bio-ucsc-api 0.2.0 → 0.2.1

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Files changed (534) hide show
  1. data/README.rdoc +79 -47
  2. data/Rakefile +4 -2
  3. data/VERSION +1 -1
  4. data/bio-ucsc-api.gemspec +408 -3
  5. data/lib/bio-ucsc.rb +162 -8
  6. data/lib/bio-ucsc/ailmel1.rb +21 -0
  7. data/lib/bio-ucsc/ailmel1/db_connection.rb +57 -0
  8. data/lib/bio-ucsc/anocar2.rb +22 -0
  9. data/lib/bio-ucsc/anocar2/db_connection.rb +57 -0
  10. data/lib/bio-ucsc/anogam1.rb +30 -0
  11. data/lib/bio-ucsc/anogam1/chaindm3.rb +81 -0
  12. data/lib/bio-ucsc/anogam1/chaindm3link.rb +81 -0
  13. data/lib/bio-ucsc/anogam1/db_connection.rb +57 -0
  14. data/lib/bio-ucsc/anogam1/est.rb +81 -0
  15. data/lib/bio-ucsc/anogam1/gap.rb +81 -0
  16. data/lib/bio-ucsc/anogam1/gold.rb +81 -0
  17. data/lib/bio-ucsc/anogam1/intronest.rb +81 -0
  18. data/lib/bio-ucsc/anogam1/mrna.rb +81 -0
  19. data/lib/bio-ucsc/anogam1/rmsk.rb +78 -0
  20. data/lib/bio-ucsc/apimel2.rb +26 -0
  21. data/lib/bio-ucsc/apimel2/chaindm2.rb +81 -0
  22. data/lib/bio-ucsc/apimel2/chaindm2link.rb +81 -0
  23. data/lib/bio-ucsc/apimel2/db_connection.rb +57 -0
  24. data/lib/bio-ucsc/aplcal1.rb +33 -0
  25. data/lib/bio-ucsc/aplcal1/chaincaepb1.rb +81 -0
  26. data/lib/bio-ucsc/aplcal1/chaincaepb1link.rb +81 -0
  27. data/lib/bio-ucsc/aplcal1/chaincaerem2.rb +81 -0
  28. data/lib/bio-ucsc/aplcal1/chaincaerem2link.rb +81 -0
  29. data/lib/bio-ucsc/aplcal1/chaincb3.rb +81 -0
  30. data/lib/bio-ucsc/aplcal1/chaincb3link.rb +81 -0
  31. data/lib/bio-ucsc/aplcal1/chaince6.rb +81 -0
  32. data/lib/bio-ucsc/aplcal1/chaince6link.rb +81 -0
  33. data/lib/bio-ucsc/aplcal1/db_connection.rb +57 -0
  34. data/lib/bio-ucsc/aplcal1/gap.rb +81 -0
  35. data/lib/bio-ucsc/aplcal1/gold.rb +81 -0
  36. data/lib/bio-ucsc/aplcal1/rmsk.rb +78 -0
  37. data/lib/bio-ucsc/bostau4.rb +24 -0
  38. data/lib/bio-ucsc/bostau4/db_connection.rb +57 -0
  39. data/lib/bio-ucsc/braflo1.rb +32 -0
  40. data/lib/bio-ucsc/braflo1/chaingalgal3.rb +81 -0
  41. data/lib/bio-ucsc/braflo1/chaingalgal3link.rb +81 -0
  42. data/lib/bio-ucsc/braflo1/chainhg18.rb +81 -0
  43. data/lib/bio-ucsc/braflo1/chainhg18link.rb +81 -0
  44. data/lib/bio-ucsc/braflo1/chainmm9.rb +81 -0
  45. data/lib/bio-ucsc/braflo1/chainmm9link.rb +81 -0
  46. data/lib/bio-ucsc/braflo1/chainpetmar1.rb +81 -0
  47. data/lib/bio-ucsc/braflo1/chainpetmar1link.rb +81 -0
  48. data/lib/bio-ucsc/braflo1/db_connection.rb +57 -0
  49. data/lib/bio-ucsc/braflo1/gap.rb +81 -0
  50. data/lib/bio-ucsc/braflo1/gold.rb +81 -0
  51. data/lib/bio-ucsc/caejap1.rb +26 -0
  52. data/lib/bio-ucsc/caejap1/chaince6.rb +81 -0
  53. data/lib/bio-ucsc/caejap1/chaince6link.rb +81 -0
  54. data/lib/bio-ucsc/caejap1/db_connection.rb +57 -0
  55. data/lib/bio-ucsc/caejap1/gap.rb +81 -0
  56. data/lib/bio-ucsc/caejap1/gold.rb +81 -0
  57. data/lib/bio-ucsc/caepb2.rb +26 -0
  58. data/lib/bio-ucsc/caepb2/chaince6.rb +81 -0
  59. data/lib/bio-ucsc/caepb2/chaince6link.rb +81 -0
  60. data/lib/bio-ucsc/caepb2/db_connection.rb +57 -0
  61. data/lib/bio-ucsc/caepb2/gap.rb +81 -0
  62. data/lib/bio-ucsc/caepb2/gold.rb +81 -0
  63. data/lib/bio-ucsc/caerem3.rb +26 -0
  64. data/lib/bio-ucsc/caerem3/chaince6.rb +81 -0
  65. data/lib/bio-ucsc/caerem3/chaince6link.rb +81 -0
  66. data/lib/bio-ucsc/caerem3/db_connection.rb +57 -0
  67. data/lib/bio-ucsc/caerem3/gap.rb +81 -0
  68. data/lib/bio-ucsc/caerem3/gold.rb +81 -0
  69. data/lib/bio-ucsc/caljac3.rb +24 -0
  70. data/lib/bio-ucsc/caljac3/db_connection.rb +55 -0
  71. data/lib/bio-ucsc/canfam2.rb +39 -0
  72. data/lib/bio-ucsc/canfam2/chainbostau4.rb +81 -0
  73. data/lib/bio-ucsc/canfam2/chainbostau4link.rb +81 -0
  74. data/lib/bio-ucsc/canfam2/chainmm9.rb +81 -0
  75. data/lib/bio-ucsc/canfam2/chainmm9link.rb +81 -0
  76. data/lib/bio-ucsc/canfam2/chainrn4.rb +81 -0
  77. data/lib/bio-ucsc/canfam2/chainrn4link.rb +81 -0
  78. data/lib/bio-ucsc/canfam2/chainself.rb +81 -0
  79. data/lib/bio-ucsc/canfam2/chainselflink.rb +81 -0
  80. data/lib/bio-ucsc/canfam2/db_connection.rb +57 -0
  81. data/lib/bio-ucsc/canfam2/est.rb +81 -0
  82. data/lib/bio-ucsc/canfam2/gap.rb +81 -0
  83. data/lib/bio-ucsc/canfam2/gold.rb +81 -0
  84. data/lib/bio-ucsc/canfam2/intronest.rb +81 -0
  85. data/lib/bio-ucsc/canfam2/mrna.rb +81 -0
  86. data/lib/bio-ucsc/canfam2/rmsk.rb +78 -0
  87. data/lib/bio-ucsc/cavpor3.rb +21 -0
  88. data/lib/bio-ucsc/cavpor3/db_connection.rb +57 -0
  89. data/lib/bio-ucsc/cb3.rb +36 -0
  90. data/lib/bio-ucsc/cb3/chaincaepb1.rb +81 -0
  91. data/lib/bio-ucsc/cb3/chaincaepb1link.rb +81 -0
  92. data/lib/bio-ucsc/cb3/chaincaerem2.rb +81 -0
  93. data/lib/bio-ucsc/cb3/chaincaerem2link.rb +81 -0
  94. data/lib/bio-ucsc/cb3/chaince6.rb +81 -0
  95. data/lib/bio-ucsc/cb3/chaince6link.rb +81 -0
  96. data/lib/bio-ucsc/cb3/chainpripac1.rb +81 -0
  97. data/lib/bio-ucsc/cb3/chainpripac1link.rb +81 -0
  98. data/lib/bio-ucsc/cb3/db_connection.rb +57 -0
  99. data/lib/bio-ucsc/cb3/est.rb +81 -0
  100. data/lib/bio-ucsc/cb3/gap.rb +81 -0
  101. data/lib/bio-ucsc/cb3/gold.rb +81 -0
  102. data/lib/bio-ucsc/cb3/intronest.rb +81 -0
  103. data/lib/bio-ucsc/cb3/mrna.rb +81 -0
  104. data/lib/bio-ucsc/cb3/rmsk.rb +78 -0
  105. data/lib/bio-ucsc/ce6/chaincaejap1.rb +2 -2
  106. data/lib/bio-ucsc/ce6/chaincaejap1link.rb +2 -2
  107. data/lib/bio-ucsc/ce6/chaincaepb2.rb +2 -2
  108. data/lib/bio-ucsc/ce6/chaincaepb2link.rb +2 -2
  109. data/lib/bio-ucsc/ce6/chaincaerem3.rb +2 -2
  110. data/lib/bio-ucsc/ce6/chaincaerem3link.rb +2 -2
  111. data/lib/bio-ucsc/ce6/chaincb3.rb +2 -2
  112. data/lib/bio-ucsc/ce6/chaincb3link.rb +2 -2
  113. data/lib/bio-ucsc/ce6/chainpripac1.rb +2 -2
  114. data/lib/bio-ucsc/ce6/chainpripac1link.rb +2 -2
  115. data/lib/bio-ucsc/ce6/chainself.rb +2 -2
  116. data/lib/bio-ucsc/ce6/chainselflink.rb +2 -2
  117. data/lib/bio-ucsc/ce6/db_connection.rb +5 -6
  118. data/lib/bio-ucsc/ce6/est.rb +2 -2
  119. data/lib/bio-ucsc/ce6/gap.rb +2 -2
  120. data/lib/bio-ucsc/ce6/gold.rb +2 -2
  121. data/lib/bio-ucsc/ce6/intronest.rb +2 -2
  122. data/lib/bio-ucsc/ce6/mrna.rb +2 -2
  123. data/lib/bio-ucsc/ce6/rmsk.rb +2 -2
  124. data/lib/bio-ucsc/ce6/t25mersrepeats.rb +2 -2
