sequenceserver 2.0.0.rc7 → 2.0.0.rc8

Sign up to get free protection for your applications and to get access to all the features.
Files changed (530) hide show
  1. checksums.yaml +4 -4
  2. data/bin/chromedriver +0 -0
  3. data/bin/geckodriver +0 -0
  4. data/bin/sequenceserver +31 -4
  5. data/lib/sequenceserver.rb +6 -1
  6. data/lib/sequenceserver/database.rb +7 -42
  7. data/lib/sequenceserver/exceptions.rb +14 -0
  8. data/lib/sequenceserver/makeblastdb.rb +121 -41
  9. data/lib/sequenceserver/routes.rb +1 -1
  10. data/lib/sequenceserver/version.rb +1 -1
  11. data/public/css/sequenceserver.css +8 -2
  12. data/public/css/sequenceserver.min.css +1 -1
  13. data/public/js/jquery_world.js +1 -1
  14. data/public/js/report.js +1 -2
  15. data/public/js/search.js +40 -18
  16. data/public/js/sidebar.js +50 -26
  17. data/public/sequenceserver-report.min.js +17 -17
  18. data/public/sequenceserver-search.min.js +2 -2
  19. data/views/layout.erb +1 -1
  20. data/views/report.erb +1 -1
  21. data/views/search.erb +1 -1
  22. metadata +4 -510
  23. data/.bootstrap/config.json +0 -433
  24. data/.codeclimate.yml +0 -31
  25. data/.csslintrc +0 -2
  26. data/.dockerignore +0 -1
  27. data/.eslintignore +0 -1
  28. data/.eslintrc.json +0 -36
  29. data/.gitignore +0 -56
  30. data/.mailmap +0 -5
  31. data/.rspec +0 -3
  32. data/.rubocop.yml +0 -61
  33. data/.travis.yml +0 -74
  34. data/AppImage/recipe.yml +0 -15
  35. data/AppImage/sequenceserver.desktop +0 -8
  36. data/AppImage/sequenceserver.png +0 -0
  37. data/AppImage/sequenceserver.sh +0 -16
  38. data/Dockerfile +0 -25
  39. data/LICENSE.txt +0 -661
  40. data/LICENSE/Apache.txt +0 -176
  41. data/LICENSE/d3.txt +0 -26
  42. data/README.md +0 -161
  43. data/package.json +0 -48
  44. data/public/vendor/.dependencies.json +0 -18
  45. data/public/vendor/.loaderversions +0 -1
  46. data/public/vendor/github/components/jquery@2.1.4/.gitignore +0 -1
  47. data/public/vendor/github/components/jquery@2.1.4/.jspm-hash +0 -1
  48. data/public/vendor/github/components/jquery@2.1.4/.jspm.json +0 -37
  49. data/public/vendor/github/components/jqueryui@1.11.4/.gitignore +0 -4
  50. data/public/vendor/github/components/jqueryui@1.11.4/.jspm-hash +0 -1
  51. data/public/vendor/github/components/jqueryui@1.11.4/.jspm.json +0 -136
  52. data/public/vendor/github/components/jqueryui@1.11.4/ui/.jshintrc +0 -24
  53. data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm-hash +0 -1
  54. data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm.json +0 -10
  55. data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm-hash +0 -1
  56. data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm.json +0 -10
  57. data/public/vendor/github/jspm/nodelibs-fs@0.1.2/.jspm-hash +0 -1
  58. data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm-hash +0 -1
  59. data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm.json +0 -3
  60. data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm-hash +0 -1
  61. data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm.json +0 -10
  62. data/public/vendor/github/jspm/nodelibs-process@0.1.1/.jspm-hash +0 -1
  63. data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm-hash +0 -1
  64. data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm.json +0 -10
  65. data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm-hash +0 -1
  66. data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm.json +0 -10
  67. data/public/vendor/github/mbostock/d3@3.5.6/.jspm-hash +0 -1
  68. data/public/vendor/github/mbostock/d3@3.5.6/.jspm.json +0 -76
  69. data/public/vendor/github/nicgirault/circosJs@1.7.0/.gitignore +0 -10
  70. data/public/vendor/github/nicgirault/circosJs@1.7.0/.jspm-hash +0 -1
  71. data/public/vendor/github/systemjs/plugin-css@0.1.15/.gitignore +0 -1
  72. data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm-hash +0 -1
  73. data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm.json +0 -4
  74. data/public/vendor/github/systemjs/plugin-json@0.1.0/.jspm-hash +0 -1
  75. data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm-hash +0 -1
  76. data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm.json +0 -100
  77. data/public/vendor/npm/amdefine@1.0.0/.jspm-hash +0 -1
