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 +1,634 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::Cb3" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::Cb3::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::Cb3::All_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::Cb3::All_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::Cb3::All_mrna" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::Cb3::All_mrna.first
24
+ pp result
25
+ result.should be_true
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::Cb3::Author" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::Cb3::Author.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::Cb3::BlastCe6SG" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::Cb3::BlastCe6SG.first
44
+ pp result
45
+ result.should be_true
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::Cb3::Cds" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::Cb3::Cds.first
54
+ pp result
55
+ result.should be_true
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::Cb3::Cell" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::Cb3::Cell.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::Cb3::ChainCaePb1" do
71
+ context ".find_by_interval" do
72
+ it 'returns the first records' do
73
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
74
+ result = Bio::Ucsc::Cb3::ChainCaePb1.find_by_interval gi
75
+ pp result
76
+ result.should be_true
77
+ end
78
+ end
79
+ end
80
+
81
+ describe "Bio::Ucsc::Cb3::ChainCaePb1Link" do
82
+ context ".find_by_interval" do
83
+ it 'returns the first records' do
84
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
85
+ result = Bio::Ucsc::Cb3::ChainCaePb1Link.find_by_interval gi
86
+ pp result
87
+ result.should be_true
88
+ end
89
+ end
90
+ end
91
+
92
+ describe "Bio::Ucsc::Cb3::ChainCaeRem2" do
93
+ context ".find_by_interval" do
94
+ it 'returns the first records' do
95
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
96
+ result = Bio::Ucsc::Cb3::ChainCaeRem2.find_by_interval gi
97
+ pp result
98
+ result.should be_true
99
+ end
100
+ end
101
+ end
102
+
103
+ describe "Bio::Ucsc::Cb3::ChainCaeRem2Link" do
104
+ context ".find_by_interval" do
105
+ it 'returns the first records' do
106
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
107
+ result = Bio::Ucsc::Cb3::ChainCaeRem2Link.find_by_interval gi
108
+ pp result
109
+ result.should be_true
110
+ end
111
+ end
112
+ end
113
+
114
+ describe "Bio::Ucsc::Cb3::ChainCe6" do
115
+ context ".find_by_interval" do
116
+ it 'returns the first records' do
117
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
118
+ result = Bio::Ucsc::Cb3::ChainCe6.find_by_interval gi
119
+ pp result
120
+ result.should be_true
121
+ end
122
+ end
123
+ end
124
+
125
+ describe "Bio::Ucsc::Cb3::ChainCe6Link" do
126
+ context ".find_by_interval" do
127
+ it 'returns the first records' do
128
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
129
+ result = Bio::Ucsc::Cb3::ChainCe6Link.find_by_interval gi
130
+ pp result
131
+ result.should be_true
132
+ end
133
+ end
134
+ end
135
+
136
+ describe "Bio::Ucsc::Cb3::ChainPriPac1" do
137
+ context ".find_by_interval" do
138
+ it 'returns the first records' do
139
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
140
+ result = Bio::Ucsc::Cb3::ChainPriPac1.find_by_interval gi
141
+ pp result
142
+ result.should be_true
143
+ end
144
+ end
145
+ end
146
+
147
+ describe "Bio::Ucsc::Cb3::ChainPriPac1Link" do
148
+ context ".find_by_interval" do
149
+ it 'returns the first records' do
150
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
151
+ result = Bio::Ucsc::Cb3::ChainPriPac1Link.find_by_interval gi
152
+ pp result
153
+ result.should be_true
154
+ end
155
+ end
156
+ end
157
+
158
+ describe "Bio::Ucsc::Cb3::ChromInfo" do
159
+ context ".first" do
160
+ it 'returns the first records' do
