wwood-bioruby 1.2.11

Sign up to get free protection for your applications and to get access to all the features.
Files changed (386) hide show
  1. data/README.rdoc +205 -0
  2. data/README_DEV.rdoc +285 -0
  3. data/VERSION.yml +4 -0
  4. data/bin/bioruby +44 -0
  5. data/bin/br_biofetch.rb +47 -0
  6. data/bin/br_bioflat.rb +293 -0
  7. data/bin/br_biogetseq.rb +45 -0
  8. data/bin/br_pmfetch.rb +421 -0
  9. data/lib/bio.rb +306 -0
  10. data/lib/bio/alignment.rb +2518 -0
  11. data/lib/bio/appl/bl2seq/report.rb +334 -0
  12. data/lib/bio/appl/blast.rb +505 -0
  13. data/lib/bio/appl/blast/ddbj.rb +142 -0
  14. data/lib/bio/appl/blast/format0.rb +1438 -0
  15. data/lib/bio/appl/blast/format8.rb +83 -0
  16. data/lib/bio/appl/blast/genomenet.rb +263 -0
  17. data/lib/bio/appl/blast/ncbioptions.rb +220 -0
  18. data/lib/bio/appl/blast/remote.rb +105 -0
  19. data/lib/bio/appl/blast/report.rb +767 -0
  20. data/lib/bio/appl/blast/rexml.rb +144 -0
  21. data/lib/bio/appl/blast/rpsblast.rb +277 -0
  22. data/lib/bio/appl/blast/wublast.rb +635 -0
  23. data/lib/bio/appl/blast/xmlparser.rb +236 -0
  24. data/lib/bio/appl/blat/report.rb +530 -0
  25. data/lib/bio/appl/clustalw.rb +219 -0
  26. data/lib/bio/appl/clustalw/report.rb +152 -0
  27. data/lib/bio/appl/emboss.rb +203 -0
  28. data/lib/bio/appl/fasta.rb +235 -0
  29. data/lib/bio/appl/fasta/format10.rb +325 -0
  30. data/lib/bio/appl/gcg/msf.rb +212 -0
  31. data/lib/bio/appl/gcg/seq.rb +195 -0
  32. data/lib/bio/appl/genscan/report.rb +552 -0
  33. data/lib/bio/appl/hmmer.rb +126 -0
  34. data/lib/bio/appl/hmmer/report.rb +683 -0
  35. data/lib/bio/appl/iprscan/report.rb +374 -0
  36. data/lib/bio/appl/mafft.rb +259 -0
  37. data/lib/bio/appl/mafft/report.rb +226 -0
  38. data/lib/bio/appl/muscle.rb +52 -0
  39. data/lib/bio/appl/paml/baseml.rb +95 -0
  40. data/lib/bio/appl/paml/baseml/report.rb +32 -0
  41. data/lib/bio/appl/paml/codeml.rb +242 -0
  42. data/lib/bio/appl/paml/codeml/rates.rb +67 -0
  43. data/lib/bio/appl/paml/codeml/report.rb +67 -0
  44. data/lib/bio/appl/paml/common.rb +348 -0
  45. data/lib/bio/appl/paml/common_report.rb +38 -0
  46. data/lib/bio/appl/paml/yn00.rb +103 -0
  47. data/lib/bio/appl/paml/yn00/report.rb +32 -0
  48. data/lib/bio/appl/phylip/alignment.rb +133 -0
  49. data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
  50. data/lib/bio/appl/probcons.rb +41 -0
  51. data/lib/bio/appl/psort.rb +548 -0
  52. data/lib/bio/appl/psort/report.rb +542 -0
  53. data/lib/bio/appl/pts1.rb +263 -0
  54. data/lib/bio/appl/sim4.rb +124 -0
  55. data/lib/bio/appl/sim4/report.rb +485 -0
  56. data/lib/bio/appl/sosui/report.rb +151 -0
  57. data/lib/bio/appl/spidey/report.rb +593 -0
  58. data/lib/bio/appl/targetp/report.rb +267 -0
  59. data/lib/bio/appl/tcoffee.rb +55 -0
  60. data/lib/bio/appl/tmhmm/report.rb +231 -0
  61. data/lib/bio/command.rb +593 -0
  62. data/lib/bio/compat/features.rb +157 -0
  63. data/lib/bio/compat/references.rb +128 -0
  64. data/lib/bio/data/aa.rb +353 -0
  65. data/lib/bio/data/codontable.rb +722 -0
  66. data/lib/bio/data/na.rb +223 -0
  67. data/lib/bio/db.rb +329 -0
  68. data/lib/bio/db/aaindex.rb +357 -0
  69. data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
  70. data/lib/bio/db/biosql/sequence.rb +508 -0
  71. data/lib/bio/db/embl/common.rb +352 -0
  72. data/lib/bio/db/embl/embl.rb +500 -0
  73. data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
  74. data/lib/bio/db/embl/format_embl.rb +190 -0
  75. data/lib/bio/db/embl/sptr.rb +1283 -0
  76. data/lib/bio/db/embl/swissprot.rb +42 -0
  77. data/lib/bio/db/embl/trembl.rb +41 -0
  78. data/lib/bio/db/embl/uniprot.rb +42 -0
  79. data/lib/bio/db/fantom.rb +597 -0
  80. data/lib/bio/db/fasta.rb +410 -0
  81. data/lib/bio/db/fasta/defline.rb +532 -0
  82. data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
  83. data/lib/bio/db/fasta/format_fasta.rb +97 -0
  84. data/lib/bio/db/genbank/common.rb +307 -0
  85. data/lib/bio/db/genbank/ddbj.rb +22 -0