  125. data/lib/bio-ucsc/ci2.rb +23 -0
  126. data/lib/bio-ucsc/ci2/db_connection.rb +55 -0
  127. data/lib/bio-ucsc/danrer7.rb +24 -0
  128. data/lib/bio-ucsc/danrer7/db_connection.rb +57 -0
  129. data/lib/bio-ucsc/dm3/chainanogam1.rb +2 -2
  130. data/lib/bio-ucsc/dm3/chainanogam1link.rb +2 -2
  131. data/lib/bio-ucsc/dm3/chainapimel3.rb +2 -2
  132. data/lib/bio-ucsc/dm3/chainapimel3link.rb +2 -2
  133. data/lib/bio-ucsc/dm3/chaindp3.rb +2 -2
  134. data/lib/bio-ucsc/dm3/chaindp3link.rb +2 -2
  135. data/lib/bio-ucsc/dm3/chaindroana2.rb +2 -2
  136. data/lib/bio-ucsc/dm3/chaindroana2link.rb +2 -2
  137. data/lib/bio-ucsc/dm3/chaindroere1.rb +2 -2
  138. data/lib/bio-ucsc/dm3/chaindroere1link.rb +2 -2
  139. data/lib/bio-ucsc/dm3/chaindroper1.rb +2 -2
  140. data/lib/bio-ucsc/dm3/chaindroper1link.rb +2 -2
  141. data/lib/bio-ucsc/dm3/chaindrosec1.rb +2 -2
  142. data/lib/bio-ucsc/dm3/chaindrosec1link.rb +2 -2
  143. data/lib/bio-ucsc/dm3/chaindrosim1.rb +2 -2
  144. data/lib/bio-ucsc/dm3/chaindrosim1link.rb +2 -2
  145. data/lib/bio-ucsc/dm3/chaindroyak2.rb +2 -2
  146. data/lib/bio-ucsc/dm3/chaindroyak2link.rb +2 -2
  147. data/lib/bio-ucsc/dm3/db_connection.rb +5 -6
  148. data/lib/bio-ucsc/dm3/est.rb +2 -2
  149. data/lib/bio-ucsc/dm3/gap.rb +2 -2
  150. data/lib/bio-ucsc/dm3/gold.rb +2 -2
  151. data/lib/bio-ucsc/dm3/intronest.rb +2 -2
  152. data/lib/bio-ucsc/dm3/mrna.rb +2 -2
  153. data/lib/bio-ucsc/dm3/rmsk.rb +2 -2
  154. data/lib/bio-ucsc/dp3.rb +33 -0
  155. data/lib/bio-ucsc/dp3/chaindm3.rb +81 -0
  156. data/lib/bio-ucsc/dp3/chaindm3link.rb +81 -0
  157. data/lib/bio-ucsc/dp3/db_connection.rb +57 -0
  158. data/lib/bio-ucsc/dp3/est.rb +81 -0
  159. data/lib/bio-ucsc/dp3/gap.rb +81 -0
  160. data/lib/bio-ucsc/dp3/gold.rb +81 -0
  161. data/lib/bio-ucsc/dp3/intronest.rb +81 -0
  162. data/lib/bio-ucsc/dp3/mrna.rb +81 -0
  163. data/lib/bio-ucsc/dp3/rmsk.rb +78 -0
  164. data/lib/bio-ucsc/droana2.rb +22 -0
  165. data/lib/bio-ucsc/droana2/db_connection.rb +57 -0
  166. data/lib/bio-ucsc/droere1.rb +22 -0
  167. data/lib/bio-ucsc/droere1/db_connection.rb +57 -0
  168. data/lib/bio-ucsc/drogri1.rb +22 -0
  169. data/lib/bio-ucsc/drogri1/db_connection.rb +57 -0
  170. data/lib/bio-ucsc/dromoj2.rb +22 -0
  171. data/lib/bio-ucsc/dromoj2/db_connection.rb +57 -0
  172. data/lib/bio-ucsc/droper1.rb +22 -0
  173. data/lib/bio-ucsc/droper1/db_connection.rb +57 -0
  174. data/lib/bio-ucsc/drosec1.rb +22 -0
  175. data/lib/bio-ucsc/drosec1/db_connection.rb +57 -0
  176. data/lib/bio-ucsc/drosim1.rb +30 -0
  177. data/lib/bio-ucsc/drosim1/chaindm3.rb +81 -0
  178. data/lib/bio-ucsc/drosim1/chaindm3link.rb +81 -0
  179. data/lib/bio-ucsc/drosim1/db_connection.rb +57 -0
  180. data/lib/bio-ucsc/drosim1/est.rb +81 -0
  181. data/lib/bio-ucsc/drosim1/gap.rb +81 -0
  182. data/lib/bio-ucsc/drosim1/gold.rb +81 -0
  183. data/lib/bio-ucsc/drosim1/intronest.rb +81 -0
  184. data/lib/bio-ucsc/drosim1/mrna.rb +81 -0
  185. data/lib/bio-ucsc/drosim1/rmsk.rb +78 -0
  186. data/lib/bio-ucsc/drovir2.rb +22 -0
  187. data/lib/bio-ucsc/drovir2/db_connection.rb +57 -0
  188. data/lib/bio-ucsc/droyak2.rb +32 -0
  189. data/lib/bio-ucsc/droyak2/chaindm3.rb +81 -0
  190. data/lib/bio-ucsc/droyak2/chaindm3link.rb +81 -0
  191. data/lib/bio-ucsc/droyak2/db_connection.rb +57 -0
  192. data/lib/bio-ucsc/droyak2/est.rb +81 -0
  193. data/lib/bio-ucsc/droyak2/gap.rb +81 -0
  194. data/lib/bio-ucsc/droyak2/gold.rb +81 -0
  195. data/lib/bio-ucsc/droyak2/intronest.rb +81 -0
  196. data/lib/bio-ucsc/droyak2/mrna.rb +81 -0
  197. data/lib/bio-ucsc/droyak2/rmsk.rb +78 -0
  198. data/lib/bio-ucsc/equcab2.rb +31 -0
  199. data/lib/bio-ucsc/equcab2/db_connection.rb +57 -0
  200. data/lib/bio-ucsc/equcab2/est.rb +81 -0
  201. data/lib/bio-ucsc/equcab2/gap.rb +81 -0
  202. data/lib/bio-ucsc/equcab2/gold.rb +81 -0
  203. data/lib/bio-ucsc/equcab2/intronest.rb +81 -0
  204. data/lib/bio-ucsc/equcab2/mrna.rb +81 -0
  205. data/lib/bio-ucsc/equcab2/rmsk.rb +78 -0
  206. data/lib/bio-ucsc/felcat4.rb +23 -0
  207. data/lib/bio-ucsc/felcat4/db_connection.rb +57 -0
  208. data/lib/bio-ucsc/fr2.rb +35 -0
  209. data/lib/bio-ucsc/fr2/chaingalgal3.rb +81 -0
  210. data/lib/bio-ucsc/fr2/chaingalgal3link.rb +81 -0
  211. data/lib/bio-ucsc/fr2/chaingasacu1.rb +81 -0
  212. data/lib/bio-ucsc/fr2/chaingasacu1link.rb +81 -0
  213. data/lib/bio-ucsc/fr2/chainmm9.rb +81 -0
  214. data/lib/bio-ucsc/fr2/chainmm9link.rb +81 -0
  215. data/lib/bio-ucsc/fr2/chainorylat2.rb +81 -0
  216. data/lib/bio-ucsc/fr2/chainorylat2link.rb +81 -0
  217. data/lib/bio-ucsc/fr2/db_connection.rb +57 -0
  218. data/lib/bio-ucsc/fr2/est.rb +81 -0
  219. data/lib/bio-ucsc/fr2/gap.rb +81 -0
  220. data/lib/bio-ucsc/fr2/gold.rb +81 -0
  221. data/lib/bio-ucsc/fr2/intronest.rb +81 -0
  222. data/lib/bio-ucsc/fr2/mrna.rb +81 -0
  223. data/lib/bio-ucsc/fr2/rmsk.rb +78 -0
  224. data/lib/bio-ucsc/galgal3.rb +54 -0
  225. data/lib/bio-ucsc/galgal3/chainanocar1.rb +81 -0
  226. data/lib/bio-ucsc/galgal3/chainanocar1link.rb +81 -0
  227. data/lib/bio-ucsc/galgal3/chainbraflo1.rb +81 -0
  228. data/lib/bio-ucsc/galgal3/chainbraflo1link.rb +81 -0
  229. data/lib/bio-ucsc/galgal3/chaincavpor3.rb +81 -0
  230. data/lib/bio-ucsc/galgal3/chaincavpor3link.rb +81 -0
  231. data/lib/bio-ucsc/galgal3/chaindanrer4.rb +81 -0
  232. data/lib/bio-ucsc/galgal3/chaindanrer4link.rb +81 -0
  233. data/lib/bio-ucsc/galgal3/chainfr2.rb +81 -0
  234. data/lib/bio-ucsc/galgal3/chainfr2link.rb +81 -0
  235. data/lib/bio-ucsc/galgal3/chaingasacu1.rb +81 -0
  236. data/lib/bio-ucsc/galgal3/chaingasacu1link.rb +81 -0
  237. data/lib/bio-ucsc/galgal3/chainmm9.rb +81 -0
  238. data/lib/bio-ucsc/galgal3/chainmm9link.rb +81 -0
  239. data/lib/bio-ucsc/galgal3/chainornana1.rb +81 -0
  240. data/lib/bio-ucsc/galgal3/chainornana1link.rb +81 -0
  241. data/lib/bio-ucsc/galgal3/chainpetmar1.rb +81 -0
  242. data/lib/bio-ucsc/galgal3/chainpetmar1link.rb +81 -0
  243. data/lib/bio-ucsc/galgal3/chainrn4.rb +81 -0
  244. data/lib/bio-ucsc/galgal3/chainrn4link.rb +81 -0
  245. data/lib/bio-ucsc/galgal3/chaintaegut1.rb +81 -0
  246. data/lib/bio-ucsc/galgal3/chaintaegut1link.rb +81 -0
  247. data/lib/bio-ucsc/galgal3/chainxentro2.rb +81 -0
