bio-ucsc-api 0.3.1 → 0.4.0

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Files changed (547) hide show
  1. data/Gemfile +4 -3
  2. data/Gemfile.lock +31 -20
  3. data/README.md +224 -0
  4. data/Rakefile +5 -8
  5. data/VERSION +1 -1
  6. data/bio-ucsc-api.gemspec +39 -122
  7. data/lib/bio-ucsc.rb +10 -5
  8. data/lib/bio-ucsc/ailmel1.rb +5 -3
  9. data/lib/bio-ucsc/anocar2.rb +7 -6
  10. data/lib/bio-ucsc/anogam1.rb +7 -5
  11. data/lib/bio-ucsc/anogam1/chaindm3.rb +11 -8
  12. data/lib/bio-ucsc/anogam1/chaindm3link.rb +11 -8
  13. data/lib/bio-ucsc/anogam1/est.rb +11 -8
  14. data/lib/bio-ucsc/anogam1/gap.rb +11 -8
  15. data/lib/bio-ucsc/anogam1/gold.rb +11 -8
  16. data/lib/bio-ucsc/anogam1/intronest.rb +11 -8
  17. data/lib/bio-ucsc/anogam1/mrna.rb +11 -8
  18. data/lib/bio-ucsc/anogam1/rmsk.rb +10 -7
  19. data/lib/bio-ucsc/apimel2.rb +5 -3
  20. data/lib/bio-ucsc/apimel2/chaindm2.rb +11 -8
  21. data/lib/bio-ucsc/apimel2/chaindm2link.rb +11 -8
  22. data/lib/bio-ucsc/aplcal1.rb +5 -3
  23. data/lib/bio-ucsc/aplcal1/chaincaepb1.rb +11 -8
  24. data/lib/bio-ucsc/aplcal1/chaincaepb1link.rb +11 -8
  25. data/lib/bio-ucsc/aplcal1/chaincaerem2.rb +11 -8
  26. data/lib/bio-ucsc/aplcal1/chaincaerem2link.rb +11 -8
  27. data/lib/bio-ucsc/aplcal1/chaincb3.rb +11 -8
  28. data/lib/bio-ucsc/aplcal1/chaincb3link.rb +11 -8
  29. data/lib/bio-ucsc/aplcal1/chaince6.rb +11 -8
  30. data/lib/bio-ucsc/aplcal1/chaince6link.rb +11 -8
  31. data/lib/bio-ucsc/aplcal1/gap.rb +11 -8
  32. data/lib/bio-ucsc/aplcal1/gold.rb +11 -8
  33. data/lib/bio-ucsc/aplcal1/rmsk.rb +10 -7
  34. data/lib/bio-ucsc/bostau4.rb +5 -3
  35. data/lib/bio-ucsc/braflo1.rb +5 -3
  36. data/lib/bio-ucsc/braflo1/chaingalgal3.rb +11 -8
  37. data/lib/bio-ucsc/braflo1/chaingalgal3link.rb +11 -8
  38. data/lib/bio-ucsc/braflo1/chainhg18.rb +11 -8
  39. data/lib/bio-ucsc/braflo1/chainhg18link.rb +11 -8
  40. data/lib/bio-ucsc/braflo1/chainmm9.rb +11 -8
  41. data/lib/bio-ucsc/braflo1/chainmm9link.rb +11 -8
  42. data/lib/bio-ucsc/braflo1/chainpetmar1.rb +11 -8
  43. data/lib/bio-ucsc/braflo1/chainpetmar1link.rb +11 -8
  44. data/lib/bio-ucsc/braflo1/gap.rb +11 -8
  45. data/lib/bio-ucsc/braflo1/gold.rb +11 -8
  46. data/lib/bio-ucsc/caejap1.rb +5 -3
  47. data/lib/bio-ucsc/caejap1/chaince6.rb +11 -8
  48. data/lib/bio-ucsc/caejap1/chaince6link.rb +11 -8
  49. data/lib/bio-ucsc/caejap1/gap.rb +11 -8
  50. data/lib/bio-ucsc/caejap1/gold.rb +11 -8
  51. data/lib/bio-ucsc/caepb2.rb +6 -4
  52. data/lib/bio-ucsc/caepb2/chaince6.rb +11 -8
  53. data/lib/bio-ucsc/caepb2/chaince6link.rb +11 -8
  54. data/lib/bio-ucsc/caepb2/gap.rb +11 -8
  55. data/lib/bio-ucsc/caepb2/gold.rb +11 -8
  56. data/lib/bio-ucsc/caerem3.rb +5 -3
  57. data/lib/bio-ucsc/caerem3/chaince6.rb +11 -8
  58. data/lib/bio-ucsc/caerem3/chaince6link.rb +11 -8
  59. data/lib/bio-ucsc/caerem3/gap.rb +11 -8
  60. data/lib/bio-ucsc/caerem3/gold.rb +11 -8
  61. data/lib/bio-ucsc/caljac3.rb +7 -4
  62. data/lib/bio-ucsc/canfam2.rb +5 -3
  63. data/lib/bio-ucsc/canfam2/chainbostau4.rb +11 -8
  64. data/lib/bio-ucsc/canfam2/chainbostau4link.rb +11 -8
  65. data/lib/bio-ucsc/canfam2/chainmm9.rb +11 -8
  66. data/lib/bio-ucsc/canfam2/chainmm9link.rb +11 -8
  67. data/lib/bio-ucsc/canfam2/chainrn4.rb +11 -8
  68. data/lib/bio-ucsc/canfam2/chainrn4link.rb +11 -8
  69. data/lib/bio-ucsc/canfam2/chainself.rb +11 -8
  70. data/lib/bio-ucsc/canfam2/chainselflink.rb +11 -8
  71. data/lib/bio-ucsc/canfam2/est.rb +11 -8
  72. data/lib/bio-ucsc/canfam2/gap.rb +11 -8
  73. data/lib/bio-ucsc/canfam2/gold.rb +11 -8
  74. data/lib/bio-ucsc/canfam2/intronest.rb +11 -8
  75. data/lib/bio-ucsc/canfam2/mrna.rb +11 -8
  76. data/lib/bio-ucsc/canfam2/rmsk.rb +10 -7
  77. data/lib/bio-ucsc/cavpor3.rb +6 -4
  78. data/lib/bio-ucsc/cb3.rb +5 -3
  79. data/lib/bio-ucsc/cb3/chaincaepb1.rb +11 -8
  80. data/lib/bio-ucsc/cb3/chaincaepb1link.rb +11 -8
  81. data/lib/bio-ucsc/cb3/chaincaerem2.rb +11 -8
  82. data/lib/bio-ucsc/cb3/chaincaerem2link.rb +11 -8
  83. data/lib/bio-ucsc/cb3/chaince6.rb +11 -8
  84. data/lib/bio-ucsc/cb3/chaince6link.rb +11 -8
  85. data/lib/bio-ucsc/cb3/chainpripac1.rb +11 -8
  86. data/lib/bio-ucsc/cb3/chainpripac1link.rb +11 -8
  87. data/lib/bio-ucsc/cb3/est.rb +11 -8
  88. data/lib/bio-ucsc/cb3/gap.rb +11 -8
  89. data/lib/bio-ucsc/cb3/gold.rb +11 -8
  90. data/lib/bio-ucsc/cb3/intronest.rb +11 -8
  91. data/lib/bio-ucsc/cb3/mrna.rb +11 -8
  92. data/lib/bio-ucsc/cb3/rmsk.rb +10 -7
  93. data/lib/bio-ucsc/ce6.rb +8 -4
  94. data/lib/bio-ucsc/ce6/chaincaejap1.rb +11 -8
  95. data/lib/bio-ucsc/ce6/chaincaejap1link.rb +11 -8
  96. data/lib/bio-ucsc/ce6/chaincaepb2.rb +11 -8