  78. data/public/vendor/npm/amdefine@1.0.0/.jspm.json +0 -55
  79. data/public/vendor/npm/babel-core@5.8.23/.jspm-hash +0 -1
  80. data/public/vendor/npm/babel-runtime@5.8.20/.jspm-hash +0 -1
  81. data/public/vendor/npm/babel-runtime@5.8.20/.npmignore +0 -2
  82. data/public/vendor/npm/base62@0.1.1/.jspm-hash +0 -1
  83. data/public/vendor/npm/base62@0.1.1/.jspm.json +0 -49
  84. data/public/vendor/npm/base62@0.1.1/.travis.yml +0 -4
  85. data/public/vendor/npm/base64-js@0.0.8/.jspm-hash +0 -1
  86. data/public/vendor/npm/base64-js@0.0.8/.jspm.json +0 -77
  87. data/public/vendor/npm/base64-js@0.0.8/.travis.yml +0 -5
  88. data/public/vendor/npm/buffer@3.4.3/.jspm-hash +0 -1
  89. data/public/vendor/npm/buffer@3.4.3/.jspm.json +0 -105
  90. data/public/vendor/npm/buffer@3.4.3/.npmignore +0 -1
  91. data/public/vendor/npm/buffer@3.4.3/.travis.yml +0 -8
  92. data/public/vendor/npm/buffer@3.4.3/.zuul.yml +0 -20
  93. data/public/vendor/npm/core-js@1.1.2/.eslintrc +0 -36
  94. data/public/vendor/npm/core-js@1.1.2/.gitattributes +0 -1
  95. data/public/vendor/npm/core-js@1.1.2/.jspm-hash +0 -1
  96. data/public/vendor/npm/core-js@1.1.2/.npmignore +0 -10
  97. data/public/vendor/npm/core-js@1.1.2/.travis.yml +0 -3
  98. data/public/vendor/npm/core-util-is@1.0.1/.jspm-hash +0 -1
  99. data/public/vendor/npm/core-util-is@1.0.1/.jspm.json +0 -58
  100. data/public/vendor/npm/envify@3.4.0/.jspm-hash +0 -1
  101. data/public/vendor/npm/envify@3.4.0/.jspm.json +0 -72
  102. data/public/vendor/npm/envify@3.4.0/.npmignore +0 -2
  103. data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm-hash +0 -1
  104. data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm.json +0 -102
  105. data/public/vendor/npm/events@1.0.2/.jspm-hash +0 -1
  106. data/public/vendor/npm/events@1.0.2/.jspm.json +0 -67
  107. data/public/vendor/npm/events@1.0.2/.npmignore +0 -1
  108. data/public/vendor/npm/events@1.0.2/.travis.yml +0 -7
  109. data/public/vendor/npm/events@1.0.2/.zuul.yml +0 -12
  110. data/public/vendor/npm/font-awesome@4.4.0/.jspm-hash +0 -1
  111. data/public/vendor/npm/font-awesome@4.4.0/.jspm.json +0 -81
  112. data/public/vendor/npm/font-awesome@4.4.0/.npmignore +0 -42
  113. data/public/vendor/npm/ieee754@1.1.6/.jspm-hash +0 -1
  114. data/public/vendor/npm/ieee754@1.1.6/.jspm.json +0 -70
  115. data/public/vendor/npm/ieee754@1.1.6/.travis.yml +0 -7
  116. data/public/vendor/npm/ieee754@1.1.6/.zuul.yml +0 -20
  117. data/public/vendor/npm/inherits@2.0.1/.jspm-hash +0 -1
  118. data/public/vendor/npm/inherits@2.0.1/.jspm.json +0 -60
  119. data/public/vendor/npm/is-array@1.0.1/.jepso-ci.json +0 -3
  120. data/public/vendor/npm/is-array@1.0.1/.jspm-hash +0 -1
  121. data/public/vendor/npm/is-array@1.0.1/.jspm.json +0 -42
  122. data/public/vendor/npm/is-array@1.0.1/.npmignore +0 -0
  123. data/public/vendor/npm/isarray@0.0.1/.jspm-hash +0 -1
  124. data/public/vendor/npm/isarray@0.0.1/.jspm.json +0 -51
  125. data/public/vendor/npm/jstransform@10.1.0/.jshintrc +0 -28
  126. data/public/vendor/npm/jstransform@10.1.0/.jspm-hash +0 -1
  127. data/public/vendor/npm/jstransform@10.1.0/.jspm.json +0 -95
  128. data/public/vendor/npm/jstransform@10.1.0/.npmignore +0 -4
  129. data/public/vendor/npm/jstransform@10.1.0/.travis.yml +0 -8
  130. data/public/vendor/npm/path-browserify@0.0.0/.jspm-hash +0 -1
  131. data/public/vendor/npm/path-browserify@0.0.0/.jspm.json +0 -56
  132. data/public/vendor/npm/process@0.10.1/.jspm-hash +0 -1
  133. data/public/vendor/npm/react@0.13.3/.jspm-hash +0 -1
  134. data/public/vendor/npm/react@0.13.3/.jspm.json +0 -77
  135. data/public/vendor/npm/readable-stream@1.1.13/.jspm-hash +0 -1
  136. data/public/vendor/npm/readable-stream@1.1.13/.jspm.json +0 -95
  137. data/public/vendor/npm/readable-stream@1.1.13/.npmignore +0 -5
  138. data/public/vendor/npm/source-map@0.1.31/.jspm-hash +0 -1
  139. data/public/vendor/npm/source-map@0.1.31/.jspm.json +0 -133
  140. data/public/vendor/npm/source-map@0.1.31/.npmignore +0 -2
  141. data/public/vendor/npm/source-map@0.1.31/.travis.yml +0 -4
  142. data/public/vendor/npm/stream-browserify@1.0.0/.jspm-hash +0 -1
  143. data/public/vendor/npm/stream-browserify@1.0.0/.jspm.json +0 -77
