Bio::Hoge
298
-
299
- Hoge ���饹�γ���������
300
-
301
- --- Bio::Hoge.new(fuga)
302
-
303
- ���饹�᥽�åɤ�������
304
-
305
- --- Bio::Hoge#to_a
306
-
307
- �᥽�åɤ�������
308
-
309
- == Bio::Hoge::Fuga
310
-
311
- �������饹 Hoge::Fuga �γ�������
312
-
313
- --- Bio::Hoge::Fuga.new(fuga)
314
-
315
- ���饹�᥽�åɤ�������
316
-
317
- --- Bio::Hoge::Fuga#to_a
318
-
319
- �᥽�åɤ�������
320
-
321
- =end
322
-
323
- ��������
324
-
325
- * ����������ˤ� ASCII �ʳ���ʸ��������ʤ����ˤΤ��ᡢ���ܸ�Υɥ����
326
- ��Ȥϡ�������ʬ�ǤϤʤ��̥ե�����˵��Ҥ���doc/ �ǥ��쥯�ȥ�ʲ�����
327
- ���ʤɤ��ޤ������κݡ���ĥ�Ҥ� .ja ���դ��ơ��ե�����̾��������ܸ��
328
- ʬ����褦�ˤ��ޤ���
329
-
330
- * ���ҤΤ褦�ˡ�������������������Ǥ� RD �ˤ��ɥ�����Ȥ϶ػߤ��ޤ���
331
- ��ͳ�Ͻ��˥����ɤ��ɤߤŤ餯�ʤ뤫��Ǥ������������ # ��Ȥä�ɬ��
332
- �ʥ����Ȥ��ɲä�����ϴ��ޤ��ޤ���(���ҤΤ褦�� RDoc ���ˤ��뤫��
333
- ����ޤ���)
334
-
335
- == ��ȯ�˻��ä���ˤ�
336
-
337
- BioRuby �Υ����֥����� ((<URL:http://bioruby.org>)) �򸫤ơ��᡼��󥰥�
338
- ���Ȥ˻��ä��뤫�������å� <staff@bioruby.org> ��Ϣ�����Ƥ���������
339
-
340
- =end
341
-