  97. data/lib/bio-ucsc/ce6/chaincaepb2link.rb +11 -8
  98. data/lib/bio-ucsc/ce6/chaincaerem3.rb +11 -8
  99. data/lib/bio-ucsc/ce6/chaincaerem3link.rb +11 -8
  100. data/lib/bio-ucsc/ce6/chaincb3.rb +11 -8
  101. data/lib/bio-ucsc/ce6/chaincb3link.rb +11 -8
  102. data/lib/bio-ucsc/ce6/chainpripac1.rb +11 -8
  103. data/lib/bio-ucsc/ce6/chainpripac1link.rb +11 -8
  104. data/lib/bio-ucsc/ce6/chainself.rb +11 -8
  105. data/lib/bio-ucsc/ce6/chainselflink.rb +11 -8
  106. data/lib/bio-ucsc/ce6/est.rb +11 -8
  107. data/lib/bio-ucsc/ce6/gap.rb +11 -8
  108. data/lib/bio-ucsc/ce6/gold.rb +11 -8
  109. data/lib/bio-ucsc/ce6/intronest.rb +11 -8
  110. data/lib/bio-ucsc/ce6/mrna.rb +11 -8
  111. data/lib/bio-ucsc/ce6/rmsk.rb +11 -8
  112. data/lib/bio-ucsc/ce6/t25mersrepeats.rb +7 -4
  113. data/lib/bio-ucsc/ci2.rb +6 -3
  114. data/lib/bio-ucsc/danrer7.rb +6 -3
  115. data/lib/bio-ucsc/{apimel2/db_connection.rb → db_connector.rb} +33 -23
  116. data/lib/bio-ucsc/dm3.rb +6 -4
  117. data/lib/bio-ucsc/dm3/chainanogam1.rb +11 -8
  118. data/lib/bio-ucsc/dm3/chainanogam1link.rb +11 -8
  119. data/lib/bio-ucsc/dm3/chainapimel3.rb +11 -8
  120. data/lib/bio-ucsc/dm3/chainapimel3link.rb +11 -8
  121. data/lib/bio-ucsc/dm3/chaindp3.rb +11 -8
  122. data/lib/bio-ucsc/dm3/chaindp3link.rb +11 -8
  123. data/lib/bio-ucsc/dm3/chaindroana2.rb +11 -8
  124. data/lib/bio-ucsc/dm3/chaindroana2link.rb +11 -8
  125. data/lib/bio-ucsc/dm3/chaindroere1.rb +11 -8
  126. data/lib/bio-ucsc/dm3/chaindroere1link.rb +11 -8
  127. data/lib/bio-ucsc/dm3/chaindroper1.rb +11 -8
  128. data/lib/bio-ucsc/dm3/chaindroper1link.rb +11 -8
  129. data/lib/bio-ucsc/dm3/chaindrosec1.rb +11 -8
  130. data/lib/bio-ucsc/dm3/chaindrosec1link.rb +11 -8
  131. data/lib/bio-ucsc/dm3/chaindrosim1.rb +11 -8
  132. data/lib/bio-ucsc/dm3/chaindrosim1link.rb +11 -8
  133. data/lib/bio-ucsc/dm3/chaindroyak2.rb +11 -8
  134. data/lib/bio-ucsc/dm3/chaindroyak2link.rb +11 -8
  135. data/lib/bio-ucsc/dm3/est.rb +11 -8
  136. data/lib/bio-ucsc/dm3/gap.rb +11 -8
  137. data/lib/bio-ucsc/dm3/gold.rb +11 -8
  138. data/lib/bio-ucsc/dm3/intronest.rb +11 -8
  139. data/lib/bio-ucsc/dm3/mrna.rb +11 -8
  140. data/lib/bio-ucsc/dm3/rmsk.rb +11 -8
  141. data/lib/bio-ucsc/dp3.rb +6 -4
  142. data/lib/bio-ucsc/dp3/chaindm3.rb +11 -8
  143. data/lib/bio-ucsc/dp3/chaindm3link.rb +11 -8
  144. data/lib/bio-ucsc/dp3/est.rb +11 -8
  145. data/lib/bio-ucsc/dp3/gap.rb +11 -8
  146. data/lib/bio-ucsc/dp3/gold.rb +11 -8
  147. data/lib/bio-ucsc/dp3/intronest.rb +11 -8
  148. data/lib/bio-ucsc/dp3/mrna.rb +11 -8
  149. data/lib/bio-ucsc/dp3/rmsk.rb +10 -7
  150. data/lib/bio-ucsc/droana2.rb +6 -4
  151. data/lib/bio-ucsc/droere1.rb +6 -4
  152. data/lib/bio-ucsc/drogri1.rb +6 -4
  153. data/lib/bio-ucsc/dromoj2.rb +7 -5
  154. data/lib/bio-ucsc/droper1.rb +7 -5
  155. data/lib/bio-ucsc/drosec1.rb +6 -4
  156. data/lib/bio-ucsc/drosim1.rb +6 -4
  157. data/lib/bio-ucsc/drosim1/chaindm3.rb +11 -8
  158. data/lib/bio-ucsc/drosim1/chaindm3link.rb +11 -8
  159. data/lib/bio-ucsc/drosim1/est.rb +11 -8
  160. data/lib/bio-ucsc/drosim1/gap.rb +11 -8
  161. data/lib/bio-ucsc/drosim1/gold.rb +11 -8
  162. data/lib/bio-ucsc/drosim1/intronest.rb +11 -8
  163. data/lib/bio-ucsc/drosim1/mrna.rb +11 -8
  164. data/lib/bio-ucsc/drosim1/rmsk.rb +10 -7
  165. data/lib/bio-ucsc/drovir2.rb +6 -4
  166. data/lib/bio-ucsc/droyak2.rb +6 -4
  167. data/lib/bio-ucsc/droyak2/chaindm3.rb +11 -8
  168. data/lib/bio-ucsc/droyak2/chaindm3link.rb +11 -8
  169. data/lib/bio-ucsc/droyak2/est.rb +11 -8
  170. data/lib/bio-ucsc/droyak2/gap.rb +11 -8
  171. data/lib/bio-ucsc/droyak2/gold.rb +11 -8
  172. data/lib/bio-ucsc/droyak2/intronest.rb +11 -8
  173. data/lib/bio-ucsc/droyak2/mrna.rb +11 -8
  174. data/lib/bio-ucsc/droyak2/rmsk.rb +10 -7
  175. data/lib/bio-ucsc/equcab2.rb +7 -4
  176. data/lib/bio-ucsc/equcab2/est.rb +11 -8
  177. data/lib/bio-ucsc/equcab2/gap.rb +11 -8
  178. data/lib/bio-ucsc/equcab2/gold.rb +11 -8
  179. data/lib/bio-ucsc/equcab2/intronest.rb +11 -8
  180. data/lib/bio-ucsc/equcab2/mrna.rb +11 -8
  181. data/lib/bio-ucsc/equcab2/rmsk.rb +10 -7
  182. data/lib/bio-ucsc/felcat4.rb +7 -4
  183. data/lib/bio-ucsc/file.rb +10 -0
  184. data/lib/bio-ucsc/file/bytequeue.rb +28 -0
  185. data/lib/bio-ucsc/file/twobit.rb +174 -0
  186. data/lib/bio-ucsc/fr2.rb +5 -3
  187. data/lib/bio-ucsc/fr2/chaingalgal3.rb +11 -8
  188. data/lib/bio-ucsc/fr2/chaingalgal3link.rb +11 -8
  189. data/lib/bio-ucsc/fr2/chaingasacu1.rb +11 -8
  190. data/lib/bio-ucsc/fr2/chaingasacu1link.rb +11 -8
  191. data/lib/bio-ucsc/fr2/chainmm9.rb +11 -8
  192. data/lib/bio-ucsc/fr2/chainmm9link.rb +11 -8
  193. data/lib/bio-ucsc/fr2/chainorylat2.rb +11 -8