  144. data/public/vendor/npm/stream-browserify@1.0.0/.travis.yml +0 -4
  145. data/public/vendor/npm/string_decoder@0.10.31/.jspm-hash +0 -1
  146. data/public/vendor/npm/string_decoder@0.10.31/.jspm.json +0 -58
  147. data/public/vendor/npm/string_decoder@0.10.31/.npmignore +0 -2
  148. data/public/vendor/npm/through@2.3.8/.jspm-hash +0 -1
  149. data/public/vendor/npm/through@2.3.8/.jspm.json +0 -72
  150. data/public/vendor/npm/through@2.3.8/.travis.yml +0 -5
  151. data/public/vendor/npm/underscore@1.8.3/.jspm-hash +0 -1
  152. data/public/vendor/npm/underscore@1.8.3/.jspm.json +0 -74
  153. data/public/vendor/npm/util@0.10.3/.jspm-hash +0 -1
  154. data/public/vendor/npm/util@0.10.3/.jspm.json +0 -58
  155. data/public/vendor/npm/util@0.10.3/.npmignore +0 -1
  156. data/public/vendor/npm/util@0.10.3/.travis.yml +0 -8
  157. data/public/vendor/npm/util@0.10.3/.zuul.yml +0 -10
  158. data/public/vendor/npm/webshim@1.15.8/.gitattributes +0 -12
  159. data/public/vendor/npm/webshim@1.15.8/.jspm-hash +0 -1
  160. data/public/vendor/npm/webshim@1.15.8/.jspm.json +0 -92
  161. data/public/vendor/npm/webshim@1.15.8/.npmignore +0 -16
  162. data/public/vendor/npm/webshim@1.15.8/.project +0 -12
  163. data/public/vendor/npm/webshim@1.15.8/demos/demos/filereader/upload/.keep +0 -0
  164. data/sequenceserver.gemspec +0 -55
  165. data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +0 -228
  166. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +0 -583
  167. data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +0 -228
  168. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +0 -587
  169. data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +0 -229
  170. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +0 -587
  171. data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +0 -228
  172. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +0 -588
  173. data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +0 -228
  174. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +0 -587
  175. data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +0 -228
  176. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +0 -587
  177. data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +0 -228
  178. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +0 -587
  179. data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +0 -228
  180. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +0 -587
  181. data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +0 -228
  182. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +0 -585
  183. data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +0 -176
  184. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +0 -237
  185. data/spec/capybara_spec.rb +0 -345
  186. data/spec/config_spec.rb +0 -87
  187. data/spec/database/funky_ids/funky_ids.fa +0 -16
  188. data/spec/database/funky_ids/v4/funky_ids.fa.nhd +0 -8
  189. data/spec/database/funky_ids/v4/funky_ids.fa.nhi +0 -0
  190. data/spec/database/funky_ids/v4/funky_ids.fa.nhr +0 -0
  191. data/spec/database/funky_ids/v4/funky_ids.fa.nin +0 -0
  192. data/spec/database/funky_ids/v4/funky_ids.fa.nog +0 -0
  193. data/spec/database/funky_ids/v4/funky_ids.fa.nsd +0 -15
  194. data/spec/database/funky_ids/v4/funky_ids.fa.nsi +0 -0
  195. data/spec/database/funky_ids/v4/funky_ids.fa.nsq +0 -0
  196. data/spec/database/funky_ids/v5/funky_ids.fa.ndb +0 -0
  197. data/spec/database/funky_ids/v5/funky_ids.fa.nhd +0 -8
  198. data/spec/database/funky_ids/v5/funky_ids.fa.nhi +0 -0
  199. data/spec/database/funky_ids/v5/funky_ids.fa.nhr +0 -0
  200. data/spec/database/funky_ids/v5/funky_ids.fa.nin +0 -0
  201. data/spec/database/funky_ids/v5/funky_ids.fa.nog +0 -0
  202. data/spec/database/funky_ids/v5/funky_ids.fa.nos +0 -0
  203. data/spec/database/funky_ids/v5/funky_ids.fa.not +0 -0
  204. data/spec/database/funky_ids/v5/funky_ids.fa.nsq +0 -0
  205. data/spec/database/funky_ids/v5/funky_ids.fa.ntf +0 -0
  206. data/spec/database/funky_ids/v5/funky_ids.fa.nto +0 -0
  207. data/spec/database/funky_sequences/README.md +0 -14
  208. data/spec/database/funky_sequences/funky_aa_sequences.fa +0 -7
  209. data/spec/database/funky_sequences/funky_aa_sequences.fa.phd +0 -3