  248. data/lib/bio-ucsc/galgal3/chainxentro2link.rb +81 -0
  249. data/lib/bio-ucsc/galgal3/db_connection.rb +57 -0
  250. data/lib/bio-ucsc/galgal3/est.rb +81 -0
  251. data/lib/bio-ucsc/galgal3/gap.rb +81 -0
  252. data/lib/bio-ucsc/galgal3/gold.rb +81 -0
  253. data/lib/bio-ucsc/galgal3/intronest.rb +81 -0
  254. data/lib/bio-ucsc/galgal3/mrna.rb +81 -0
  255. data/lib/bio-ucsc/galgal3/rmsk.rb +78 -0
  256. data/lib/bio-ucsc/gasacu1.rb +39 -0
  257. data/lib/bio-ucsc/gasacu1/chainanocar1.rb +81 -0
  258. data/lib/bio-ucsc/gasacu1/chainanocar1link.rb +81 -0
  259. data/lib/bio-ucsc/gasacu1/chainfr2.rb +81 -0
  260. data/lib/bio-ucsc/gasacu1/chainfr2link.rb +81 -0
  261. data/lib/bio-ucsc/gasacu1/chaingalgal3.rb +81 -0
  262. data/lib/bio-ucsc/gasacu1/chaingalgal3link.rb +81 -0
  263. data/lib/bio-ucsc/gasacu1/chainmm9.rb +81 -0
  264. data/lib/bio-ucsc/gasacu1/chainmm9link.rb +81 -0
  265. data/lib/bio-ucsc/gasacu1/chainorylat2.rb +81 -0
  266. data/lib/bio-ucsc/gasacu1/chainorylat2link.rb +81 -0
  267. data/lib/bio-ucsc/gasacu1/db_connection.rb +57 -0
  268. data/lib/bio-ucsc/gasacu1/est.rb +81 -0
  269. data/lib/bio-ucsc/gasacu1/intronest.rb +81 -0
  270. data/lib/bio-ucsc/gasacu1/mrna.rb +81 -0
  271. data/lib/bio-ucsc/gasacu1/rmsk.rb +78 -0
  272. data/lib/bio-ucsc/go/db_connection.rb +5 -6
  273. data/lib/bio-ucsc/hg18/chainanocar1.rb +2 -2
  274. data/lib/bio-ucsc/hg18/chainbostau4.rb +2 -2
  275. data/lib/bio-ucsc/hg18/chainbraflo1.rb +2 -2
  276. data/lib/bio-ucsc/hg18/chaincaljac1.rb +2 -2
  277. data/lib/bio-ucsc/hg18/chaincanfam2.rb +2 -2
  278. data/lib/bio-ucsc/hg18/chaincavpor3.rb +2 -2
  279. data/lib/bio-ucsc/hg18/chaindanrer5.rb +2 -2
  280. data/lib/bio-ucsc/hg18/chainequcab1.rb +2 -2
  281. data/lib/bio-ucsc/hg18/chainfelcat3.rb +2 -2
  282. data/lib/bio-ucsc/hg18/chainfr2.rb +2 -2
  283. data/lib/bio-ucsc/hg18/chaingalgal3.rb +2 -2
  284. data/lib/bio-ucsc/hg18/chaingasacu1.rb +2 -2
  285. data/lib/bio-ucsc/hg18/chainmm9.rb +2 -2
  286. data/lib/bio-ucsc/hg18/chainmondom4.rb +2 -2
  287. data/lib/bio-ucsc/hg18/chainornana1.rb +2 -2
  288. data/lib/bio-ucsc/hg18/chainorylat2.rb +2 -2
  289. data/lib/bio-ucsc/hg18/chainpantro2.rb +2 -2
  290. data/lib/bio-ucsc/hg18/chainpetmar1.rb +2 -2
  291. data/lib/bio-ucsc/hg18/chainponabe2.rb +2 -2
  292. data/lib/bio-ucsc/hg18/chainrhemac2.rb +2 -2
  293. data/lib/bio-ucsc/hg18/chainrn4.rb +2 -2
  294. data/lib/bio-ucsc/hg18/chainself.rb +2 -2
  295. data/lib/bio-ucsc/hg18/chainstrpur2.rb +2 -2
  296. data/lib/bio-ucsc/hg18/chaintaegut1.rb +2 -2
  297. data/lib/bio-ucsc/hg18/chaintetnig2.rb +2 -2
  298. data/lib/bio-ucsc/hg18/chainxentro2.rb +2 -2
  299. data/lib/bio-ucsc/hg18/db_connection.rb +5 -7
  300. data/lib/bio-ucsc/hg18/gap.rb +2 -2
  301. data/lib/bio-ucsc/hg18/gold.rb +2 -2
  302. data/lib/bio-ucsc/hg18/intronest.rb +2 -2
  303. data/lib/bio-ucsc/hg18/rmsk.rb +2 -2
  304. data/lib/bio-ucsc/hg18/rmskrm327.rb +2 -2
  305. data/lib/bio-ucsc/hgfixed/db_connection.rb +5 -6
  306. data/lib/bio-ucsc/loxafr3.rb +20 -0
  307. data/lib/bio-ucsc/loxafr3/db_connection.rb +57 -0
  308. data/lib/bio-ucsc/mm9/chainanocar1.rb +2 -2
  309. data/lib/bio-ucsc/mm9/chainanocar1link.rb +2 -2
  310. data/lib/bio-ucsc/mm9/chainbostau4.rb +2 -2
  311. data/lib/bio-ucsc/mm9/chainbostau4link.rb +3 -3
  312. data/lib/bio-ucsc/mm9/chainbraflo1.rb +2 -2
  313. data/lib/bio-ucsc/mm9/chainbraflo1link.rb +2 -2
  314. data/lib/bio-ucsc/mm9/chaincanfam2.rb +2 -2
  315. data/lib/bio-ucsc/mm9/chaincanfam2link.rb +2 -2
  316. data/lib/bio-ucsc/mm9/chaincavpor3.rb +2 -2
  317. data/lib/bio-ucsc/mm9/chaincavpor3link.rb +2 -2
  318. data/lib/bio-ucsc/mm9/chainfr2.rb +2 -2
  319. data/lib/bio-ucsc/mm9/chainfr2link.rb +2 -2
  320. data/lib/bio-ucsc/mm9/chaingalgal3.rb +2 -2
  321. data/lib/bio-ucsc/mm9/chaingalgal3link.rb +2 -2
  322. data/lib/bio-ucsc/mm9/chaingasacu1.rb +2 -2
  323. data/lib/bio-ucsc/mm9/chaingasacu1link.rb +2 -2
  324. data/lib/bio-ucsc/mm9/chainornana1.rb +2 -2
  325. data/lib/bio-ucsc/mm9/chainornana1link.rb +2 -2
  326. data/lib/bio-ucsc/mm9/chainorylat2.rb +2 -2
  327. data/lib/bio-ucsc/mm9/chainorylat2link.rb +2 -2
  328. data/lib/bio-ucsc/mm9/chainpantro2.rb +2 -2
  329. data/lib/bio-ucsc/mm9/chainpantro2link.rb +2 -2
  330. data/lib/bio-ucsc/mm9/chainpetmar1.rb +2 -2
  331. data/lib/bio-ucsc/mm9/chainpetmar1link.rb +2 -2
  332. data/lib/bio-ucsc/mm9/chainponabe2.rb +2 -2
  333. data/lib/bio-ucsc/mm9/chainponabe2link.rb +2 -2
  334. data/lib/bio-ucsc/mm9/chainrhemac2.rb +2 -2
  335. data/lib/bio-ucsc/mm9/chainrhemac2link.rb +2 -2
  336. data/lib/bio-ucsc/mm9/chainrn4.rb +2 -2
  337. data/lib/bio-ucsc/mm9/chainrn4link.rb +2 -2
  338. data/lib/bio-ucsc/mm9/chainxentro2.rb +2 -2
  339. data/lib/bio-ucsc/mm9/chainxentro2link.rb +2 -2
  340. data/lib/bio-ucsc/mm9/db_connection.rb +6 -7
  341. data/lib/bio-ucsc/mm9/est.rb +2 -2
  342. data/lib/bio-ucsc/mm9/gap.rb +2 -2
  343. data/lib/bio-ucsc/mm9/gold.rb +2 -2
  344. data/lib/bio-ucsc/mm9/intronest.rb +2 -2
  345. data/lib/bio-ucsc/mm9/mrna.rb +2 -2
  346. data/lib/bio-ucsc/mm9/rmsk.rb +2 -2
  347. data/lib/bio-ucsc/mondom5.rb +21 -0
  348. data/lib/bio-ucsc/mondom5/db_connection.rb +57 -0
  349. data/lib/bio-ucsc/ornana1.rb +20 -0
  350. data/lib/bio-ucsc/ornana1/db_connection.rb +57 -0
  351. data/lib/bio-ucsc/orycun2.rb +24 -0
  352. data/lib/bio-ucsc/orycun2/db_connection.rb +57 -0
  353. data/lib/bio-ucsc/orylat2.rb +24 -0
  354. data/lib/bio-ucsc/orylat2/db_connection.rb +55 -0
  355. data/lib/bio-ucsc/oviari1.rb +24 -0
  356. data/lib/bio-ucsc/oviari1/db_connection.rb +57 -0
  357. data/lib/bio-ucsc/pantro3.rb +24 -0
  358. data/lib/bio-ucsc/pantro3/db_connection.rb +55 -0
  359. data/lib/bio-ucsc/petmar1.rb +22 -0
  360. data/lib/bio-ucsc/petmar1/db_connection.rb +57 -0
  361. data/lib/bio-ucsc/ponabe2.rb +36 -0
  362. data/lib/bio-ucsc/ponabe2/chainmm9.rb +81 -0
  363. data/lib/bio-ucsc/ponabe2/chainmm9link.rb +81 -0
  364. data/lib/bio-ucsc/ponabe2/chainornana1.rb +81 -0
  365. data/lib/bio-ucsc/ponabe2/chainornana1link.rb +81 -0
  366. data/lib/bio-ucsc/ponabe2/chainrhemac2.rb +81 -0
  367. data/lib/bio-ucsc/ponabe2/chainrhemac2link.rb +81 -0
  368. data/lib/bio-ucsc/ponabe2/db_connection.rb +55 -0