  194. data/lib/bio-ucsc/fr2/chainorylat2link.rb +11 -8
  195. data/lib/bio-ucsc/fr2/est.rb +11 -8
  196. data/lib/bio-ucsc/fr2/gap.rb +11 -8
  197. data/lib/bio-ucsc/fr2/gold.rb +11 -8
  198. data/lib/bio-ucsc/fr2/intronest.rb +11 -8
  199. data/lib/bio-ucsc/fr2/mrna.rb +11 -8
  200. data/lib/bio-ucsc/fr2/rmsk.rb +10 -7
  201. data/lib/bio-ucsc/galgal3.rb +8 -5
  202. data/lib/bio-ucsc/galgal3/chainanocar1.rb +11 -8
  203. data/lib/bio-ucsc/galgal3/chainanocar1link.rb +11 -8
  204. data/lib/bio-ucsc/galgal3/chainbraflo1.rb +11 -8
  205. data/lib/bio-ucsc/galgal3/chainbraflo1link.rb +11 -8
  206. data/lib/bio-ucsc/galgal3/chaincavpor3.rb +11 -8
  207. data/lib/bio-ucsc/galgal3/chaincavpor3link.rb +11 -8
  208. data/lib/bio-ucsc/galgal3/chaindanrer4.rb +11 -8
  209. data/lib/bio-ucsc/galgal3/chaindanrer4link.rb +11 -8
  210. data/lib/bio-ucsc/galgal3/chainfr2.rb +11 -8
  211. data/lib/bio-ucsc/galgal3/chainfr2link.rb +11 -8
  212. data/lib/bio-ucsc/galgal3/chaingasacu1.rb +11 -8
  213. data/lib/bio-ucsc/galgal3/chaingasacu1link.rb +11 -8
  214. data/lib/bio-ucsc/galgal3/chainmm9.rb +11 -8
  215. data/lib/bio-ucsc/galgal3/chainmm9link.rb +11 -8
  216. data/lib/bio-ucsc/galgal3/chainornana1.rb +11 -8
  217. data/lib/bio-ucsc/galgal3/chainornana1link.rb +11 -8
  218. data/lib/bio-ucsc/galgal3/chainpetmar1.rb +11 -8
  219. data/lib/bio-ucsc/galgal3/chainpetmar1link.rb +11 -8
  220. data/lib/bio-ucsc/galgal3/chainrn4.rb +11 -8
  221. data/lib/bio-ucsc/galgal3/chainrn4link.rb +11 -8
  222. data/lib/bio-ucsc/galgal3/chaintaegut1.rb +11 -8
  223. data/lib/bio-ucsc/galgal3/chaintaegut1link.rb +11 -8
  224. data/lib/bio-ucsc/galgal3/chainxentro2.rb +11 -8
  225. data/lib/bio-ucsc/galgal3/chainxentro2link.rb +11 -8
  226. data/lib/bio-ucsc/galgal3/est.rb +11 -8
  227. data/lib/bio-ucsc/galgal3/gap.rb +11 -8
  228. data/lib/bio-ucsc/galgal3/gold.rb +11 -8
  229. data/lib/bio-ucsc/galgal3/intronest.rb +11 -8
  230. data/lib/bio-ucsc/galgal3/mrna.rb +11 -8
  231. data/lib/bio-ucsc/galgal3/rmsk.rb +10 -7
  232. data/lib/bio-ucsc/gasacu1.rb +6 -4
  233. data/lib/bio-ucsc/gasacu1/chainanocar1.rb +11 -8
  234. data/lib/bio-ucsc/gasacu1/chainanocar1link.rb +11 -8
  235. data/lib/bio-ucsc/gasacu1/chainfr2.rb +11 -8
  236. data/lib/bio-ucsc/gasacu1/chainfr2link.rb +11 -8
  237. data/lib/bio-ucsc/gasacu1/chaingalgal3.rb +11 -8
  238. data/lib/bio-ucsc/gasacu1/chaingalgal3link.rb +11 -8
  239. data/lib/bio-ucsc/gasacu1/chainmm9.rb +11 -8
  240. data/lib/bio-ucsc/gasacu1/chainmm9link.rb +11 -8
  241. data/lib/bio-ucsc/gasacu1/chainorylat2.rb +11 -8
  242. data/lib/bio-ucsc/gasacu1/chainorylat2link.rb +11 -8
  243. data/lib/bio-ucsc/gasacu1/est.rb +11 -8
  244. data/lib/bio-ucsc/gasacu1/intronest.rb +11 -8
  245. data/lib/bio-ucsc/gasacu1/mrna.rb +11 -8
  246. data/lib/bio-ucsc/gasacu1/rmsk.rb +10 -7
  247. data/lib/bio-ucsc/gi.rb +27 -0
  248. data/lib/bio-ucsc/go.rb +7 -4
  249. data/lib/bio-ucsc/hg18.rb +7 -4
  250. data/lib/bio-ucsc/hg18/chainanocar1.rb +11 -8
  251. data/lib/bio-ucsc/hg18/chainbostau4.rb +11 -8
  252. data/lib/bio-ucsc/hg18/chainbraflo1.rb +11 -8
  253. data/lib/bio-ucsc/hg18/chaincaljac1.rb +11 -8
  254. data/lib/bio-ucsc/hg18/chaincanfam2.rb +11 -8
  255. data/lib/bio-ucsc/hg18/chaincavpor3.rb +11 -8
  256. data/lib/bio-ucsc/hg18/chaindanrer5.rb +11 -8
  257. data/lib/bio-ucsc/hg18/chainequcab1.rb +11 -8
  258. data/lib/bio-ucsc/hg18/chainfelcat3.rb +11 -8
  259. data/lib/bio-ucsc/hg18/chainfr2.rb +12 -9
  260. data/lib/bio-ucsc/hg18/chaingalgal3.rb +11 -8
  261. data/lib/bio-ucsc/hg18/chaingasacu1.rb +11 -8
  262. data/lib/bio-ucsc/hg18/chainmm9.rb +11 -8
  263. data/lib/bio-ucsc/hg18/chainmondom4.rb +11 -8
  264. data/lib/bio-ucsc/hg18/chainornana1.rb +11 -8
  265. data/lib/bio-ucsc/hg18/chainorylat2.rb +11 -8
  266. data/lib/bio-ucsc/hg18/chainpantro2.rb +11 -8
  267. data/lib/bio-ucsc/hg18/chainpetmar1.rb +11 -8
  268. data/lib/bio-ucsc/hg18/chainponabe2.rb +11 -8
  269. data/lib/bio-ucsc/hg18/chainrhemac2.rb +11 -8
  270. data/lib/bio-ucsc/hg18/chainrn4.rb +11 -8
  271. data/lib/bio-ucsc/hg18/chainself.rb +11 -8
  272. data/lib/bio-ucsc/hg18/chainstrpur2.rb +11 -8
  273. data/lib/bio-ucsc/hg18/chaintaegut1.rb +11 -8
  274. data/lib/bio-ucsc/hg18/chaintetnig2.rb +11 -8
  275. data/lib/bio-ucsc/hg18/chainxentro2.rb +11 -8
  276. data/lib/bio-ucsc/hg18/gap.rb +11 -8
  277. data/lib/bio-ucsc/hg18/gold.rb +11 -8
  278. data/lib/bio-ucsc/hg18/intronest.rb +11 -8
  279. data/lib/bio-ucsc/hg18/rmsk.rb +10 -7
  280. data/lib/bio-ucsc/hg18/rmskrm327.rb +10 -7
  281. data/lib/bio-ucsc/hg19.rb +7 -6
  282. data/lib/bio-ucsc/hg19/description.rb +1 -1
  283. data/lib/bio-ucsc/hg19/gbcdnainfo.rb +2 -2