  86. data/lib/bio/db/genbank/format_genbank.rb +187 -0
  87. data/lib/bio/db/genbank/genbank.rb +250 -0
  88. data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
  89. data/lib/bio/db/genbank/genpept.rb +60 -0
  90. data/lib/bio/db/genbank/refseq.rb +18 -0
  91. data/lib/bio/db/gff.rb +1846 -0
  92. data/lib/bio/db/go.rb +481 -0
  93. data/lib/bio/db/kegg/brite.rb +41 -0
  94. data/lib/bio/db/kegg/compound.rb +131 -0
  95. data/lib/bio/db/kegg/drug.rb +98 -0
  96. data/lib/bio/db/kegg/enzyme.rb +148 -0
  97. data/lib/bio/db/kegg/expression.rb +155 -0
  98. data/lib/bio/db/kegg/genes.rb +263 -0
  99. data/lib/bio/db/kegg/genome.rb +241 -0
  100. data/lib/bio/db/kegg/glycan.rb +166 -0
  101. data/lib/bio/db/kegg/keggtab.rb +357 -0
  102. data/lib/bio/db/kegg/kgml.rb +256 -0
  103. data/lib/bio/db/kegg/orthology.rb +136 -0
  104. data/lib/bio/db/kegg/reaction.rb +82 -0
  105. data/lib/bio/db/kegg/taxonomy.rb +331 -0
  106. data/lib/bio/db/lasergene.rb +209 -0
  107. data/lib/bio/db/litdb.rb +107 -0
  108. data/lib/bio/db/medline.rb +326 -0
  109. data/lib/bio/db/nbrf.rb +191 -0
  110. data/lib/bio/db/newick.rb +658 -0
  111. data/lib/bio/db/nexus.rb +1854 -0
  112. data/lib/bio/db/pdb.rb +29 -0
  113. data/lib/bio/db/pdb/atom.rb +77 -0
  114. data/lib/bio/db/pdb/chain.rb +210 -0
  115. data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
  116. data/lib/bio/db/pdb/model.rb +148 -0
  117. data/lib/bio/db/pdb/pdb.rb +1911 -0
  118. data/lib/bio/db/pdb/residue.rb +176 -0
  119. data/lib/bio/db/pdb/utils.rb +399 -0
  120. data/lib/bio/db/prosite.rb +597 -0
  121. data/lib/bio/db/rebase.rb +456 -0
  122. data/lib/bio/db/soft.rb +404 -0
  123. data/lib/bio/db/transfac.rb +375 -0
  124. data/lib/bio/db/url.rb +42 -0
  125. data/lib/bio/feature.rb +139 -0
  126. data/lib/bio/io/biosql/biodatabase.rb +64 -0
  127. data/lib/bio/io/biosql/bioentry.rb +29 -0
  128. data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
  129. data/lib/bio/io/biosql/bioentry_path.rb +12 -0
  130. data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
  131. data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
  132. data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
  133. data/lib/bio/io/biosql/biosequence.rb +11 -0
  134. data/lib/bio/io/biosql/comment.rb +7 -0
  135. data/lib/bio/io/biosql/config/database.yml +20 -0
  136. data/lib/bio/io/biosql/dbxref.rb +13 -0
  137. data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
  138. data/lib/bio/io/biosql/location.rb +32 -0
  139. data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
  140. data/lib/bio/io/biosql/ontology.rb +10 -0
  141. data/lib/bio/io/biosql/reference.rb +9 -0
  142. data/lib/bio/io/biosql/seqfeature.rb +32 -0
  143. data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
  144. data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
  145. data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
  146. data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
  147. data/lib/bio/io/biosql/taxon.rb +12 -0
  148. data/lib/bio/io/biosql/taxon_name.rb +9 -0
  149. data/lib/bio/io/biosql/term.rb +27 -0
  150. data/lib/bio/io/biosql/term_dbxref.rb +11 -0
  151. data/lib/bio/io/biosql/term_path.rb +12 -0
  152. data/lib/bio/io/biosql/term_relationship.rb +13 -0
  153. data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
  154. data/lib/bio/io/biosql/term_synonym.rb +10 -0
  155. data/lib/bio/io/das.rb +461 -0
  156. data/lib/bio/io/dbget.rb +194 -0
  157. data/lib/bio/io/ddbjxml.rb +638 -0
  158. data/lib/bio/io/ebisoap.rb +158 -0
  159. data/lib/bio/io/ensembl.rb +229 -0
  160. data/lib/bio/io/fastacmd.rb +163 -0
  161. data/lib/bio/io/fetch.rb +195 -0
  162. data/lib/bio/io/flatfile.rb +482 -0
  163. data/lib/bio/io/flatfile/autodetection.rb +545 -0
  164. data/lib/bio/io/flatfile/bdb.rb +253 -0
  165. data/lib/bio/io/flatfile/buffer.rb +237 -0
  166. data/lib/bio/io/flatfile/index.rb +1381 -0