  369. data/lib/bio-ucsc/ponabe2/est.rb +81 -0
  370. data/lib/bio-ucsc/ponabe2/gap.rb +81 -0
  371. data/lib/bio-ucsc/ponabe2/gold.rb +81 -0
  372. data/lib/bio-ucsc/ponabe2/intronest.rb +81 -0
  373. data/lib/bio-ucsc/ponabe2/mrna.rb +81 -0
  374. data/lib/bio-ucsc/ponabe2/rmsk.rb +78 -0
  375. data/lib/bio-ucsc/pripac1.rb +33 -0
  376. data/lib/bio-ucsc/pripac1/chaincaepb1.rb +81 -0
  377. data/lib/bio-ucsc/pripac1/chaincaepb1link.rb +81 -0
  378. data/lib/bio-ucsc/pripac1/chaincaerem2.rb +81 -0
  379. data/lib/bio-ucsc/pripac1/chaincaerem2link.rb +81 -0
  380. data/lib/bio-ucsc/pripac1/chaincb3.rb +81 -0
  381. data/lib/bio-ucsc/pripac1/chaincb3link.rb +81 -0
  382. data/lib/bio-ucsc/pripac1/chaince6.rb +81 -0
  383. data/lib/bio-ucsc/pripac1/chaince6link.rb +81 -0
  384. data/lib/bio-ucsc/pripac1/db_connection.rb +57 -0
  385. data/lib/bio-ucsc/pripac1/gap.rb +81 -0
  386. data/lib/bio-ucsc/pripac1/gold.rb +81 -0
  387. data/lib/bio-ucsc/pripac1/rmsk.rb +78 -0
  388. data/lib/bio-ucsc/proteome/db_connection.rb +5 -7
  389. data/lib/bio-ucsc/rhemac2.rb +32 -0
  390. data/lib/bio-ucsc/rhemac2/chainmm9.rb +81 -0
  391. data/lib/bio-ucsc/rhemac2/chainmm9link.rb +81 -0
  392. data/lib/bio-ucsc/rhemac2/chainpantro2.rb +81 -0
  393. data/lib/bio-ucsc/rhemac2/chainpantro2link.rb +81 -0
  394. data/lib/bio-ucsc/rhemac2/chainponabe2.rb +81 -0
  395. data/lib/bio-ucsc/rhemac2/chainponabe2link.rb +81 -0
  396. data/lib/bio-ucsc/rhemac2/chainrn4.rb +81 -0
  397. data/lib/bio-ucsc/rhemac2/chainrn4link.rb +81 -0
  398. data/lib/bio-ucsc/rhemac2/db_connection.rb +55 -0
  399. data/lib/bio-ucsc/rn4.rb +52 -0
  400. data/lib/bio-ucsc/rn4/chainbostau3.rb +79 -0
  401. data/lib/bio-ucsc/rn4/chainbostau3link.rb +79 -0
  402. data/lib/bio-ucsc/rn4/chaincanfam2.rb +82 -0
  403. data/lib/bio-ucsc/rn4/chaincanfam2link.rb +82 -0
  404. data/lib/bio-ucsc/rn4/chaincavpor3.rb +81 -0
  405. data/lib/bio-ucsc/rn4/chaincavpor3link.rb +81 -0
  406. data/lib/bio-ucsc/rn4/chaindanrer4.rb +81 -0
  407. data/lib/bio-ucsc/rn4/chaindanrer4link.rb +81 -0
  408. data/lib/bio-ucsc/rn4/chainequcab1.rb +81 -0
  409. data/lib/bio-ucsc/rn4/chainequcab1link.rb +81 -0
  410. data/lib/bio-ucsc/rn4/chaingalgal3.rb +81 -0
  411. data/lib/bio-ucsc/rn4/chaingalgal3link.rb +81 -0
  412. data/lib/bio-ucsc/rn4/chainmm9.rb +81 -0
  413. data/lib/bio-ucsc/rn4/chainmm9link.rb +81 -0
  414. data/lib/bio-ucsc/rn4/chainmondom4.rb +81 -0
  415. data/lib/bio-ucsc/rn4/chainmondom4link.rb +81 -0
  416. data/lib/bio-ucsc/rn4/chainpantro2.rb +81 -0
  417. data/lib/bio-ucsc/rn4/chainpantro2link.rb +82 -0
  418. data/lib/bio-ucsc/rn4/chainrhemac2.rb +81 -0
  419. data/lib/bio-ucsc/rn4/chainrhemac2link.rb +81 -0
  420. data/lib/bio-ucsc/rn4/chainxentro2.rb +81 -0
  421. data/lib/bio-ucsc/rn4/chainxentro2link.rb +81 -0
  422. data/lib/bio-ucsc/rn4/db_connection.rb +55 -0
  423. data/lib/bio-ucsc/rn4/est.rb +81 -0
  424. data/lib/bio-ucsc/rn4/gap.rb +81 -0
  425. data/lib/bio-ucsc/rn4/gold.rb +81 -0
  426. data/lib/bio-ucsc/rn4/intronest.rb +81 -0
  427. data/lib/bio-ucsc/rn4/mrna.rb +81 -0
  428. data/lib/bio-ucsc/rn4/rmsk.rb +78 -0
  429. data/lib/bio-ucsc/saccer2.rb +33 -0
  430. data/lib/bio-ucsc/saccer2/db_connection.rb +55 -0
  431. data/lib/bio-ucsc/saccer2/est.rb +83 -0
  432. data/lib/bio-ucsc/saccer2/gap.rb +83 -0
  433. data/lib/bio-ucsc/saccer2/gold.rb +83 -0
  434. data/lib/bio-ucsc/saccer2/intronest.rb +83 -0
  435. data/lib/bio-ucsc/saccer2/mrna.rb +83 -0
  436. data/lib/bio-ucsc/saccer2/t2micron_est.rb +57 -0
  437. data/lib/bio-ucsc/saccer2/t2micron_gap.rb +57 -0
  438. data/lib/bio-ucsc/saccer2/t2micron_gold.rb +58 -0
  439. data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb +57 -0
  440. data/lib/bio-ucsc/saccer2/t2micron_mrna.rb +57 -0
  441. data/lib/bio-ucsc/strpur2.rb +32 -0
  442. data/lib/bio-ucsc/strpur2/chaingalgal3.rb +81 -0
  443. data/lib/bio-ucsc/strpur2/chaingalgal3link.rb +81 -0
  444. data/lib/bio-ucsc/strpur2/chainhg18.rb +81 -0
  445. data/lib/bio-ucsc/strpur2/chainhg18link.rb +81 -0
  446. data/lib/bio-ucsc/strpur2/chainmm9.rb +81 -0
  447. data/lib/bio-ucsc/strpur2/chainmm9link.rb +81 -0
  448. data/lib/bio-ucsc/strpur2/chainpetmar1.rb +81 -0
  449. data/lib/bio-ucsc/strpur2/chainpetmar1link.rb +81 -0
  450. data/lib/bio-ucsc/strpur2/db_connection.rb +57 -0
  451. data/lib/bio-ucsc/strpur2/gap.rb +81 -0
  452. data/lib/bio-ucsc/strpur2/gold.rb +81 -0
  453. data/lib/bio-ucsc/susscr2.rb +26 -0
  454. data/lib/bio-ucsc/susscr2/db_connection.rb +57 -0
  455. data/lib/bio-ucsc/susscr2/est.rb +81 -0
  456. data/lib/bio-ucsc/susscr2/intronest.rb +81 -0
  457. data/lib/bio-ucsc/susscr2/mrna.rb +81 -0
  458. data/lib/bio-ucsc/table_class_detector.rb +18 -22
  459. data/lib/bio-ucsc/taegut1.rb +33 -0
  460. data/lib/bio-ucsc/taegut1/chaingalgal3.rb +81 -0
  461. data/lib/bio-ucsc/taegut1/chaingalgal3link.rb +81 -0
  462. data/lib/bio-ucsc/taegut1/db_connection.rb +57 -0
  463. data/lib/bio-ucsc/taegut1/est.rb +81 -0
  464. data/lib/bio-ucsc/taegut1/gap.rb +81 -0
  465. data/lib/bio-ucsc/taegut1/gold.rb +81 -0
  466. data/lib/bio-ucsc/taegut1/intronest.rb +81 -0
  467. data/lib/bio-ucsc/taegut1/mrna.rb +81 -0
  468. data/lib/bio-ucsc/taegut1/rmsk.rb +78 -0
  469. data/lib/bio-ucsc/tetnig2.rb +25 -0
  470. data/lib/bio-ucsc/tetnig2/db_connection.rb +57 -0
  471. data/lib/bio-ucsc/tetnig2/mrna.rb +81 -0
  472. data/lib/bio-ucsc/uniprot/db_connection.rb +5 -7
  473. data/lib/bio-ucsc/visigene/db_connection.rb +5 -6
  474. data/lib/bio-ucsc/xentro2.rb +30 -0
  475. data/lib/bio-ucsc/xentro2/chaingalgal3.rb +81 -0
  476. data/lib/bio-ucsc/xentro2/chaingalgal3link.rb +81 -0
  477. data/lib/bio-ucsc/xentro2/db_connection.rb +57 -0
  478. data/lib/bio-ucsc/xentro2/est.rb +81 -0
  479. data/lib/bio-ucsc/xentro2/gap.rb +81 -0
  480. data/lib/bio-ucsc/xentro2/gold.rb +81 -0
  481. data/lib/bio-ucsc/xentro2/intronest.rb +81 -0
  482. data/lib/bio-ucsc/xentro2/mrna.rb +81 -0
  483. data/lib/bio-ucsc/xentro2/rmsk.rb +78 -0
  484. data/samples/hg19-2bit-retrieve.rb +5 -2
  485. data/spec/ailmel1_spec.rb +770 -0
  486. data/spec/anocar2_spec.rb +750 -0
  487. data/spec/anogam1_spec.rb +568 -0
  488. data/spec/apimel2_spec.rb +542 -0
  489. data/spec/aplcal1_spec.rb +530 -0