  284. data/lib/bio-ucsc/hgfixed.rb +7 -4
  285. data/lib/bio-ucsc/loxafr3.rb +7 -4
  286. data/lib/bio-ucsc/mm9.rb +7 -12
  287. data/lib/bio-ucsc/mm9/chainbraflo1.rb +11 -8
  288. data/lib/bio-ucsc/mm9/chainbraflo1link.rb +11 -8
  289. data/lib/bio-ucsc/mm9/chaincanfam2.rb +11 -8
  290. data/lib/bio-ucsc/mm9/chaincanfam2link.rb +11 -8
  291. data/lib/bio-ucsc/mm9/chaincavpor3.rb +11 -8
  292. data/lib/bio-ucsc/mm9/chaincavpor3link.rb +11 -8
  293. data/lib/bio-ucsc/mm9/chainfr2.rb +11 -8
  294. data/lib/bio-ucsc/mm9/chainfr2link.rb +11 -8
  295. data/lib/bio-ucsc/mm9/chaingalgal3.rb +11 -8
  296. data/lib/bio-ucsc/mm9/chaingalgal3link.rb +11 -8
  297. data/lib/bio-ucsc/mm9/chaingasacu1.rb +11 -8
  298. data/lib/bio-ucsc/mm9/chaingasacu1link.rb +11 -8
  299. data/lib/bio-ucsc/mm9/chainornana1.rb +11 -8
  300. data/lib/bio-ucsc/mm9/chainornana1link.rb +11 -8
  301. data/lib/bio-ucsc/mm9/chainorylat2.rb +11 -8
  302. data/lib/bio-ucsc/mm9/chainorylat2link.rb +11 -8
  303. data/lib/bio-ucsc/mm9/chainpetmar1.rb +11 -8
  304. data/lib/bio-ucsc/mm9/chainpetmar1link.rb +11 -8
  305. data/lib/bio-ucsc/mm9/chainponabe2.rb +11 -8
  306. data/lib/bio-ucsc/mm9/chainponabe2link.rb +11 -8
  307. data/lib/bio-ucsc/mm9/chainrhemac2.rb +11 -8
  308. data/lib/bio-ucsc/mm9/chainrhemac2link.rb +11 -8
  309. data/lib/bio-ucsc/mm9/chainrn4.rb +11 -8
  310. data/lib/bio-ucsc/mm9/chainrn4link.rb +11 -8
  311. data/lib/bio-ucsc/mm9/est.rb +11 -8
  312. data/lib/bio-ucsc/mm9/gap.rb +11 -8
  313. data/lib/bio-ucsc/mm9/gold.rb +11 -8
  314. data/lib/bio-ucsc/mm9/intronest.rb +11 -8
  315. data/lib/bio-ucsc/mm9/mrna.rb +11 -8
  316. data/lib/bio-ucsc/mm9/rmsk.rb +10 -7
  317. data/lib/bio-ucsc/mondom5.rb +7 -4
  318. data/lib/bio-ucsc/ornana1.rb +6 -3
  319. data/lib/bio-ucsc/orycun2.rb +5 -3
  320. data/lib/bio-ucsc/orylat2.rb +7 -5
  321. data/lib/bio-ucsc/oviari1.rb +6 -4
  322. data/lib/bio-ucsc/pantro3.rb +7 -5
  323. data/lib/bio-ucsc/petmar1.rb +6 -5
  324. data/lib/bio-ucsc/ponabe2.rb +6 -4
  325. data/lib/bio-ucsc/ponabe2/chainmm9.rb +11 -8
  326. data/lib/bio-ucsc/ponabe2/chainmm9link.rb +11 -8
  327. data/lib/bio-ucsc/ponabe2/chainornana1.rb +11 -8
  328. data/lib/bio-ucsc/ponabe2/chainornana1link.rb +11 -8
  329. data/lib/bio-ucsc/ponabe2/chainrhemac2.rb +11 -8
  330. data/lib/bio-ucsc/ponabe2/chainrhemac2link.rb +11 -8
  331. data/lib/bio-ucsc/ponabe2/est.rb +11 -8
  332. data/lib/bio-ucsc/ponabe2/gap.rb +11 -8
  333. data/lib/bio-ucsc/ponabe2/gold.rb +11 -8
  334. data/lib/bio-ucsc/ponabe2/intronest.rb +11 -8
  335. data/lib/bio-ucsc/ponabe2/mrna.rb +11 -8
  336. data/lib/bio-ucsc/ponabe2/rmsk.rb +10 -7
  337. data/lib/bio-ucsc/pripac1.rb +7 -5
  338. data/lib/bio-ucsc/pripac1/chaincaepb1.rb +11 -8
  339. data/lib/bio-ucsc/pripac1/chaincaepb1link.rb +11 -8
  340. data/lib/bio-ucsc/pripac1/chaincaerem2.rb +11 -8
  341. data/lib/bio-ucsc/pripac1/chaincaerem2link.rb +11 -8
  342. data/lib/bio-ucsc/pripac1/chaincb3.rb +11 -8
  343. data/lib/bio-ucsc/pripac1/chaincb3link.rb +11 -8
  344. data/lib/bio-ucsc/pripac1/chaince6.rb +11 -8
  345. data/lib/bio-ucsc/pripac1/chaince6link.rb +11 -8
  346. data/lib/bio-ucsc/pripac1/gap.rb +11 -8
  347. data/lib/bio-ucsc/pripac1/gold.rb +11 -8
  348. data/lib/bio-ucsc/pripac1/rmsk.rb +10 -7
  349. data/lib/bio-ucsc/proteome.rb +7 -4
  350. data/lib/bio-ucsc/reference.rb +5 -160
  351. data/lib/bio-ucsc/rhemac2.rb +5 -5
  352. data/lib/bio-ucsc/rhemac2/chainmm9.rb +11 -8
  353. data/lib/bio-ucsc/rhemac2/chainmm9link.rb +11 -8
  354. data/lib/bio-ucsc/rhemac2/chainponabe2.rb +11 -8
  355. data/lib/bio-ucsc/rhemac2/chainponabe2link.rb +11 -8
  356. data/lib/bio-ucsc/rhemac2/chainrn4.rb +11 -8
  357. data/lib/bio-ucsc/rhemac2/chainrn4link.rb +11 -8
  358. data/lib/bio-ucsc/rn4.rb +6 -8
  359. data/lib/bio-ucsc/rn4/chaincanfam2.rb +11 -8
  360. data/lib/bio-ucsc/rn4/chaincanfam2link.rb +11 -8
  361. data/lib/bio-ucsc/rn4/chaincavpor3.rb +11 -8
  362. data/lib/bio-ucsc/rn4/chaincavpor3link.rb +11 -8
  363. data/lib/bio-ucsc/rn4/chaindanrer4.rb +11 -8
  364. data/lib/bio-ucsc/rn4/chaindanrer4link.rb +11 -8
  365. data/lib/bio-ucsc/rn4/chainequcab1.rb +11 -8
  366. data/lib/bio-ucsc/rn4/chainequcab1link.rb +11 -8
  367. data/lib/bio-ucsc/rn4/chaingalgal3.rb +11 -8
  368. data/lib/bio-ucsc/rn4/chaingalgal3link.rb +11 -8
  369. data/lib/bio-ucsc/rn4/chainmm9.rb +11 -8
  370. data/lib/bio-ucsc/rn4/chainmm9link.rb +11 -8
  371. data/lib/bio-ucsc/rn4/chainmondom4.rb +11 -8
  372. data/lib/bio-ucsc/rn4/chainmondom4link.rb +11 -8
  373. data/lib/bio-ucsc/rn4/chainpantro2.rb +11 -8
  374. data/lib/bio-ucsc/rn4/chainpantro2link.rb +11 -8
  375. data/lib/bio-ucsc/rn4/chainrhemac2.rb +11 -8
  376. data/lib/bio-ucsc/rn4/chainrhemac2link.rb +11 -8