  210. data/spec/database/funky_sequences/funky_aa_sequences.fa.phi +0 -0
  211. data/spec/database/funky_sequences/funky_aa_sequences.fa.phr +0 -0
  212. data/spec/database/funky_sequences/funky_aa_sequences.fa.pin +0 -0
  213. data/spec/database/funky_sequences/funky_aa_sequences.fa.pog +0 -0
  214. data/spec/database/funky_sequences/funky_aa_sequences.fa.psd +0 -6
  215. data/spec/database/funky_sequences/funky_aa_sequences.fa.psi +0 -0
  216. data/spec/database/funky_sequences/funky_aa_sequences.fa.psq +0 -0
  217. data/spec/database/funky_sequences/funky_na_sequences.fa +0 -2
  218. data/spec/database/funky_sequences/funky_na_sequences.fa.nhr +0 -0
  219. data/spec/database/funky_sequences/funky_na_sequences.fa.nin +0 -0
  220. data/spec/database/funky_sequences/funky_na_sequences.fa.nog +0 -0
  221. data/spec/database/funky_sequences/funky_na_sequences.fa.nsd +0 -2
  222. data/spec/database/funky_sequences/funky_na_sequences.fa.nsi +0 -0
  223. data/spec/database/funky_sequences/funky_na_sequences.fa.nsq +0 -0
  224. data/spec/database/ox_parse_error/query.fa +0 -1
  225. data/spec/database/ox_parse_error/rand1.fa +0 -2
  226. data/spec/database/ox_parse_error/rand1.fa.nhd +0 -1
  227. data/spec/database/ox_parse_error/rand1.fa.nhi +0 -0
  228. data/spec/database/ox_parse_error/rand1.fa.nhr +0 -0
  229. data/spec/database/ox_parse_error/rand1.fa.nin +0 -0
  230. data/spec/database/ox_parse_error/rand1.fa.nog +0 -0
  231. data/spec/database/ox_parse_error/rand1.fa.nsd +0 -2
  232. data/spec/database/ox_parse_error/rand1.fa.nsi +0 -0
  233. data/spec/database/ox_parse_error/rand1.fa.nsq +0 -0
  234. data/spec/database/ox_parse_error/rand2.fa +0 -2
  235. data/spec/database/ox_parse_error/rand2.fa.nhd +0 -1
  236. data/spec/database/ox_parse_error/rand2.fa.nhi +0 -0
  237. data/spec/database/ox_parse_error/rand2.fa.nhr +0 -0
  238. data/spec/database/ox_parse_error/rand2.fa.nin +0 -0
  239. data/spec/database/ox_parse_error/rand2.fa.nog +0 -0
  240. data/spec/database/ox_parse_error/rand2.fa.nsd +0 -2
  241. data/spec/database/ox_parse_error/rand2.fa.nsi +0 -0
  242. data/spec/database/ox_parse_error/rand2.fa.nsq +0 -0
  243. data/spec/database/ox_parse_error_unique_ids/query.fa +0 -1
  244. data/spec/database/ox_parse_error_unique_ids/rand1.fa +0 -2
  245. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhd +0 -1
  246. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhi +0 -0
  247. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhr +0 -0
  248. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nin +0 -0
  249. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nog +0 -0
  250. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsd +0 -2
  251. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsi +0 -0
  252. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsq +0 -0
  253. data/spec/database/ox_parse_error_unique_ids/rand2.fa +0 -2
  254. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhd +0 -1
  255. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhi +0 -0
  256. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhr +0 -0
  257. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nin +0 -0
  258. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nog +0 -0
  259. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsd +0 -2
  260. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsi +0 -0
  261. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsq +0 -0
  262. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa +0 -6
  263. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhd +0 -1
  264. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhi +0 -0
  265. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhr +0 -0
  266. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nin +0 -0
  267. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nog +0 -0
  268. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsd +0 -2
  269. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsi +0 -0
  270. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsq +0 -0
  271. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ndb +0 -0
  272. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +0 -8