  490. data/spec/bostau4_spec.rb +920 -0
  491. data/spec/braflo1_spec.rb +660 -0
  492. data/spec/caejap1_spec.rb +524 -0
  493. data/spec/caepb2_spec.rb +515 -0
  494. data/spec/caerem3_spec.rb +524 -0
  495. data/spec/caljac3_spec.rb +860 -0
  496. data/spec/canfam2_spec.rb +1145 -0
  497. data/spec/cavpor3_spec.rb +880 -0
  498. data/spec/cb3_spec.rb +634 -0
  499. data/spec/ci2_spec.rb +520 -0
  500. data/spec/danrer7_spec.rb +810 -0
  501. data/spec/dp3_spec.rb +617 -0
  502. data/spec/droana2_spec.rb +500 -0
  503. data/spec/droere1_spec.rb +510 -0
  504. data/spec/drogri1_spec.rb +470 -0
  505. data/spec/dromoj2_spec.rb +510 -0
  506. data/spec/droper1_spec.rb +470 -0
  507. data/spec/drosec1_spec.rb +470 -0
  508. data/spec/drosim1_spec.rb +588 -0
  509. data/spec/drovir2_spec.rb +540 -0
  510. data/spec/droyak2_spec.rb +558 -0
  511. data/spec/equcab2_spec.rb +936 -0
  512. data/spec/felcat4_spec.rb +770 -0
  513. data/spec/fr2_spec.rb +835 -0
  514. data/spec/galgal3_spec.rb +1351 -0
  515. data/spec/gasacu1_spec.rb +924 -0
  516. data/spec/loxafr3_spec.rb +550 -0
  517. data/spec/mondom5_spec.rb +1230 -0
  518. data/spec/ornana1_spec.rb +980 -0
  519. data/spec/orycun2_spec.rb +770 -0
  520. data/spec/orylat2_spec.rb +930 -0
  521. data/spec/oviari1_spec.rb +670 -0
  522. data/spec/pantro3_spec.rb +810 -0
  523. data/spec/petmar1_spec.rb +770 -0
  524. data/spec/ponabe2_spec.rb +962 -0
  525. data/spec/pripac1_spec.rb +621 -0
  526. data/spec/rhemac2_spec.rb +958 -0
  527. data/spec/rn4_spec.rb +2038 -0
  528. data/spec/saccer2_spec.rb +925 -0
  529. data/spec/strpur2_spec.rb +600 -0
  530. data/spec/susscr2_spec.rb +623 -0
  531. data/spec/taegut1_spec.rb +768 -0
  532. data/spec/tetnig2_spec.rb +721 -0
  533. data/spec/xentro2_spec.rb +900 -0
  534. metadata +477 -23
@@ -0,0 +1,936 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::EquCab2" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::EquCab2::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::EquCab2::All_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::EquCab2::All_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::EquCab2::All_mrna" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::EquCab2::All_mrna.first
24
+ pp result
25
+ result.should be_true
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::EquCab2::Author" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::EquCab2::Author.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::EquCab2::BlastHg18KG" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::EquCab2::BlastHg18KG.first
44
+ pp result
45
+ result.should be_true
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::EquCab2::Cds" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::EquCab2::Cds.first
54
+ pp result
55
+ result.should be_true
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::EquCab2::Cell" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::EquCab2::Cell.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::EquCab2::ChainCanFam2" do
71
+ context ".first" do
72
+ it 'returns the first records' do
73
+ result = Bio::Ucsc::EquCab2::ChainCanFam2.first
74
+ pp result
75
+ result.should be_true
76
+ end
77
+ end
78
+ end
79
+
80
+ describe "Bio::Ucsc::EquCab2::ChainCanFam2Link" do
81
+ context ".first" do
82
+ it 'returns the first records' do
83
+ result = Bio::Ucsc::EquCab2::ChainCanFam2Link.first
84
+ pp result
85
+ result.should be_true
86
+ end
87
+ end
88
+ end
89
+
90
+ describe "Bio::Ucsc::EquCab2::ChainGalGal3" do
91
+ context ".first" do
92
+ it 'returns the first records' do
93
+ result = Bio::Ucsc::EquCab2::ChainGalGal3.first
94
+ pp result
95
+ result.should be_true
96
+ end
97
+ end
98
+ end
99
+
100
+ describe "Bio::Ucsc::EquCab2::ChainGalGal3Link" do
101
+ context ".first" do
102
+ it 'returns the first records' do
103
+ result = Bio::Ucsc::EquCab2::ChainGalGal3Link.first
104
+ pp result
105
+ result.should be_true
106
+ end
107
+ end
108
+ end
109
+
110
+ describe "Bio::Ucsc::EquCab2::ChainHg19" do
111
+ context ".first" do
112
+ it 'returns the first records' do
113
+ result = Bio::Ucsc::EquCab2::ChainHg19.first
114
+ pp result
115
+ result.should be_true
116
+ end
117
+ end
118
+ end
119
+
120
+ describe "Bio::Ucsc::EquCab2::ChainHg19Link" do
121
+ context ".first" do
122
+ it 'returns the first records' do
123
+ result = Bio::Ucsc::EquCab2::ChainHg19Link.first
124
+ pp result
125
+ result.should be_true
126
+ end
127
+ end
128
+ end
129
+
130
+ describe "Bio::Ucsc::EquCab2::ChainMm9" do
131
+ context ".first" do
132
+ it 'returns the first records' do
133
+ result = Bio::Ucsc::EquCab2::ChainMm9.first
134
+ pp result
135
+ result.should be_true
136
+ end
137
+ end
138
+ end
139
+
140
+ describe "Bio::Ucsc::EquCab2::ChainMm9Link" do
141
+ context ".first" do
142
+ it 'returns the first records' do
143
+ result = Bio::Ucsc::EquCab2::ChainMm9Link.first
144
+ pp result
145
+ result.should be_true
146
+ end
147
+ end
148
+ end
149
+
150
+ describe "Bio::Ucsc::EquCab2::ChainMonDom5" do
151
+ context ".first" do
152
+ it 'returns the first records' do
153
+ result = Bio::Ucsc::EquCab2::ChainMonDom5.first
154
+ pp result
155
+ result.should be_true
156
+ end
157
+ end
158
+ end
159
+
160
+ describe "Bio::Ucsc::EquCab2::ChainMonDom5Link" do
161
+ context ".first" do
162
+ it 'returns the first records' do
163
+ result = Bio::Ucsc::EquCab2::ChainMonDom5Link.first
164
+ pp result
165
+ result.should be_true
166
+ end
167
+ end
168
+ end
169
+
170
+ describe "Bio::Ucsc::EquCab2::ChainOrnAna1" do
171
+ context ".first" do
172
+ it 'returns the first records' do
173
+ result = Bio::Ucsc::EquCab2::ChainOrnAna1.first
174
+ pp result
175
+ result.should be_true
176
+ end
177
+ end
178
+ end
179
+
180
+ describe "Bio::Ucsc::EquCab2::ChainOrnAna1Link" do
181
+ context ".first" do
182
+ it 'returns the first records' do
183
+ result = Bio::Ucsc::EquCab2::ChainOrnAna1Link.first
184
+ pp result
185
+ result.should be_true
186
+ end
187
+ end
188
+ end
189
+
190
+ describe "Bio::Ucsc::EquCab2::ChainOviAri1" do
191
+ context ".first" do
192
+ it 'returns the first records' do
193
+ result = Bio::Ucsc::EquCab2::ChainOviAri1.first
194
+ pp result
195
+ result.should be_true