  377. data/lib/bio-ucsc/rn4/est.rb +11 -8
  378. data/lib/bio-ucsc/rn4/gap.rb +11 -8
  379. data/lib/bio-ucsc/rn4/gold.rb +11 -8
  380. data/lib/bio-ucsc/rn4/intronest.rb +11 -8
  381. data/lib/bio-ucsc/rn4/mrna.rb +11 -8
  382. data/lib/bio-ucsc/rn4/rmsk.rb +10 -7
  383. data/lib/bio-ucsc/saccer2.rb +6 -4
  384. data/lib/bio-ucsc/saccer2/est.rb +11 -8
  385. data/lib/bio-ucsc/saccer2/gap.rb +11 -8
  386. data/lib/bio-ucsc/saccer2/gold.rb +11 -8
  387. data/lib/bio-ucsc/saccer2/intronest.rb +11 -8
  388. data/lib/bio-ucsc/saccer2/mrna.rb +11 -8
  389. data/lib/bio-ucsc/saccer2/t2micron_est.rb +4 -4
  390. data/lib/bio-ucsc/saccer2/t2micron_gap.rb +4 -4
  391. data/lib/bio-ucsc/saccer2/t2micron_gold.rb +4 -4
  392. data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb +4 -4
  393. data/lib/bio-ucsc/saccer2/t2micron_mrna.rb +4 -4
  394. data/lib/bio-ucsc/strpur2.rb +7 -15
  395. data/lib/bio-ucsc/susscr2.rb +6 -4
  396. data/lib/bio-ucsc/susscr2/est.rb +11 -8
  397. data/lib/bio-ucsc/susscr2/intronest.rb +11 -8
  398. data/lib/bio-ucsc/susscr2/mrna.rb +11 -8
  399. data/lib/bio-ucsc/table_class_detector.rb +250 -475
  400. data/lib/bio-ucsc/taegut1.rb +6 -4
  401. data/lib/bio-ucsc/taegut1/chaingalgal3.rb +14 -13
  402. data/lib/bio-ucsc/taegut1/chaingalgal3link.rb +13 -10
  403. data/lib/bio-ucsc/taegut1/est.rb +13 -10
  404. data/lib/bio-ucsc/taegut1/gap.rb +13 -10
  405. data/lib/bio-ucsc/taegut1/gold.rb +13 -10
  406. data/lib/bio-ucsc/taegut1/intronest.rb +13 -10
  407. data/lib/bio-ucsc/taegut1/mrna.rb +13 -10
  408. data/lib/bio-ucsc/taegut1/rmsk.rb +12 -9
  409. data/lib/bio-ucsc/tetnig2.rb +6 -4
  410. data/lib/bio-ucsc/tetnig2/mrna.rb +11 -8
  411. data/lib/bio-ucsc/uniprot.rb +7 -4
  412. data/lib/bio-ucsc/visigene.rb +6 -3
  413. data/lib/bio-ucsc/xentro2.rb +6 -12
  414. data/samples/num-gene-exon.rb +1 -2
  415. data/samples/snp2genes.rb +1 -7
  416. data/samples/symbol2summary.rb +7 -1
  417. data/spec/ailmel1_spec.rb +245 -245
  418. data/spec/aplcal1_spec.rb +0 -30
  419. data/spec/braflo1_spec.rb +1 -1
  420. data/spec/canfam2_spec.rb +6 -6
  421. data/spec/danrer7_spec.rb +6 -6
  422. data/spec/file/twobit.rb +167 -0
  423. data/spec/galgal3_spec.rb +12 -12
  424. data/spec/gasacu1_spec.rb +6 -6
  425. data/spec/hg18/find_by_spec.rb +14 -20
  426. data/spec/hg19/all_mrna_spec.rb +0 -8
  427. data/spec/hg19/altseqliftoverpsl_spec.rb +0 -8
  428. data/spec/hg19/altseqpatches_spec.rb +0 -8
  429. data/spec/hg19/{chainanocar1_spec.rb → chainanocar2_spec.rb} +2 -2
  430. data/spec/hg19/{chainbostau4_spec.rb → chainbostau6_spec.rb} +2 -2
  431. data/spec/hg19/{chainxentro2_spec.rb → chainxentro3_spec.rb} +2 -2
  432. data/spec/hg19/connect_spec.rb +20 -0
  433. data/spec/hg19/find_by_spec.rb +14 -14
  434. data/spec/hg19/gwascatalog_spec.rb +0 -7
  435. data/spec/hg19/hgikmcextra_spec.rb +2 -1
  436. data/spec/hg19/mrnaorinetinfo_spec.rb +0 -8
  437. data/spec/hg19/{netanocar1_spec.rb → netanocar2_spec.rb} +2 -2
  438. data/spec/hg19/{netbostau4_spec.rb → netbostau6_spec.rb} +2 -2
  439. data/spec/hg19/{netxentro2_spec.rb → netxentro3_spec.rb} +2 -2
  440. data/spec/hg19/sibtxgraph_spec.rb +0 -8
  441. data/spec/hg19/snp132_spec.rb +9 -0
  442. data/spec/hg19/xenorefflat_spec.rb +0 -8
  443. data/spec/hg19/xenorefgene_spec.rb +0 -8
  444. data/spec/hg19/xenorefseqali_spec.rb +0 -8
  445. data/spec/mm9_spec.rb +32 -32
  446. data/spec/ornana1_spec.rb +12 -12
  447. data/spec/{named_scope_spec.rb → relation_objects_spec.rb} +14 -0
  448. data/spec/rhemac2_spec.rb +16 -6
  449. data/spec/rn4_spec.rb +12 -12
  450. data/spec/spec_helper.rb +3 -1
  451. data/spec/susscr2_spec.rb +6 -6
  452. data/spec/taegut1_spec.rb +8 -8
  453. data/spec/xentro2_spec.rb +6 -6
  454. metadata +63 -138
  455. data/README.rdoc +0 -202
  456. data/lib/bio-ucsc/ailmel1/db_connection.rb +0 -57
  457. data/lib/bio-ucsc/anocar2/db_connection.rb +0 -57
  458. data/lib/bio-ucsc/anogam1/db_connection.rb +0 -57
  459. data/lib/bio-ucsc/aplcal1/db_connection.rb +0 -57
  460. data/lib/bio-ucsc/bostau4/db_connection.rb +0 -57
  461. data/lib/bio-ucsc/braflo1/db_connection.rb +0 -57
  462. data/lib/bio-ucsc/caejap1/db_connection.rb +0 -57
  463. data/lib/bio-ucsc/caepb2/db_connection.rb +0 -57
  464. data/lib/bio-ucsc/caerem3/db_connection.rb +0 -57
  465. data/lib/bio-ucsc/caljac3/db_connection.rb +0 -55
  466. data/lib/bio-ucsc/canfam2/db_connection.rb +0 -57
  467. data/lib/bio-ucsc/cavpor3/db_connection.rb +0 -57
  468. data/lib/bio-ucsc/cb3/db_connection.rb +0 -57
  469. data/lib/bio-ucsc/ce6/db_connection.rb +0 -55
  470. data/lib/bio-ucsc/ci2/db_connection.rb +0 -55
  471. data/lib/bio-ucsc/danrer7/db_connection.rb +0 -57