  273. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  274. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  275. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  276. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  277. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nos +0 -0
  278. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.not +0 -0
  279. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  280. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ntf +0 -0
  281. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nto +0 -0
  282. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
  283. data/spec/database/sample/links.rb +0 -23
  284. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
  285. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pdb +0 -0
  286. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
  287. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
  288. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  289. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  290. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  291. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pos +0 -0
  292. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pot +0 -0
  293. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  294. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.ptf +0 -0
  295. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pto +0 -0
  296. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pdb +0 -0
  297. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +0 -9140
  298. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
  299. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  300. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  301. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
  302. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pos +0 -0
  303. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pot +0 -0
  304. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
  305. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.ptf +0 -0
  306. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pto +0 -0
  307. data/spec/database/sample/proteins/uniprot/URL +0 -1
  308. data/spec/database/sample/si_uniprot_idmap.yml +0 -14180
  309. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +0 -5486
  310. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ndb +0 -0
  311. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +0 -473
  312. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
  313. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  314. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  315. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  316. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nos +0 -0
  317. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.not +0 -0
  318. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  319. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ntf +0 -0
  320. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nto +0 -0
  321. data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +0 -148303
  322. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +0 -8
  323. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  324. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  325. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  326. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  327. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +0 -16
  328. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
  329. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  330. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
  331. data/spec/database/v4/links.rb +0 -23
  332. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
  333. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
  334. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
  335. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  336. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  337. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  338. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +0 -2378
  339. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  340. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  341. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +0 -9140