196
+ end
197
+ end
198
+ end
199
+
200
+ describe "Bio::Ucsc::EquCab2::ChainOviAri1Link" do
201
+ context ".first" do
202
+ it 'returns the first records' do
203
+ result = Bio::Ucsc::EquCab2::ChainOviAri1Link.first
204
+ pp result
205
+ result.should be_true
206
+ end
207
+ end
208
+ end
209
+
210
+ describe "Bio::Ucsc::EquCab2::ChainPanTro3" do
211
+ context ".first" do
212
+ it 'returns the first records' do
213
+ result = Bio::Ucsc::EquCab2::ChainPanTro3.first
214
+ pp result
215
+ result.should be_true
216
+ end
217
+ end
218
+ end
219
+
220
+ describe "Bio::Ucsc::EquCab2::ChainPanTro3Link" do
221
+ context ".first" do
222
+ it 'returns the first records' do
223
+ result = Bio::Ucsc::EquCab2::ChainPanTro3Link.first
224
+ pp result
225
+ result.should be_true
226
+ end
227
+ end
228
+ end
229
+
230
+ describe "Bio::Ucsc::EquCab2::ChromInfo" do
231
+ context ".first" do
232
+ it 'returns the first records' do
233
+ result = Bio::Ucsc::EquCab2::ChromInfo.first
234
+ pp result
235
+ result.should be_true
236
+ end
237
+ end
238
+ end
239
+
240
+ describe "Bio::Ucsc::EquCab2::CtgPos2" do
241
+ context ".first" do
242
+ it 'returns the first records' do
243
+ result = Bio::Ucsc::EquCab2::CtgPos2.first
244
+ pp result
245
+ result.should be_true
246
+ end
247
+ end
248
+ end
249
+
250
+ describe "Bio::Ucsc::EquCab2::Description" do
251
+ context ".first" do
252
+ it 'returns the first records' do
253
+ result = Bio::Ucsc::EquCab2::Description.first
254
+ pp result
255
+ result.should be_true
256
+ end
257
+ end
258
+ end
259
+
260
+ describe "Bio::Ucsc::EquCab2::Development" do
261
+ context ".first" do
262
+ it 'returns the first records' do
263
+ result = Bio::Ucsc::EquCab2::Development.first
264
+ pp result
265
+ result.should be_true
266
+ end
267
+ end
268
+ end
269
+
270
+ describe "Bio::Ucsc::EquCab2::EnsGene" do
271
+ context ".first" do
272
+ it 'returns the first records' do
273
+ result = Bio::Ucsc::EquCab2::EnsGene.first
274
+ pp result
275
+ result.should be_true
276
+ end
277
+ end
278
+ end
279
+
280
+ describe "Bio::Ucsc::EquCab2::EnsGtp" do
281
+ context ".first" do
282
+ it 'returns the first records' do
283
+ result = Bio::Ucsc::EquCab2::EnsGtp.first
284
+ pp result
285
+ result.should be_true
286
+ end
287
+ end
288
+ end
289
+
290
+ describe "Bio::Ucsc::EquCab2::EnsPep" do
291
+ context ".first" do
292
+ it 'returns the first records' do
293
+ result = Bio::Ucsc::EquCab2::EnsPep.first
294
+ pp result
295
+ result.should be_true
296
+ end
297
+ end
298
+ end
299
+
300
+ describe "Bio::Ucsc::EquCab2::Est" do
301
+ context ".first" do
302
+ it 'returns the first records' do
303
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
304
+ result = Bio::Ucsc::EquCab2::Est.find_by_interval gi
305
+ pp result
306
+ result.should be_true
307
+ end
308
+ end
309
+ end
310
+
311
+ describe "Bio::Ucsc::EquCab2::EstOrientInfo" do
312
+ context ".first" do
313
+ it 'returns the first records' do
314
+ result = Bio::Ucsc::EquCab2::EstOrientInfo.first
315
+ pp result
316
+ result.should be_true
317
+ end
318
+ end
319
+ end
320
+
321
+ describe "Bio::Ucsc::EquCab2::ExtFile" do
322
+ context ".first" do
323
+ it 'returns the first records' do
324
+ result = Bio::Ucsc::EquCab2::ExtFile.first
325
+ pp result
326
+ result.should be_true
327
+ end
328
+ end
329
+ end
330
+
331
+ describe "Bio::Ucsc::EquCab2::Gap" do
332
+ context ".find_by_interval" do
333
+ it 'returns the first records' do
334
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
335
+ result = Bio::Ucsc::EquCab2::Gap.find_by_interval gi
336
+ pp result
337
+ result.should be_true
338
+ end
339
+ end
340
+ end
341
+
342
+ describe "Bio::Ucsc::EquCab2::GbCdnaInfo" do
343
+ context ".first" do
344
+ it 'returns the first records' do
345
+ result = Bio::Ucsc::EquCab2::GbCdnaInfo.first
346
+ pp result
347
+ result.should be_true
348
+ end
349
+ end
350
+ end
351
+
352
+ describe "Bio::Ucsc::EquCab2::GbExtFile" do
353
+ context ".first" do
354
+ it 'returns the first records' do
355
+ result = Bio::Ucsc::EquCab2::GbExtFile.first
356
+ pp result
357
+ result.should be_true
358
+ end
359
+ end
360
+ end
361
+
362
+ describe "Bio::Ucsc::EquCab2::GbLoaded" do
363
+ context ".first" do
364
+ it 'returns the first records' do
365
+ result = Bio::Ucsc::EquCab2::GbLoaded.first
366
+ pp result
367
+ result.should be_true
368
+ end
369
+ end
370
+ end
371
+
372
+ describe "Bio::Ucsc::EquCab2::GbMiscDiff" do
373
+ context ".first" do
374
+ it 'returns the first records' do
375
+ result = Bio::Ucsc::EquCab2::GbMiscDiff.first
376
+ pp result
377
+ result.should be_true
378
+ end
379
+ end
380
+ end
381
+
382
+ describe "Bio::Ucsc::EquCab2::GbSeq" do
383
+ context ".first" do
384
+ it 'returns the first records' do
385
+ result = Bio::Ucsc::EquCab2::GbSeq.first
386
+ pp result
387
+ result.should be_true
388
+ end
389
+ end
390
+ end
391
+
392
+ describe "Bio::Ucsc::EquCab2::GbStatus" do
393
+ context ".first" do
394
+ it 'returns the first records' do
395
+ result = Bio::Ucsc::EquCab2::GbStatus.first
396
+ pp result
397
+ result.should be_true
398
+ end
399
+ end
400
+ end
401
+
402
+ describe "Bio::Ucsc::EquCab2::GbWarn" do
403
+ context ".first" do
404
+ it 'returns the first records' do
405
+ result = Bio::Ucsc::EquCab2::GbWarn.first
406
+ pp result
407
+ result.should be_true
408
+ end
409
+ end
410
+ end
411
+
412
+ describe "Bio::Ucsc::EquCab2::Gc5Base" do
413
+ context ".first" do
414
+ it 'returns the first records' do
415
+ result = Bio::Ucsc::EquCab2::Gc5Base.first
416
+ pp result
417
+ result.should be_true
418
+ end
419
+ end
420
+ end
421
+
422
+ describe "Bio::Ucsc::EquCab2::GeneName" do
423
+ context ".first" do
424
+ it 'returns the first records' do
425
+ result = Bio::Ucsc::EquCab2::GeneName.first
426
+ pp result
427
+ result.should be_true
428
+ end
429
+ end
430
+ end
431
+
432
+ describe "Bio::Ucsc::EquCab2::Gold" do
433
+ context ".find_by_interval" do
434
+ it 'returns the first records' do
435
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
436
+ result = Bio::Ucsc::EquCab2::Gold.find_by_interval gi
437
+ pp result
438
+ result.should be_true
439
+ end
440
+ end
441
+ end
442
+
443
+ describe "Bio::Ucsc::EquCab2::Grp" do
444