  472. data/lib/bio-ucsc/dm3/db_connection.rb +0 -55
  473. data/lib/bio-ucsc/dp3/db_connection.rb +0 -57
  474. data/lib/bio-ucsc/droana2/db_connection.rb +0 -57
  475. data/lib/bio-ucsc/droere1/db_connection.rb +0 -57
  476. data/lib/bio-ucsc/drogri1/db_connection.rb +0 -57
  477. data/lib/bio-ucsc/dromoj2/db_connection.rb +0 -57
  478. data/lib/bio-ucsc/droper1/db_connection.rb +0 -57
  479. data/lib/bio-ucsc/drosec1/db_connection.rb +0 -57
  480. data/lib/bio-ucsc/drosim1/db_connection.rb +0 -57
  481. data/lib/bio-ucsc/drovir2/db_connection.rb +0 -57
  482. data/lib/bio-ucsc/droyak2/db_connection.rb +0 -57
  483. data/lib/bio-ucsc/equcab2/db_connection.rb +0 -57
  484. data/lib/bio-ucsc/felcat4/db_connection.rb +0 -57
  485. data/lib/bio-ucsc/fr2/db_connection.rb +0 -57
  486. data/lib/bio-ucsc/galgal3/db_connection.rb +0 -57
  487. data/lib/bio-ucsc/gasacu1/db_connection.rb +0 -57
  488. data/lib/bio-ucsc/go/db_connection.rb +0 -55
  489. data/lib/bio-ucsc/hg18/db_connection.rb +0 -59
  490. data/lib/bio-ucsc/hg19/db_connection.rb +0 -61
  491. data/lib/bio-ucsc/hgfixed/db_connection.rb +0 -55
  492. data/lib/bio-ucsc/loxafr3/db_connection.rb +0 -57
  493. data/lib/bio-ucsc/mm9/chainanocar1.rb +0 -79
  494. data/lib/bio-ucsc/mm9/chainanocar1link.rb +0 -79
  495. data/lib/bio-ucsc/mm9/chainbostau4.rb +0 -79
  496. data/lib/bio-ucsc/mm9/chainbostau4link.rb +0 -79
  497. data/lib/bio-ucsc/mm9/chainpantro2.rb +0 -81
  498. data/lib/bio-ucsc/mm9/chainpantro2link.rb +0 -82
  499. data/lib/bio-ucsc/mm9/chainxentro2.rb +0 -81
  500. data/lib/bio-ucsc/mm9/chainxentro2link.rb +0 -81
  501. data/lib/bio-ucsc/mm9/db_connection.rb +0 -55
  502. data/lib/bio-ucsc/mondom5/db_connection.rb +0 -57
  503. data/lib/bio-ucsc/ornana1/db_connection.rb +0 -57
  504. data/lib/bio-ucsc/orycun2/db_connection.rb +0 -57
  505. data/lib/bio-ucsc/orylat2/db_connection.rb +0 -55
  506. data/lib/bio-ucsc/oviari1/db_connection.rb +0 -57
  507. data/lib/bio-ucsc/pantro3/db_connection.rb +0 -55
  508. data/lib/bio-ucsc/petmar1/db_connection.rb +0 -57
  509. data/lib/bio-ucsc/ponabe2/db_connection.rb +0 -55
  510. data/lib/bio-ucsc/pripac1/db_connection.rb +0 -57
  511. data/lib/bio-ucsc/proteome/db_connection.rb +0 -59
  512. data/lib/bio-ucsc/rhemac2/chainpantro2.rb +0 -81
  513. data/lib/bio-ucsc/rhemac2/chainpantro2link.rb +0 -81
  514. data/lib/bio-ucsc/rhemac2/db_connection.rb +0 -55
  515. data/lib/bio-ucsc/rn4/chainbostau3.rb +0 -79
  516. data/lib/bio-ucsc/rn4/chainbostau3link.rb +0 -79
  517. data/lib/bio-ucsc/rn4/chainxentro2.rb +0 -81
  518. data/lib/bio-ucsc/rn4/chainxentro2link.rb +0 -81
  519. data/lib/bio-ucsc/rn4/db_connection.rb +0 -55
  520. data/lib/bio-ucsc/saccer2/db_connection.rb +0 -55
  521. data/lib/bio-ucsc/strpur2/chaingalgal3.rb +0 -81
  522. data/lib/bio-ucsc/strpur2/chaingalgal3link.rb +0 -81
  523. data/lib/bio-ucsc/strpur2/chainhg18.rb +0 -81
  524. data/lib/bio-ucsc/strpur2/chainhg18link.rb +0 -81
  525. data/lib/bio-ucsc/strpur2/chainmm9.rb +0 -81
  526. data/lib/bio-ucsc/strpur2/chainmm9link.rb +0 -81
  527. data/lib/bio-ucsc/strpur2/chainpetmar1.rb +0 -81
  528. data/lib/bio-ucsc/strpur2/chainpetmar1link.rb +0 -81
  529. data/lib/bio-ucsc/strpur2/db_connection.rb +0 -57
  530. data/lib/bio-ucsc/strpur2/gap.rb +0 -81
  531. data/lib/bio-ucsc/strpur2/gold.rb +0 -81
  532. data/lib/bio-ucsc/susscr2/db_connection.rb +0 -57
  533. data/lib/bio-ucsc/taegut1/db_connection.rb +0 -57
  534. data/lib/bio-ucsc/tetnig2/db_connection.rb +0 -57
  535. data/lib/bio-ucsc/uniprot/db_connection.rb +0 -59
  536. data/lib/bio-ucsc/visigene/db_connection.rb +0 -55
  537. data/lib/bio-ucsc/xentro2/chaingalgal3.rb +0 -81
  538. data/lib/bio-ucsc/xentro2/chaingalgal3link.rb +0 -81
  539. data/lib/bio-ucsc/xentro2/db_connection.rb +0 -57
  540. data/lib/bio-ucsc/xentro2/est.rb +0 -81
  541. data/lib/bio-ucsc/xentro2/gap.rb +0 -81
  542. data/lib/bio-ucsc/xentro2/gold.rb +0 -81
  543. data/lib/bio-ucsc/xentro2/intronest.rb +0 -81
  544. data/lib/bio-ucsc/xentro2/mrna.rb +0 -81
  545. data/lib/bio-ucsc/xentro2/rmsk.rb +0 -78
  546. data/spec/hg19/chainaplcal1_spec.rb +0 -16
  547. data/spec/hg19/netaplcal1_spec.rb +0 -16
@@ -1,55 +0,0 @@
1
- #
2
- # = db_connection.rb - UCSC DB connection
3
- #
4
- # Copyright:: Cioyrught (C) 2011
5
- # MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # Copyright:: Copyright (C) 2010
7
- # Jan Aerts <jan.aerts@gmail.com>
8
- # License:: Ruby licence (Ryby's / GPLv2 dual)
9
-
10
- require 'rubygems'
11
- require 'active_record'
12
-
13
- module Bio
14
- module Ucsc
15
-
16
- module RheMac2
17
- # = DESCRIPTION
18
- # Actual connection established to the UCSC mysql server.