  342. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
  343. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  344. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  345. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
  346. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd +0 -18280
  347. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
  348. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
  349. data/spec/database/v4/proteins/uniprot/URL +0 -1
  350. data/spec/database/v4/si_uniprot_idmap.yml +0 -14180
  351. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +0 -5486
  352. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +0 -473
  353. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
  354. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  355. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  356. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  357. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +0 -946
  358. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  359. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  360. data/spec/database/without_parse_seqids/without_parse_seqids.fa +0 -10
  361. data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
  362. data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
  363. data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
  364. data/spec/database_spec.rb +0 -51
  365. data/spec/doctor_spec.disabled.rb +0 -107
  366. data/spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml +0 -1201
  367. data/spec/dotdir/blast_2.2.30/blastn/job.yaml +0 -8
  368. data/spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml +0 -866
  369. data/spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml +0 -8
  370. data/spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml +0 -1181
  371. data/spec/dotdir/blast_2.2.30/blastp/job.yaml +0 -8
  372. data/spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml +0 -1181
  373. data/spec/dotdir/blast_2.2.30/blastx/job.yaml +0 -8
  374. data/spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml +0 -1181
  375. data/spec/dotdir/blast_2.2.30/tblastn/job.yaml +0 -8
  376. data/spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml +0 -8857
  377. data/spec/dotdir/blast_2.2.30/tblastx/job.yaml +0 -8
  378. data/spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml +0 -1201
  379. data/spec/dotdir/blast_2.2.31/blastn/job.yaml +0 -8
  380. data/spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml +0 -866
  381. data/spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml +0 -8
  382. data/spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml +0 -1181
  383. data/spec/dotdir/blast_2.2.31/blastp/job.yaml +0 -8
  384. data/spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml +0 -1181
  385. data/spec/dotdir/blast_2.2.31/blastx/job.yaml +0 -8
  386. data/spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml +0 -1181
  387. data/spec/dotdir/blast_2.2.31/tblastn/job.yaml +0 -8
  388. data/spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml +0 -8857
  389. data/spec/dotdir/blast_2.2.31/tblastx/job.yaml +0 -8
  390. data/spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml +0 -1201
  391. data/spec/dotdir/blast_2.3.0/blastn/job.yaml +0 -8
  392. data/spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml +0 -866
  393. data/spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml +0 -8
  394. data/spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml +0 -1181
  395. data/spec/dotdir/blast_2.3.0/blastp/job.yaml +0 -8
  396. data/spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml +0 -1181
  397. data/spec/dotdir/blast_2.3.0/blastx/job.yaml +0 -8
  398. data/spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml +0 -1181
  399. data/spec/dotdir/blast_2.3.0/tblastn/job.yaml +0 -8
  400. data/spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml +0 -8857
  401. data/spec/dotdir/blast_2.3.0/tblastx/job.yaml +0 -8
  402. data/spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml +0 -1201
  403. data/spec/dotdir/blast_2.4.0/blastn/job.yaml +0 -8
  404. data/spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml +0 -866