+ context ".first" do
445
+ it 'returns the first records' do
446
+ result = Bio::Ucsc::EquCab2::Grp.first
447
+ pp result
448
+ result.should be_true
449
+ end
450
+ end
451
+ end
452
+
453
+ describe "Bio::Ucsc::EquCab2::HgFindSpec" do
454
+ context ".first" do
455
+ it 'returns the first records' do
456
+ result = Bio::Ucsc::EquCab2::HgFindSpec.first
457
+ pp result
458
+ result.should be_true
459
+ end
460
+ end
461
+ end
462
+
463
+ describe "Bio::Ucsc::EquCab2::History" do
464
+ context ".first" do
465
+ it 'returns the first records' do
466
+ result = Bio::Ucsc::EquCab2::History.first
467
+ pp result
468
+ result.should be_true
469
+ end
470
+ end
471
+ end
472
+
473
+ describe "Bio::Ucsc::EquCab2::ImageClone" do
474
+ context ".first" do
475
+ it 'returns the first records' do
476
+ result = Bio::Ucsc::EquCab2::ImageClone.first
477
+ pp result
478
+ result.should be_true
479
+ end
480
+ end
481
+ end
482
+
483
+ describe "Bio::Ucsc::EquCab2::IntronEst" do
484
+ context ".find_by_interval" do
485
+ it 'returns the first records' do
486
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
487
+ result = Bio::Ucsc::EquCab2::IntronEst.find_by_interval gi
488
+ pp result
489
+ result.should be_true
490
+ end
491
+ end
492
+ end
493
+
494
+ describe "Bio::Ucsc::EquCab2::Keyword" do
495
+ context ".first" do
496
+ it 'returns the first records' do
497
+ result = Bio::Ucsc::EquCab2::Keyword.first
498
+ pp result
499
+ result.should be_true
500
+ end
501
+ end
502
+ end
503
+
504
+ describe "Bio::Ucsc::EquCab2::Library" do
505
+ context ".first" do
506
+ it 'returns the first records' do
507
+ result = Bio::Ucsc::EquCab2::Library.first
508
+ pp result
509
+ result.should be_true
510
+ end
511
+ end
512
+ end
513
+
514
+ describe "Bio::Ucsc::EquCab2::Mrna" do
515
+ context ".find_by_interval" do
516
+ it 'returns the first records' do
517
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
518
+ result = Bio::Ucsc::EquCab2::Mrna.find_by_interval gi
519
+ pp result
520
+ result.should be_true
521
+ end
522
+ end
523
+ end
524
+
525
+ describe "Bio::Ucsc::EquCab2::MrnaClone" do
526
+ context ".first" do
527
+ it 'returns the first records' do
528
+ result = Bio::Ucsc::EquCab2::MrnaClone.first
529
+ pp result
530
+ result.should be_true
531
+ end
532
+ end
533
+ end
534
+
535
+ describe "Bio::Ucsc::EquCab2::MrnaOrientInfo" do
536
+ context ".first" do
537
+ it 'returns the first records' do
538
+ result = Bio::Ucsc::EquCab2::MrnaOrientInfo.first
539
+ pp result
540
+ result.should be_true
541
+ end
542
+ end
543
+ end
544
+
545
+ describe "Bio::Ucsc::EquCab2::NestedRepeats" do
546
+ context ".first" do
547
+ it 'returns the first records' do
548
+ result = Bio::Ucsc::EquCab2::NestedRepeats.first
549
+ pp result
550
+ result.should be_true
551
+ end
552
+ end
553
+ end
554
+
555
+ describe "Bio::Ucsc::EquCab2::NetCanFam2" do
556
+ context ".first" do
557
+ it 'returns the first records' do
558
+ result = Bio::Ucsc::EquCab2::NetCanFam2.first
559
+ pp result
560
+ result.should be_true
561
+ end
562
+ end
563
+ end
564
+
565
+ describe "Bio::Ucsc::EquCab2::NetGalGal3" do
566
+ context ".first" do
567
+ it 'returns the first records' do
568
+ result = Bio::Ucsc::EquCab2::NetGalGal3.first
569
+ pp result
570
+ result.should be_true
571
+ end
572
+ end
573
+ end
574
+
575
+ describe "Bio::Ucsc::EquCab2::NetHg19" do
576
+ context ".first" do
577
+ it 'returns the first records' do
578
+ result = Bio::Ucsc::EquCab2::NetHg19.first
579
+ pp result
580
+ result.should be_true
581
+ end
582
+ end
583
+ end
584
+
585
+ describe "Bio::Ucsc::EquCab2::NetMm9" do
586
+ context ".first" do
587
+ it 'returns the first records' do
588
+ result = Bio::Ucsc::EquCab2::NetMm9.first
589
+ pp result
590
+ result.should be_true
591
+ end
592
+ end
593
+ end
594
+
595
+ describe "Bio::Ucsc::EquCab2::NetMonDom5" do
596
+ context ".first" do
597
+ it 'returns the first records' do
598
+ result = Bio::Ucsc::EquCab2::NetMonDom5.first
599
+ pp result
600
+ result.should be_true
601
+ end
602
+ end
603
+ end
604
+
605
+ describe "Bio::Ucsc::EquCab2::NetOrnAna1" do
606
+ context ".first" do
607
+ it 'returns the first records' do
608
+ result = Bio::Ucsc::EquCab2::NetOrnAna1.first
609
+ pp result
610
+ result.should be_true
611
+ end
612
+ end
613
+ end
614
+
615
+ describe "Bio::Ucsc::EquCab2::NetOviAri1" do
616
+ context ".first" do
617
+ it 'returns the first records' do
618
+ result = Bio::Ucsc::EquCab2::NetOviAri1.first
619
+ pp result
620
+ result.should be_true
621
+ end
622
+ end
623
+ end
624
+
625
+ describe "Bio::Ucsc::EquCab2::NetPanTro3" do
626
+ context ".first" do
627
+ it 'returns the first records' do
628
+ result = Bio::Ucsc::EquCab2::NetPanTro3.first
629
+ pp result
630
+ result.should be_true
631
+ end
632
+ end
633
+ end
634
+
635
+ describe "Bio::Ucsc::EquCab2::NscanGene" do
636
+ context ".first" do
637
+ it 'returns the first records' do
638
+ result = Bio::Ucsc::EquCab2::NscanGene.first
639
+ pp result
640
+ result.should be_true
641
+ end
642
+ end
643
+ end
644
+
645
+ describe "Bio::Ucsc::EquCab2::NscanPep" do
646
+ context ".first" do
647
+ it 'returns the first records' do
648
+ result = Bio::Ucsc::EquCab2::NscanPep.first
649
+ pp result
650
+ result.should be_true
651
+ end
652
+ end
653
+ end
654
+
655
+ describe "Bio::Ucsc::EquCab2::Organism" do
656
+ context ".first" do
657
+ it 'returns the first records' do
658
+ result = Bio::Ucsc::EquCab2::Organism.first
659
+ pp result
660
+ result.should be_true
661
+ end
662
+ end
663
+ end
664
+
665
+ describe "Bio::Ucsc::EquCab2::ProductName" do
666
+ context ".first" do
667
+ it 'returns the first records' do
668
+ result = Bio::Ucsc::EquCab2::ProductName.first
669
+ pp result
670
+ result.should be_true
671
+ end
672
+ end
673
+ end
674
+
675
+ describe "Bio::Ucsc::EquCab2::Quality" do
676
+ context ".first" do
677
+ it 'returns the first records' do
678
+ result = Bio::Ucsc::EquCab2::Quality.first
679
+ pp result
680
+ result.should be_true
681
+ end
682
+ end
683
+ end
684
+
685
+ describe "Bio::Ucsc::EquCab2::RefFlat" do
686
+ context ".first" do
687
+ it 'returns the first records' do
688
+ result = Bio::Ucsc::EquCab2::RefFlat.first
689
+ pp result
690
+ result.should be_true