  167. data/lib/bio/io/flatfile/indexer.rb +805 -0
  168. data/lib/bio/io/flatfile/splitter.rb +297 -0
  169. data/lib/bio/io/higet.rb +73 -0
  170. data/lib/bio/io/hinv.rb +442 -0
  171. data/lib/bio/io/keggapi.rb +805 -0
  172. data/lib/bio/io/ncbirest.rb +733 -0
  173. data/lib/bio/io/ncbisoap.rb +155 -0
  174. data/lib/bio/io/pubmed.rb +307 -0
  175. data/lib/bio/io/registry.rb +292 -0
  176. data/lib/bio/io/soapwsdl.rb +119 -0
  177. data/lib/bio/io/sql.rb +186 -0
  178. data/lib/bio/location.rb +867 -0
  179. data/lib/bio/map.rb +410 -0
  180. data/lib/bio/pathway.rb +960 -0
  181. data/lib/bio/reference.rb +602 -0
  182. data/lib/bio/sequence.rb +456 -0
  183. data/lib/bio/sequence/aa.rb +152 -0
  184. data/lib/bio/sequence/adapter.rb +108 -0
  185. data/lib/bio/sequence/common.rb +310 -0
  186. data/lib/bio/sequence/compat.rb +123 -0
  187. data/lib/bio/sequence/dblink.rb +54 -0
  188. data/lib/bio/sequence/format.rb +358 -0
  189. data/lib/bio/sequence/format_raw.rb +23 -0
  190. data/lib/bio/sequence/generic.rb +24 -0
  191. data/lib/bio/sequence/na.rb +491 -0
  192. data/lib/bio/shell.rb +44 -0
  193. data/lib/bio/shell/core.rb +578 -0
  194. data/lib/bio/shell/demo.rb +146 -0
  195. data/lib/bio/shell/interface.rb +218 -0
  196. data/lib/bio/shell/irb.rb +95 -0
  197. data/lib/bio/shell/object.rb +71 -0
  198. data/lib/bio/shell/plugin/blast.rb +42 -0
  199. data/lib/bio/shell/plugin/codon.rb +218 -0
  200. data/lib/bio/shell/plugin/das.rb +58 -0
  201. data/lib/bio/shell/plugin/emboss.rb +23 -0
  202. data/lib/bio/shell/plugin/entry.rb +105 -0
  203. data/lib/bio/shell/plugin/flatfile.rb +101 -0
  204. data/lib/bio/shell/plugin/keggapi.rb +181 -0
  205. data/lib/bio/shell/plugin/midi.rb +430 -0
  206. data/lib/bio/shell/plugin/obda.rb +45 -0
  207. data/lib/bio/shell/plugin/psort.rb +56 -0
  208. data/lib/bio/shell/plugin/seq.rb +247 -0
  209. data/lib/bio/shell/plugin/soap.rb +87 -0
  210. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
  211. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
  212. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
  213. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
  214. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
  215. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
  216. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  217. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  218. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  219. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
  220. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
  221. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
  222. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
  223. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
  224. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
  225. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
  226. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  227. data/lib/bio/shell/script.rb +25 -0
  228. data/lib/bio/shell/setup.rb +109 -0
  229. data/lib/bio/shell/web.rb +102 -0
  230. data/lib/bio/tree.rb +852 -0
  231. data/lib/bio/util/color_scheme.rb +191 -0
  232. data/lib/bio/util/color_scheme/buried.rb +59 -0
  233. data/lib/bio/util/color_scheme/helix.rb +59 -0
  234. data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
  235. data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
  236. data/lib/bio/util/color_scheme/strand.rb +59 -0
  237. data/lib/bio/util/color_scheme/taylor.rb +50 -0
  238. data/lib/bio/util/color_scheme/turn.rb +59 -0
  239. data/lib/bio/util/color_scheme/zappo.rb +50 -0
  240. data/lib/bio/util/contingency_table.rb +370 -0
  241. data/lib/bio/util/restriction_enzyme.rb +228 -0
  242. data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
  243. data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
  244. data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
  245. data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