161
+ result = Bio::Ucsc::Cb3::ChromInfo.first
162
+ pp result
163
+ result.should be_true
164
+ end
165
+ end
166
+ end
167
+
168
+ describe "Bio::Ucsc::Cb3::Description" do
169
+ context ".first" do
170
+ it 'returns the first records' do
171
+ result = Bio::Ucsc::Cb3::Description.first
172
+ pp result
173
+ result.should be_true
174
+ end
175
+ end
176
+ end
177
+
178
+ describe "Bio::Ucsc::Cb3::Development" do
179
+ context ".first" do
180
+ it 'returns the first records' do
181
+ result = Bio::Ucsc::Cb3::Development.first
182
+ pp result
183
+ result.should be_true
184
+ end
185
+ end
186
+ end
187
+
188
+ describe "Bio::Ucsc::Cb3::Est" do
189
+ context ".find_by_interval" do
190
+ it 'returns the first records' do
191
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
192
+ result = Bio::Ucsc::Cb3::Est.find_by_interval gi
193
+ pp result
194
+ result.should be_true
195
+ end
196
+ end
197
+ end
198
+
199
+ describe "Bio::Ucsc::Cb3::EstOrientInfo" do
200
+ context ".first" do
201
+ it 'returns the first records' do
202
+ result = Bio::Ucsc::Cb3::EstOrientInfo.first
203
+ pp result
204
+ result.should be_true
205
+ end
206
+ end
207
+ end
208
+
209
+ describe "Bio::Ucsc::Cb3::Gap" do
210
+ context ".find_by_interval" do
211
+ it 'returns the first records' do
212
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
213
+ result = Bio::Ucsc::Cb3::Gap.find_by_interval gi
214
+ pp result
215
+ result.should be_true
216
+ end
217
+ end
218
+ end
219
+
220
+ describe "Bio::Ucsc::Cb3::GbCdnaInfo" do
221
+ context ".first" do
222
+ it 'returns the first records' do
223
+ result = Bio::Ucsc::Cb3::GbCdnaInfo.first
224
+ pp result
225
+ result.should be_true
226
+ end
227
+ end
228
+ end
229
+
230
+ describe "Bio::Ucsc::Cb3::GbExtFile" do
231
+ context ".first" do
232
+ it 'returns the first records' do
233
+ result = Bio::Ucsc::Cb3::GbExtFile.first
234
+ pp result
235
+ result.should be_true
236
+ end
237
+ end
238
+ end
239
+
240
+ describe "Bio::Ucsc::Cb3::GbLoaded" do
241
+ context ".first" do
242
+ it 'returns the first records' do
243
+ result = Bio::Ucsc::Cb3::GbLoaded.first
244
+ pp result
245
+ result.should be_true
246
+ end
247
+ end
248
+ end
249
+
250
+ describe "Bio::Ucsc::Cb3::GbMiscDiff" do
251
+ context ".first" do
252
+ it 'returns the first records' do
253
+ result = Bio::Ucsc::Cb3::GbMiscDiff.first
254
+ pp result
255
+ result.should be_true
256
+ end
257
+ end
258
+ end
259
+
260
+ describe "Bio::Ucsc::Cb3::GbSeq" do
261
+ context ".first" do
262
+ it 'returns the first records' do
263
+ result = Bio::Ucsc::Cb3::GbSeq.first
264
+ pp result
265
+ result.should be_true
266
+ end
267
+ end
268
+ end
269
+
270
+ describe "Bio::Ucsc::Cb3::GbStatus" do
271
+ context ".first" do
272
+ it 'returns the first records' do
273
+ result = Bio::Ucsc::Cb3::GbStatus.first
274
+ pp result
275
+ result.should be_true
276
+ end
277
+ end
278
+ end
279
+
280
+ describe "Bio::Ucsc::Cb3::GbWarn" do
281
+ context ".first" do
282
+ it 'returns the first records' do
283
+ result = Bio::Ucsc::Cb3::GbWarn.first
284
+ pp result
285
+ result.should be_true
286
+ end
287
+ end
288
+ end
289
+
290
+ describe "Bio::Ucsc::Cb3::Gc5Base" do
291
+ context ".first" do
292
+ it 'returns the first records' do
293
+ result = Bio::Ucsc::Cb3::Gc5Base.first
294
+ pp result
295
+ result.should be_true
296
+ end
297
+ end
298
+ end
299
+
300
+ describe "Bio::Ucsc::Cb3::GeneName" do
301
+ context ".first" do
302
+ it 'returns the first records' do
303
+ result = Bio::Ucsc::Cb3::GeneName.first
304
+ pp result
305
+ result.should be_true
306
+ end
307
+ end
308
+ end
309
+
310
+ describe "Bio::Ucsc::Cb3::Gold" do
311
+ context ".find_by_interval" do
312
+ it 'returns the first records' do
313
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
314
+ result = Bio::Ucsc::Cb3::Gold.find_by_interval gi
315
+ pp result
316