19
- class DBConnection < ActiveRecord::Base
20
- # = DESCRIPTION
21
- # The #connect method make the connection
22
- #
23
- # = USAGE
24
- # Bin::Ucsc::DB_NAME::DBConnection.connect
25
- #
26
- # ---
27
- # *Arguments*: none
28
- @@db_adapter ||= 'mysql'
29
- @@db_host ||= 'genome-mysql.cse.ucsc.edu'
30
- @@db_username ||= 'genome'
31
- @@db_password ||= ''
32
-
33
- cattr_accessor :db_adapter, :db_host, :db_username, :db_password
34
-
35
- self.abstract_class = true
36
-
37
- def self.default
38
- @@db_adapter = 'mysql'
39
- @@db_host = 'genome-mysql.cse.ucsc.edu'
40
- @@db_username = 'genome'
41
- @@db_password = ''
42
- end
43
-
44
- def self.connect
45
- establish_connection({ :adapter => @@db_adapter,
46
- :host => @@db_host,
47
- :database => 'rheMac2',
48
- :username => @@db_username,
49
- :password => @@db_password, })
50
- end
51
- end
52
- end # module
53
-
54
- end # module Ucsc
55
- end # module Bio
@@ -1,79 +0,0 @@
1
- # = chainbostau4.rb
2
- # Copyright::
3
- # Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
4
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
5
- #
6
- # In the hg18 database, this table is actually separated
7
- # into "chr1_*", "chr2_*", etc. This class dynamically
8
- # define *::Chr1_*, *::Chr2_*, etc. The
9
- # Rmsk.find_by_interval calls an appropreate class automatically.
10
-
11
- module Bio
12
- module Ucsc
13
- module Rn4
14
-
15
- class ChainBosTau3
16
- Bio::Ucsc::Rn4::CHROMS.each do |chr|
17
- class_eval %!
18
- class #{chr[0..0].upcase + chr[1..-1]}_ChainBosTau3 < DBConnection
19
- set_table_name "#{chr[0..0].downcase + chr[1..-1]}_chainBosTau3"
20
- set_primary_key nil
21
- set_inheritance_column nil
22
-
23
- def self.find_by_interval(interval, opt = {:partial => true})
24
- find_first_or_all_by_interval(interval, :first, opt)
25
- end
26
-
27
- def self.find_all_by_interval(interval, opt = {:partial => true})
28
- find_first_or_all_by_interval(interval, :all, opt)
29
- end
30
-
31
- def self.find_first_or_all_by_interval(interval, first_all, opt)
32
- zstart = interval.zero_start
33
- zend = interval.zero_end
34
- if opt[:partial] == true
35
- where = <<-SQL
36
- tName = :chrom
37
- AND bin in (:bins)
38
- AND ((tStart BETWEEN :zstart AND :zend)
39
- OR (tEnd BETWEEN :zstart AND :zend)
40
- OR (tStart <= :zstart AND tEnd >= :zend))
41
- SQL
42
- else
43
- where = <<-SQL
44
- tName = :chrom
45
- AND bin in (:bins)
46
- AND ((tStart BETWEEN :zstart AND :zend)
47
- AND (tEnd BETWEEN :zstart AND :zend))
48
- SQL
49
- end
50
- cond = {
51
- :chrom => interval.chrom,
52
- :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
53
- :zstart => zstart,
54
- :zend => zend,
55
- }
56
- self.find(first_all,
57
- { :select => "*",
58
- :conditions => [where, cond], })
59
- end
60
- end
61
- !
62
- end # each chromosome
63
-
64
- def self.find_by_interval(interval, opt = {:partial => true})
65
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
66
- chr_klass = self.const_get("#{chrom}_ChainBosTau3")
67
- chr_klass.__send__(:find_by_interval, interval, opt)
68
- end
69
-
70
- def self.find_all_by_interval(interval, opt = {:partial => true})
71
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
72
- chr_klass = self.const_get("#{chrom}_ChainBosTau3")
73
- chr_klass.__send__(:find_all_by_interval, interval, opt)
74
- end
75
- end # class
76
-
77
- end # module Hg18
78
- end # module Ucsc
79
- end # module Bio
@@ -1,79 +0,0 @@
1
- # = chainbostau3link.rb
2
- # Copyright::
3
- # Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
4
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
5
- #
6
- # In the hg18 database, this table is actually separated
7
- # into "chr1_*", "chr2_*", etc. This class dynamically
8
- # define *::Chr1_*, *::Chr2_*, etc. The
9
- # Rmsk.find_by_interval calls an appropreate class automatically.
10
-
11
- module Bio
12
- module Ucsc
13
- module Rn4
14
-
15
- class ChainBosTau3Link
16
- Bio::Ucsc::Rn4::CHROMS.each do |chr|
17
- class_eval %!
18
- class #{chr[0..0].upcase + chr[1..-1]}_ChainBosTau3Link < DBConnection
19
- set_table_name "#{chr[0..0].downcase + chr[1..-1]}_chainBosTau3Link"
20
- set_primary_key nil
21
- set_inheritance_column nil
22
-
23
- def self.find_by_interval(interval, opt = {:partial => true})
24
- find_first_or_all_by_interval(interval, :first, opt)
25
- end
26
-
27
- def self.find_all_by_interval(interval, opt = {:partial => true})
28
- find_first_or_all_by_interval(interval, :all, opt)
29
- end
30
-
31
- def self.find_first_or_all_by_interval(interval, first_all, opt)
32
- zstart = interval.zero_start
33
- zend = interval.zero_end
34
- if opt[:partial] == true
35
- where = <<-SQL
36
- tName = :chrom
37
- AND bin in (:bins)
38
- AND ((tStart BETWEEN :zstart AND :zend)
39
- OR (tEnd BETWEEN :zstart AND :zend)
40
- OR (tStart <= :zstart AND tEnd >= :zend))
41
- SQL
42
- else
43
- where = <<-SQL
44
- tName = :chrom
45
- AND bin in (:bins)
46
- AND ((tStart BETWEEN :zstart AND :zend)
47
- AND (tEnd BETWEEN :zstart AND :zend))
48
- SQL
49
- end
50
- cond = {
51
- :chrom => interval.chrom,
52
- :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
53
- :zstart => zstart,
54
- :zend => zend,
55
- }
56
- self.find(first_all,
57
- { :select => "*",
58
- :conditions => [where, cond], })
59
- end
60
- end
61
- !
62
- end # each chromosome
63
-
64
- def self.find_by_interval(interval, opt = {:partial => true})
65
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
66
- chr_klass = self.const_get("#{chrom}_ChainBosTau3Link")
67
- chr_klass.__send__(:find_by_interval, interval, opt)
68
- end
69
-
70
- def self.find_all_by_interval(interval, opt = {:partial => true})
71
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
72
- chr_klass = self.const_get("#{chrom}_ChainBosTau3Link")
73
- chr_klass.__send__(:find_all_by_interval, interval, opt)
74
- end
75
- end # class
76
-
77
- end # module
78
- end # module Ucsc
79
- end # module Bio
@@ -1,81 +0,0 @@
1
- # Copyright::
2
- # Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
3
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
4
- #
5
- # In the hg18 database, this table is actually separated
6
- # into "chr1_*", "chr2_*", etc. This class dynamically
7
- # define *::Chr1_*, *::Chr2_*, etc. The
8
- # Rmsk.find_by_interval calls an appropreate class automatically.
9
-
10
- module Bio
11
- module Ucsc
12
- module Rn4
13
-
14
- class ChainXenTro2
15
- KLASS = "ChainXenTro2"
16
- KLASS_S = "chainXenTro2"
17
-
18
- Bio::Ucsc::Rn4::CHROMS.each do |chr|
19
- class_eval %!
20
- class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
21
- set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
22
- set_primary_key nil
23
- set_inheritance_column nil
24
-
25
- def self.find_by_interval(interval, opt = {:partial => true})
26
- find_first_or_all_by_interval(interval, :first, opt)
27
- end
28
-
29
- def self.find_all_by_interval(interval, opt = {:partial => true})
30
- find_first_or_all_by_interval(interval, :all, opt)
31
- end
32
-
33
- def self.find_first_or_all_by_interval(interval, first_all, opt)
34
- zstart = interval.zero_start
35
- zend = interval.zero_end
36
- if opt[:partial] == true
37
- where = <<-SQL
38
- tName = :chrom
39
- AND bin in (:bins)
40
- AND ((tStart BETWEEN :zstart AND :zend)
41
- OR (tEnd BETWEEN :zstart AND :zend)
42
- OR (tStart <= :zstart AND tEnd >= :zend))
43
- SQL
44
- else
45
- where = <<-SQL
46
- tName = :chrom
47
- AND bin in (:bins)
48
- AND ((tStart BETWEEN :zstart AND :zend)
49
- AND (tEnd BETWEEN :zstart AND :zend))
50
- SQL
51
- end
52
- cond = {
53
- :chrom => interval.chrom,
54
- :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
55
- :zstart => zstart,
56
- :zend => zend,
57
- }
58
- self.find(first_all,
59
- { :select => "*",
60
- :conditions => [where, cond], })
61
- end
62
- end
63
- !