  405. data/spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml +0 -8
  406. data/spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml +0 -1181
  407. data/spec/dotdir/blast_2.4.0/blastp/job.yaml +0 -8
  408. data/spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml +0 -1181
  409. data/spec/dotdir/blast_2.4.0/blastx/job.yaml +0 -8
  410. data/spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml +0 -1181
  411. data/spec/dotdir/blast_2.4.0/tblastn/job.yaml +0 -8
  412. data/spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml +0 -8857
  413. data/spec/dotdir/blast_2.4.0/tblastx/job.yaml +0 -8
  414. data/spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml +0 -1201
  415. data/spec/dotdir/blast_2.5.0/blastn/job.yaml +0 -8
  416. data/spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml +0 -866
  417. data/spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml +0 -8
  418. data/spec/dotdir/blast_2.5.0/blastp/BLASTP +0 -2161
  419. data/spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml +0 -1181
  420. data/spec/dotdir/blast_2.5.0/blastp/job.yaml +0 -8
  421. data/spec/dotdir/blast_2.5.0/blastx/BLASTX +0 -28080
  422. data/spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml +0 -1181
  423. data/spec/dotdir/blast_2.5.0/blastx/job.yaml +0 -8
  424. data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN +0 -29486
  425. data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml +0 -1181
  426. data/spec/dotdir/blast_2.5.0/tblastn/job.yaml +0 -8
  427. data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX +0 -180859
  428. data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml +0 -8857
  429. data/spec/dotdir/blast_2.5.0/tblastx/job.yaml +0 -8
  430. data/spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml +0 -1201
  431. data/spec/dotdir/blast_2.6.0/blastn/job.yaml +0 -8
  432. data/spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml +0 -866
  433. data/spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml +0 -8
  434. data/spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml +0 -1181
  435. data/spec/dotdir/blast_2.6.0/blastp/job.yaml +0 -8
  436. data/spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml +0 -1181
  437. data/spec/dotdir/blast_2.6.0/blastx/job.yaml +0 -8
  438. data/spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml +0 -1181
  439. data/spec/dotdir/blast_2.6.0/tblastn/job.yaml +0 -8
  440. data/spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml +0 -8857
  441. data/spec/dotdir/blast_2.6.0/tblastx/job.yaml +0 -8
  442. data/spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml +0 -1201
  443. data/spec/dotdir/blast_2.7.1/blastn/job.yaml +0 -8
  444. data/spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml +0 -866
  445. data/spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml +0 -8
  446. data/spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml +0 -1181
  447. data/spec/dotdir/blast_2.7.1/blastp/job.yaml +0 -8
  448. data/spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml +0 -1181
  449. data/spec/dotdir/blast_2.7.1/blastx/job.yaml +0 -8
  450. data/spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml +0 -1181
  451. data/spec/dotdir/blast_2.7.1/tblastn/job.yaml +0 -8
  452. data/spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml +0 -8857
  453. data/spec/dotdir/blast_2.7.1/tblastx/job.yaml +0 -8
  454. data/spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml +0 -1201
  455. data/spec/dotdir/blast_2.8.1/blastn/job.yaml +0 -8
  456. data/spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml +0 -866
  457. data/spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml +0 -8
  458. data/spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml +0 -1181
  459. data/spec/dotdir/blast_2.8.1/blastp/job.yaml +0 -8
  460. data/spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml +0 -1181
  461. data/spec/dotdir/blast_2.8.1/blastx/job.yaml +0 -8
  462. data/spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml +0 -1181
  463. data/spec/dotdir/blast_2.8.1/tblastn/job.yaml +0 -8
  464. data/spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml +0 -8857