  246. data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
  247. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
  248. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
  249. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
  250. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
  251. data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
  252. data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
  253. data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
  254. data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
  255. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
  256. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
  257. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
  258. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
  259. data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
  260. data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
  261. data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
  262. data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
  263. data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
  264. data/lib/bio/util/sirna.rb +288 -0
  265. data/test/data/HMMER/hmmpfam.out +64 -0
  266. data/test/data/HMMER/hmmsearch.out +88 -0
  267. data/test/data/SOSUI/sample.report +11 -0
  268. data/test/data/TMHMM/sample.report +21 -0
  269. data/test/data/aaindex/DAYM780301 +30 -0
  270. data/test/data/aaindex/PRAM900102 +20 -0
  271. data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
  272. data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
  273. data/test/data/blast/2.2.15.blastp.m7 +876 -0
  274. data/test/data/blast/b0002.faa +15 -0
  275. data/test/data/blast/b0002.faa.m0 +128 -0
  276. data/test/data/blast/b0002.faa.m7 +65 -0
  277. data/test/data/blast/b0002.faa.m8 +1 -0
  278. data/test/data/blast/blastp-multi.m7 +188 -0
  279. data/test/data/command/echoarg2.bat +1 -0
  280. data/test/data/embl/AB090716.embl +65 -0
  281. data/test/data/embl/AB090716.embl.rel89 +63 -0
  282. data/test/data/fasta/example1.txt +75 -0
  283. data/test/data/fasta/example2.txt +21 -0
  284. data/test/data/genscan/sample.report +63 -0
  285. data/test/data/iprscan/merged.raw +32 -0
  286. data/test/data/iprscan/merged.txt +74 -0
  287. data/test/data/paml/codeml/control_file.txt +30 -0
  288. data/test/data/paml/codeml/output.txt +78 -0
  289. data/test/data/paml/codeml/rates +217 -0
  290. data/test/data/prosite/prosite.dat +2233 -0
  291. data/test/data/refseq/nm_126355.entret +64 -0
  292. data/test/data/rpsblast/misc.rpsblast +193 -0
  293. data/test/data/soft/GDS100_partial.soft +92 -0
  294. data/test/data/soft/GSE3457_family_partial.soft +874 -0
  295. data/test/data/uniprot/p53_human.uniprot +1456 -0
  296. data/test/functional/bio/appl/test_pts1.rb +115 -0
  297. data/test/functional/bio/io/test_ensembl.rb +229 -0
  298. data/test/functional/bio/io/test_soapwsdl.rb +52 -0
  299. data/test/functional/bio/sequence/test_output_embl.rb +51 -0
  300. data/test/functional/bio/test_command.rb +301 -0
  301. data/test/runner.rb +14 -0
  302. data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
  303. data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
  304. data/test/unit/bio/appl/blast/test_report.rb +1135 -0
  305. data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
  306. data/test/unit/bio/appl/genscan/test_report.rb +182 -0
  307. data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
  308. data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
  309. data/test/unit/bio/appl/mafft/test_report.rb +63 -0
  310. data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
  311. data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
  312. data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
  313. data/test/unit/bio/appl/sosui/test_report.rb +81 -0
  314. data/test/unit/bio/appl/targetp/test_report.rb +146 -0
  315. data/test/unit/bio/appl/test_blast.rb +277 -0
  316. data/test/unit/bio/appl/test_fasta.rb +130 -0