64
- end # each chromosome
65
-
66
- def self.find_by_interval(interval, opt = {:partial => true})
67
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
68
- chr_klass = self.const_get("#{chrom}_#{KLASS}")
69
- chr_klass.__send__(:find_by_interval, interval, opt)
70
- end
71
-
72
- def self.find_all_by_interval(interval, opt = {:partial => true})
73
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
74
- chr_klass = self.const_get("#{chrom}_#{KLASS}")
75
- chr_klass.__send__(:find_all_by_interval, interval, opt)
76
- end
77
- end # class
78
-
79
- end # module Hg18
80
- end # module Ucsc
81
- end # module Bio
@@ -1,81 +0,0 @@
1
- # Copyright::
2
- # Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
3
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
4
- #
5
- # In the hg18 database, this table is actually separated
6
- # into "chr1_*", "chr2_*", etc. This class dynamically
7
- # define *::Chr1_*, *::Chr2_*, etc. The
8
- # Rmsk.find_by_interval calls an appropreate class automatically.
9
-
10
- module Bio
11
- module Ucsc
12
- module Rn4
13
-
14
- class ChainXenTro2Link
15
- KLASS = "ChainXenTro2Link"
16
- KLASS_S = "chainXenTro2Link"
17
-
18
- Bio::Ucsc::Rn4::CHROMS.each do |chr|
19
- class_eval %!
20
- class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
21
- set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
22
- set_primary_key nil
23
- set_inheritance_column nil
24
-
25
- def self.find_by_interval(interval, opt = {:partial => true})
26
- find_first_or_all_by_interval(interval, :first, opt)
27
- end
28
-
29
- def self.find_all_by_interval(interval, opt = {:partial => true})
30
- find_first_or_all_by_interval(interval, :all, opt)
31
- end
32
-
33
- def self.find_first_or_all_by_interval(interval, first_all, opt)
34
- zstart = interval.zero_start
35
- zend = interval.zero_end
36
- if opt[:partial] == true
37
- where = <<-SQL
38
- tName = :chrom
39
- AND bin in (:bins)
40
- AND ((tStart BETWEEN :zstart AND :zend)
41
- OR (tEnd BETWEEN :zstart AND :zend)
42
- OR (tStart <= :zstart AND tEnd >= :zend))
43
- SQL
44
- else
45
- where = <<-SQL
46
- tName = :chrom
47
- AND bin in (:bins)
48
- AND ((tStart BETWEEN :zstart AND :zend)
49
- AND (tEnd BETWEEN :zstart AND :zend))
50
- SQL
51
- end
52
- cond = {
53
- :chrom => interval.chrom,
54
- :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
55
- :zstart => zstart,
56
- :zend => zend,
57
- }
58
- self.find(first_all,
59
- { :select => "*",
60
- :conditions => [where, cond], })
61
- end
62
- end
63
- !
64
- end # each chromosome
65
-
66
- def self.find_by_interval(interval, opt = {:partial => true})
67
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
68
- chr_klass = self.const_get("#{chrom}_#{KLASS}")
69
- chr_klass.__send__(:find_by_interval, interval, opt)
70
- end
71
-
72
- def self.find_all_by_interval(interval, opt = {:partial => true})
73
- chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
74
- chr_klass = self.const_get("#{chrom}_#{KLASS}")
75
- chr_klass.__send__(:find_all_by_interval, interval, opt)
76
- end
77
- end # class
78
-
79
- end # module Hg18
80
- end # module Ucsc
81
- end # module Bio
@@ -1,55 +0,0 @@
1
- #
2
- # = db_connection.rb - UCSC DB connection
3
- #
4
- # Copyright:: Cioyrught (C) 2011
5
- # MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # Copyright:: Copyright (C) 2010
7
- # Jan Aerts <jan.aerts@gmail.com>
8
- # License:: Ruby licence (Ryby's / GPLv2 dual)
9
-
10
- require 'rubygems'
11
- require 'active_record'
12
-
13
- module Bio
14
- module Ucsc
15
-
16
- module Rn4
17
- # = DESCRIPTION
18
- # Actual connection established to the UCSC mysql server.
19
- class DBConnection < ActiveRecord::Base
20
- # = DESCRIPTION
21
- # The #connect method make the connection
22
- #
23
- # = USAGE
24
- # Bin::Ucsc::DB_NAME::DBConnection.connect
25
- #
26
- # ---
27
- # *Arguments*: none
28
- @@db_adapter ||= 'mysql'
29
- @@db_host ||= 'genome-mysql.cse.ucsc.edu'
30
- @@db_username ||= 'genome'
31
- @@db_password ||= ''
32
-
33
- cattr_accessor :db_adapter, :db_host, :db_username, :db_password
34
-
35
- self.abstract_class = true
36
-
37
- def self.default
38
- @@db_adapter = 'mysql'
39
- @@db_host = 'genome-mysql.cse.ucsc.edu'
40
- @@db_username = 'genome'
41
- @@db_password = ''
42
- end
43
-
44
- def self.connect
45
- establish_connection({ :adapter => @@db_adapter,
46
- :host => @@db_host,
47
- :database => 'rn4',
48
- :username => @@db_username,
49
- :password => @@db_password, })
50
- end
51
- end
52
- end # module
53
-
54
- end # module Ucsc
55
- end # module Bio
@@ -1,55 +0,0 @@
1
- #
2
- # = db_connection.rb - UCSC DB connection
3
- #
4
- # Copyright:: Cioyrught (C) 2011
5
- # MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # Copyright:: Copyright (C) 2010
7
- # Jan Aerts <jan.aerts@gmail.com>
8
- # License:: Ruby licence (Ryby's / GPLv2 dual)
9
-
10
- require 'rubygems'
11
- require 'active_record'
12
-
13
- module Bio
14
- module Ucsc
15
-
16
- module SacCer2
17
- # = DESCRIPTION
18
- # Actual connection established to the UCSC mysql server.
19
- class DBConnection < ActiveRecord::Base
20
- # = DESCRIPTION
21
- # The #connect method make the connection
22
- #
23
- # = USAGE
24
- # Bin::Ucsc::DB_NAME::DBConnection.connect
25
- #
26
- # ---
27
- # *Arguments*: none
28
- @@db_adapter ||= 'mysql'
29
- @@db_host ||= 'genome-mysql.cse.ucsc.edu'
30
- @@db_username ||= 'genome'
31
- @@db_password ||= ''
32
-
33
- cattr_accessor :db_adapter, :db_host, :db_username, :db_password
34
-
35
- self.abstract_class = true
36
-
37
- def self.default
38
- @@db_adapter = 'mysql'
39
- @@db_host = 'genome-mysql.cse.ucsc.edu'
40
- @@db_username = 'genome'
41
- @@db_password = ''
42
- end
43
-
44
- def self.connect
45
- establish_connection({ :adapter => @@db_adapter,
46
- :host => @@db_host,
47
- :database => 'sacCer2',
48
- :username => @@db_username,
49
- :password => @@db_password, })
50
- end
51
- end
52
- end # module
53
-
54
- end # module Ucsc
55
- end # module Bio