691
+ end
692
+ end
693
+ end
694
+
695
+ describe "Bio::Ucsc::EquCab2::RefGene" do
696
+ context ".first" do
697
+ it 'returns the first records' do
698
+ result = Bio::Ucsc::EquCab2::RefGene.first
699
+ pp result
700
+ result.should be_true
701
+ end
702
+ end
703
+ end
704
+
705
+ describe "Bio::Ucsc::EquCab2::RefLink" do
706
+ context ".first" do
707
+ it 'returns the first records' do
708
+ result = Bio::Ucsc::EquCab2::RefLink.first
709
+ pp result
710
+ result.should be_true
711
+ end
712
+ end
713
+ end
714
+
715
+ describe "Bio::Ucsc::EquCab2::RefSeqAli" do
716
+ context ".first" do
717
+ it 'returns the first records' do
718
+ result = Bio::Ucsc::EquCab2::RefSeqAli.first
719
+ pp result
720
+ result.should be_true
721
+ end
722
+ end
723
+ end
724
+
725
+ describe "Bio::Ucsc::EquCab2::RefSeqStatus" do
726
+ context ".first" do
727
+ it 'returns the first records' do
728
+ result = Bio::Ucsc::EquCab2::RefSeqStatus.first
729
+ pp result
730
+ result.should be_true
731
+ end
732
+ end
733
+ end
734
+
735
+ describe "Bio::Ucsc::EquCab2::RefSeqSummary" do
736
+ context ".first" do
737
+ it 'returns the first records' do
738
+ result = Bio::Ucsc::EquCab2::RefSeqSummary.first
739
+ pp result
740
+ result.should be_true
741
+ end
742
+ end
743
+ end
744
+
745
+ describe "Bio::Ucsc::EquCab2::Rmsk" do
746
+ context ".find_by_interval" do
747
+ it 'returns the first records' do
748
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
749
+ result = Bio::Ucsc::EquCab2::Rmsk.find_by_interval gi
750
+ pp result
751
+ result.should be_true
752
+ end
753
+ end
754
+ end
755
+
756
+ describe "Bio::Ucsc::EquCab2::Sex" do
757
+ context ".first" do
758
+ it 'returns the first records' do
759
+ result = Bio::Ucsc::EquCab2::Sex.first
760
+ pp result
761
+ result.should be_true
762
+ end
763
+ end
764
+ end
765
+
766
+ describe "Bio::Ucsc::EquCab2::SimpleRepeat" do
767
+ context ".first" do
768
+ it 'returns the first records' do
769
+ result = Bio::Ucsc::EquCab2::SimpleRepeat.first
770
+ pp result
771
+ result.should be_true
772
+ end
773
+ end
774
+ end
775
+
776
+ describe "Bio::Ucsc::EquCab2::Source" do
777
+ context ".first" do
778
+ it 'returns the first records' do
779
+ result = Bio::Ucsc::EquCab2::Source.first
780
+ pp result
781
+ result.should be_true
782
+ end
783
+ end
784
+ end
785
+
786
+ describe "Bio::Ucsc::EquCab2::TableDescriptions" do
787
+ context ".first" do
788
+ it 'returns the first records' do
789
+ result = Bio::Ucsc::EquCab2::TableDescriptions.first
790
+ pp result
791
+ result.should be_true
792
+ end
793
+ end
794
+ end
795
+
796
+ describe "Bio::Ucsc::EquCab2::Tissue" do
797
+ context ".first" do
798
+ it 'returns the first records' do
799
+ result = Bio::Ucsc::EquCab2::Tissue.first
800
+ pp result
801
+ result.should be_true
802
+ end
803
+ end
804
+ end
805
+
806
+ describe "Bio::Ucsc::EquCab2::TrackDb" do
807
+ context ".first" do
808
+ it 'returns the first records' do
809
+ result = Bio::Ucsc::EquCab2::TrackDb.first
810
+ pp result
811
+ result.should be_true
812
+ end
813
+ end
814
+ end
815
+
816
+ describe "Bio::Ucsc::EquCab2::TransMapAlnMRna" do
817
+ context ".first" do
818
+ it 'returns the first records' do
819
+ result = Bio::Ucsc::EquCab2::TransMapAlnMRna.first
820
+ pp result
821
+ result.should be_true
822
+ end
823
+ end
824
+ end
825
+
826
+ describe "Bio::Ucsc::EquCab2::TransMapAlnRefSeq" do
827
+ context ".first" do
828
+ it 'returns the first records' do
829
+ result = Bio::Ucsc::EquCab2::TransMapAlnRefSeq.first
830
+ pp result
831
+ result.should be_true
832
+ end
833
+ end
834
+ end
835
+
836
+ describe "Bio::Ucsc::EquCab2::TransMapAlnSplicedEst" do
837
+ context ".first" do
838
+ it 'returns the first records' do
839
+ result = Bio::Ucsc::EquCab2::TransMapAlnSplicedEst.first
840
+ pp result
841
+ result.should be_true
842
+ end
843
+ end
844
+ end
845
+
846
+ describe "Bio::Ucsc::EquCab2::TransMapAlnUcscGenes" do
847
+ context ".first" do
848
+ it 'returns the first records' do
849
+ result = Bio::Ucsc::EquCab2::TransMapAlnUcscGenes.first
850
+ pp result
851
+ result.should be_true
852
+ end
853
+ end
854
+ end
855
+
856
+ describe "Bio::Ucsc::EquCab2::TransMapInfoMRna" do
857
+ context ".first" do
858
+ it 'returns the first records' do
859
+ result = Bio::Ucsc::EquCab2::TransMapInfoMRna.first
860
+ pp result
861
+ result.should be_true
862
+ end
863
+ end
864
+ end
865
+
866
+ describe "Bio::Ucsc::EquCab2::TransMapInfoRefSeq" do
867
+ context ".first" do
868
+ it 'returns the first records' do
869
+ result = Bio::Ucsc::EquCab2::TransMapInfoRefSeq.first
870
+ pp result
871
+ result.should be_true
872
+ end
873
+ end
874
+ end
875
+
876
+ describe "Bio::Ucsc::EquCab2::TransMapInfoSplicedEst" do
877
+ context ".first" do
878
+ it 'returns the first records' do
879
+ result = Bio::Ucsc::EquCab2::TransMapInfoSplicedEst.first
880
+ pp result
881
+ result.should be_true
882
+ end
883
+ end
884
+ end
885
+
886
+ describe "Bio::Ucsc::EquCab2::TransMapInfoUcscGenes" do
887
+ context ".first" do
888
+ it 'returns the first records' do
889
+ result = Bio::Ucsc::EquCab2::TransMapInfoUcscGenes.first
890
+ pp result
891
+ result.should be_true
892
+ end
893
+ end
894
+ end
895
+
896
+ describe "Bio::Ucsc::EquCab2::XenoMrna" do
897
+ context ".first" do
898
+ it 'returns the first records' do
899
+ result = Bio::Ucsc::EquCab2::XenoMrna.first
900
+ pp result
901
+ result.should be_true
902
+ end
903
+ end
904
+ end
905
+
906
+ describe "Bio::Ucsc::EquCab2::XenoRefFlat" do
907
+ context ".first" do
908
+ it 'returns the first records' do
909
+ result = Bio::Ucsc::EquCab2::XenoRefFlat.first
910
+ pp result
911
+ result.should be_true
912
+ end
913
+ end
914
+ end
915
+
916
+ describe "Bio::Ucsc::EquCab2::XenoRefGene" do
917
+ context ".first" do
918
+ it 'returns the first records' do
919
+ result = Bio::Ucsc::EquCab2::XenoRefGene.first
920
+ pp result
921
+ result.should be_true
922
+ end
923
+ end
924
+ end
925
+
926
+ describe "Bio::Ucsc::EquCab2::XenoRefSeqAli" do
927
+ context ".first" do
928
+ it 'returns the first records' do
929
+ result = Bio::Ucsc::EquCab2::XenoRefSeqAli.first
930
+ pp result
931
+ result.should be_true
932
+ end
933
+ end
934
+ end
935
+
936
+ end