  465. data/spec/dotdir/blast_2.8.1/tblastx/job.yaml +0 -8
  466. data/spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml +0 -1201
  467. data/spec/dotdir/blast_2.9.0/blastn/job.yaml +0 -8
  468. data/spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml +0 -866
  469. data/spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml +0 -8
  470. data/spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml +0 -1181
  471. data/spec/dotdir/blast_2.9.0/blastp/job.yaml +0 -8
  472. data/spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml +0 -1181
  473. data/spec/dotdir/blast_2.9.0/blastx/job.yaml +0 -8
  474. data/spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml +0 -1181
  475. data/spec/dotdir/blast_2.9.0/tblastn/job.yaml +0 -8
  476. data/spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml +0 -8857
  477. data/spec/dotdir/blast_2.9.0/tblastx/job.yaml +0 -8
  478. data/spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml +0 -1040
  479. data/spec/dotdir/diamond_0.9.24/blastp/job.yaml +0 -8
  480. data/spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml +0 -1040
  481. data/spec/dotdir/diamond_0.9.24/blastx/job.yaml +0 -8
  482. data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml +0 -41
  483. data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml +0 -8
  484. data/spec/download_helper.rb +0 -35
  485. data/spec/empty_config.yml +0 -0
  486. data/spec/makeblastdb_spec.rb +0 -121
  487. data/spec/routes_spec.rb +0 -93
  488. data/spec/sample.conf +0 -2
  489. data/spec/sequence_spec.rb +0 -99
  490. data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt +0 -6
  491. data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt +0 -6
  492. data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt +0 -30
  493. data/spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt +0 -6
  494. data/spec/sequences/Nucleotide_TP53_COX41.fasta +0 -15
  495. data/spec/sequences/Protein_TP53_COX41.fasta +0 -12
  496. data/spec/sequences/Query_1_SI2_2_0_06267.txt +0 -6
  497. data/spec/sequences/alignment-2_hits.txt +0 -12
  498. data/spec/sequences/alignment-35_hits_diamond_blastp.txt +0 -210
  499. data/spec/sequences/alignment-35_hits_diamond_blastx.txt +0 -210
  500. data/spec/sequences/alignment-3_hits.txt +0 -18
  501. data/spec/sequences/alignment-40_hits_blastn.txt +0 -246
  502. data/spec/sequences/alignment-40_hits_blastp.txt +0 -240
  503. data/spec/sequences/alignment-40_hits_blastp_2.2.30.txt +0 -240
  504. data/spec/sequences/alignment-40_hits_blastx.txt +0 -240
  505. data/spec/sequences/alignment-40_hits_tblastn.txt +0 -240
  506. data/spec/sequences/alignment-40_hits_tblastn_2.2.30.txt +0 -240
  507. data/spec/sequences/alignment-40_hits_tblastx.txt +0 -2664
  508. data/spec/sequences/alignment-4_hits.txt +0 -24
  509. data/spec/sequences/alignment-4_hits_blastn.txt +0 -24
  510. data/spec/sequences/alignment-4_hits_blastp.txt +0 -24
  511. data/spec/sequences/alignment-4_hits_blastp_2.2.30.txt +0 -24
  512. data/spec/sequences/alignment-4_hits_blastx.txt +0 -24
  513. data/spec/sequences/alignment-4_hits_diamond_blastp.txt +0 -24
  514. data/spec/sequences/alignment-4_hits_diamond_blastx.txt +0 -24
  515. data/spec/sequences/alignment-4_hits_tblastn.txt +0 -24
  516. data/spec/sequences/alignment-4_hits_tblastn_2.2.30.txt +0 -24
  517. data/spec/sequences/alignment-4_hits_tblastx.txt +0 -318
  518. data/spec/sequences/nucleotide_query.fa +0 -21
  519. data/spec/sequences/problematic_query.fa +0 -5
  520. data/spec/sequences/protein_query.fa +0 -9
  521. data/spec/sequences/sample_query_fire_ant_obps.fa +0 -44
  522. data/spec/sequences/sequenceserver-2_hits.fa +0 -10
  523. data/spec/sequences/sequenceserver-SI2.2.0_06267.fa +0 -5
  524. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt +0 -6
  525. data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt +0 -6
  526. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt +0 -6
  527. data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt +0 -6
  528. data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt +0 -6
  529. data/spec/sequenceserver_spec.rb +0 -90
  530. data/spec/spec_helper.rb +0 -63

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.