  317. data/test/unit/bio/appl/test_psort.rb +57 -0
  318. data/test/unit/bio/appl/test_pts1.rb +77 -0
  319. data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
  320. data/test/unit/bio/data/test_aa.rb +90 -0
  321. data/test/unit/bio/data/test_codontable.rb +107 -0
  322. data/test/unit/bio/data/test_na.rb +80 -0
  323. data/test/unit/bio/db/embl/test_common.rb +117 -0
  324. data/test/unit/bio/db/embl/test_embl.rb +214 -0
  325. data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
  326. data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
  327. data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
  328. data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
  329. data/test/unit/bio/db/kegg/test_genes.rb +45 -0
  330. data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
  331. data/test/unit/bio/db/test_aaindex.rb +197 -0
  332. data/test/unit/bio/db/test_fasta.rb +250 -0
  333. data/test/unit/bio/db/test_gff.rb +1190 -0
  334. data/test/unit/bio/db/test_lasergene.rb +95 -0
  335. data/test/unit/bio/db/test_medline.rb +127 -0
  336. data/test/unit/bio/db/test_newick.rb +293 -0
  337. data/test/unit/bio/db/test_nexus.rb +364 -0
  338. data/test/unit/bio/db/test_prosite.rb +1437 -0
  339. data/test/unit/bio/db/test_rebase.rb +101 -0
  340. data/test/unit/bio/db/test_soft.rb +138 -0
  341. data/test/unit/bio/db/test_url.rb +36 -0
  342. data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
  343. data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
  344. data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
  345. data/test/unit/bio/io/test_ddbjxml.rb +80 -0
  346. data/test/unit/bio/io/test_ensembl.rb +109 -0
  347. data/test/unit/bio/io/test_fastacmd.rb +42 -0
  348. data/test/unit/bio/io/test_flatfile.rb +505 -0
  349. data/test/unit/bio/io/test_soapwsdl.rb +32 -0
  350. data/test/unit/bio/sequence/test_aa.rb +115 -0
  351. data/test/unit/bio/sequence/test_common.rb +373 -0
  352. data/test/unit/bio/sequence/test_compat.rb +69 -0
  353. data/test/unit/bio/sequence/test_dblink.rb +58 -0
  354. data/test/unit/bio/sequence/test_na.rb +330 -0
  355. data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
  356. data/test/unit/bio/test_alignment.rb +1025 -0
  357. data/test/unit/bio/test_command.rb +349 -0
  358. data/test/unit/bio/test_db.rb +96 -0
  359. data/test/unit/bio/test_feature.rb +144 -0
  360. data/test/unit/bio/test_location.rb +599 -0
  361. data/test/unit/bio/test_map.rb +230 -0
  362. data/test/unit/bio/test_pathway.rb +499 -0
  363. data/test/unit/bio/test_reference.rb +252 -0
  364. data/test/unit/bio/test_sequence.rb +329 -0
  365. data/test/unit/bio/test_shell.rb +18 -0
  366. data/test/unit/bio/test_tree.rb +593 -0
  367. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
  368. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
  369. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
  370. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
  371. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
  372. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
  373. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
  374. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
  375. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
  376. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
  377. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
  378. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
  379. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
  380. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
  381. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
  382. data/test/unit/bio/util/test_color_scheme.rb +33 -0
  383. data/test/unit/bio/util/test_contingency_table.rb +94 -0
  384. data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
  385. data/test/unit/bio/util/test_sirna.rb +245 -0
  386. metadata +543 -0

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the gem file manually.