+ result.should be_true
317
+ end
318
+ end
319
+ end
320
+
321
+ describe "Bio::Ucsc::Cb3::Grp" do
322
+ context ".first" do
323
+ it 'returns the first records' do
324
+ result = Bio::Ucsc::Cb3::Grp.first
325
+ pp result
326
+ result.should be_true
327
+ end
328
+ end
329
+ end
330
+
331
+ describe "Bio::Ucsc::Cb3::HgFindSpec" do
332
+ context ".first" do
333
+ it 'returns the first records' do
334
+ result = Bio::Ucsc::Cb3::HgFindSpec.first
335
+ pp result
336
+ result.should be_true
337
+ end
338
+ end
339
+ end
340
+
341
+ describe "Bio::Ucsc::Cb3::History" do
342
+ context ".first" do
343
+ it 'returns the first records' do
344
+ result = Bio::Ucsc::Cb3::History.first
345
+ pp result
346
+ result.should be_true
347
+ end
348
+ end
349
+ end
350
+
351
+ describe "Bio::Ucsc::Cb3::ImageClone" do
352
+ context ".first" do
353
+ it 'returns the first records' do
354
+ result = Bio::Ucsc::Cb3::ImageClone.first
355
+ pp result
356
+ result.should be_true
357
+ end
358
+ end
359
+ end
360
+
361
+ describe "Bio::Ucsc::Cb3::IntronEst" do
362
+ context ".find_by_interval" do
363
+ it 'returns the first records' do
364
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
365
+ result = Bio::Ucsc::Cb3::IntronEst.find_by_interval gi
366
+ pp result
367
+ result.should be_true
368
+ end
369
+ end
370
+ end
371
+
372
+ describe "Bio::Ucsc::Cb3::Keyword" do
373
+ context ".first" do
374
+ it 'returns the first records' do
375
+ result = Bio::Ucsc::Cb3::Keyword.first
376
+ pp result
377
+ result.should be_true
378
+ end
379
+ end
380
+ end
381
+
382
+ describe "Bio::Ucsc::Cb3::Library" do
383
+ context ".first" do
384
+ it 'returns the first records' do
385
+ result = Bio::Ucsc::Cb3::Library.first
386
+ pp result
387
+ result.should be_true
388
+ end
389
+ end
390
+ end
391
+
392
+ describe "Bio::Ucsc::Cb3::Mrna" do
393
+ context ".find_by_interval" do
394
+ it 'returns the first records' do
395
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
396
+ result = Bio::Ucsc::Cb3::Mrna.find_by_interval gi
397
+ pp result
398
+ result.should be_true
399
+ end
400
+ end
401
+ end
402
+
403
+ describe "Bio::Ucsc::Cb3::MrnaClone" do
404
+ context ".first" do
405
+ it 'returns the first records' do
406
+ result = Bio::Ucsc::Cb3::MrnaClone.first
407
+ pp result
408
+ result.should be_true
409
+ end
410
+ end
411
+ end
412
+
413
+ describe "Bio::Ucsc::Cb3::MrnaOrientInfo" do
414
+ context ".first" do
415
+ it 'returns the first records' do
416
+ result = Bio::Ucsc::Cb3::MrnaOrientInfo.first
417
+ pp result
418
+ result.should be_true
419
+ end
420
+ end
421
+ end
422
+
423
+ describe "Bio::Ucsc::Cb3::NetCaePb1" do
424
+ context ".first" do
425
+ it 'returns the first records' do
426
+ result = Bio::Ucsc::Cb3::NetCaePb1.first
427
+ pp result
428
+ result.should be_true
429
+ end
430
+ end
431
+ end
432
+
433
+ describe "Bio::Ucsc::Cb3::NetCaeRem2" do
434
+ context ".first" do
435
+ it 'returns the first records' do
436
+ result = Bio::Ucsc::Cb3::NetCaeRem2.first
437
+ pp result
438
+ result.should be_true
439
+ end
440
+ end
441
+ end
442
+
443
+ describe "Bio::Ucsc::Cb3::NetCe6" do
444
+ context ".first" do
445
+ it 'returns the first records' do
446
+ result = Bio::Ucsc::Cb3::NetCe6.first
447
+ pp result
448
+ result.should be_true
449
+ end
450
+ end
451
+ end
452
+
453
+ describe "Bio::Ucsc::Cb3::NetPriPac1" do
454
+ context ".first" do
455
+ it 'returns the first records' do
456
+ result = Bio::Ucsc::Cb3::NetPriPac1.first
457
+ pp result
458
+ result.should be_true
459
+ end
460
+ end
461
+ end
462
+
463
+ describe "Bio::Ucsc::Cb3::Organism" do
464
+ context ".first" do
465
+ it 'returns the first records' do
466
+ result = Bio::Ucsc::Cb3::Organism.first
467
+ pp result
468
+ result.should be_true
469
+ end
470
+ end
471
+ end
472
+
473
+ describe "Bio::Ucsc::Cb3::ProductName" do
474
+ context ".first" do
475
