bio 1.0.0 → 1.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
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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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- �����ȥѡ�����������Ϥ���ѥ����������Ϥޤ��͡��ʷ׻����ʤɤ�ɬ�פȤʤ�
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- �͡��ʵ�ǽ�� Ruby ����Ǽ���������ñ�˰�����褦�ˤ���ץ��������ȤǤ���
12
-
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- 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
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- �Υץ��������Ȥˤ⤽�줾������������Ȼפ��ޤ�����������ˤ��Ƥ��ȯ�dz�
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- ���ƹԤäƤ⽽ʬ���ɤ��դ���Ȼפ��ޤ���
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-
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- 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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46
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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
-
54
- 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
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- | | |- class Bio::KEGG::ENZYME bio/db/kegg/enzyme.rb alpha
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- | | `- 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
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- | | `- 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
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- |- 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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-
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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
-