+ it 'returns the first records' do
476
+ result = Bio::Ucsc::Cb3::ProductName.first
477
+ pp result
478
+ result.should be_true
479
+ end
480
+ end
481
+ end
482
+
483
+ describe "Bio::Ucsc::Cb3::RefLink" do
484
+ context ".first" do
485
+ it 'returns the first records' do
486
+ result = Bio::Ucsc::Cb3::RefLink.first
487
+ pp result
488
+ result.should be_true
489
+ end
490
+ end
491
+ end
492
+
493
+ describe "Bio::Ucsc::Cb3::RefSeqStatus" do
494
+ context ".first" do
495
+ it 'returns the first records' do
496
+ result = Bio::Ucsc::Cb3::RefSeqStatus.first
497
+ pp result
498
+ result.should be_true
499
+ end
500
+ end
501
+ end
502
+
503
+ describe "Bio::Ucsc::Cb3::RefSeqSummary" do
504
+ context ".first" do
505
+ it 'returns the first records' do
506
+ result = Bio::Ucsc::Cb3::RefSeqSummary.first
507
+ pp result
508
+ result.should be_true
509
+ end
510
+ end
511
+ end
512
+
513
+ describe "Bio::Ucsc::Cb3::Rmsk" do
514
+ context ".find_by_interval" do
515
+ it 'returns the first records' do
516
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
517
+ result = Bio::Ucsc::Cb3::Rmsk.find_by_interval gi
518
+ pp result
519
+ result.should be_true
520
+ end
521
+ end
522
+ end
523
+
524
+ describe "Bio::Ucsc::Cb3::Sex" do
525
+ context ".first" do
526
+ it 'returns the first records' do
527
+ result = Bio::Ucsc::Cb3::Sex.first
528
+ pp result
529
+ result.should be_true
530
+ end
531
+ end
532
+ end
533
+
534
+ describe "Bio::Ucsc::Cb3::SimpleRepeat" do
535
+ context ".first" do
536
+ it 'returns the first records' do
537
+ result = Bio::Ucsc::Cb3::SimpleRepeat.first
538
+ pp result
539
+ result.should be_true
540
+ end
541
+ end
542
+ end
543
+
544
+ describe "Bio::Ucsc::Cb3::Source" do
545
+ context ".first" do
546
+ it 'returns the first records' do
547
+ result = Bio::Ucsc::Cb3::Source.first
548
+ pp result
549
+ result.should be_true
550
+ end
551
+ end
552
+ end
553
+
554
+ describe "Bio::Ucsc::Cb3::TableDescriptions" do
555
+ context ".first" do
556
+ it 'returns the first records' do
557
+ result = Bio::Ucsc::Cb3::TableDescriptions.first
558
+ pp result
559
+ result.should be_true
560
+ end
561
+ end
562
+ end
563
+
564
+ describe "Bio::Ucsc::Cb3::Tissue" do
565
+ context ".first" do
566
+ it 'returns the first records' do
567
+ result = Bio::Ucsc::Cb3::Tissue.first
568
+ pp result
569
+ result.should be_true
570
+ end
571
+ end
572
+ end
573
+
574
+ describe "Bio::Ucsc::Cb3::TrackDb" do
575
+ context ".first" do
576
+ it 'returns the first records' do
577
+ result = Bio::Ucsc::Cb3::TrackDb.first
578
+ pp result
579
+ result.should be_true
580
+ end
581
+ end
582
+ end
583
+
584
+ describe "Bio::Ucsc::Cb3::WindowmaskerSdust" do
585
+ context ".first" do
586
+ it 'returns the first records' do
587
+ result = Bio::Ucsc::Cb3::WindowmaskerSdust.first
588
+ pp result
589
+ result.should be_true
590
+ end
591
+ end
592
+ end
593
+
594
+ describe "Bio::Ucsc::Cb3::XenoMrna" do
595
+ context ".first" do
596
+ it 'returns the first records' do
597
+ result = Bio::Ucsc::Cb3::XenoMrna.first
598
+ pp result
599
+ result.should be_true
600
+ end
601
+ end
602
+ end
603
+
604
+ describe "Bio::Ucsc::Cb3::XenoRefFlat" do
605
+ context ".first" do
606
+ it 'returns the first records' do
607
+ result = Bio::Ucsc::Cb3::XenoRefFlat.first
608
+ pp result
609
+ result.should be_true
610
+ end
611
+ end
612
+ end
613
+
614
+ describe "Bio::Ucsc::Cb3::XenoRefGene" do
615
+ context ".first" do
616
+ it 'returns the first records' do
617
+ result = Bio::Ucsc::Cb3::XenoRefGene.first
618
+ pp result
619
+ result.should be_true
620
+ end
621
+ end
622
+ end
623
+
624
+ describe "Bio::Ucsc::Cb3::XenoRefSeqAli" do
625
+ context ".first" do
626
+ it 'returns the first records' do
627
+ result = Bio::Ucsc::Cb3::XenoRefSeqAli.first
628
+ pp result
629
+ result.should be_true
630
+ end
631
+ end
632
+ end
633
+
634
+ end