bio-ucsc-api 0.2.0 → 0.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 +1,925 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::SacCer2" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::SacCer2::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::SacCer2::T2micron_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::SacCer2::T2micron_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::SacCer2::T2micron_gap" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::SacCer2::T2micron_gap.first
24
+ pp result
25
+ result.should be_nil
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::SacCer2::T2micron_gold" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::SacCer2::T2micron_gold.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::SacCer2::T2micron_intronEst" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::SacCer2::T2micron_intronEst.first
44
+ pp result
45
+ result.should be_nil
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::SacCer2::T2micron_mrna" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::SacCer2::T2micron_mrna.first
54
+ pp result
55
+ result.should be_nil
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::SacCer2::All_est" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::SacCer2::All_est.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::SacCer2::All_mrna" do
71
+ context ".first" do
72
+ it 'returns the first records' do
73
+ result = Bio::Ucsc::SacCer2::All_mrna.first
74
+ pp result
75
+ result.should be_true
76
+ end
77
+ end
78
+ end
79
+
80
+ describe "Bio::Ucsc::SacCer2::Author" do
81
+ context ".first" do
82
+ it 'returns the first records' do
83
+ result = Bio::Ucsc::SacCer2::Author.first
84
+ pp result
85
+ result.should be_true
86
+ end
87
+ end
88
+ end
89
+
90
+ describe "Bio::Ucsc::SacCer2::BlastHg18KG" do
91
+ context ".first" do
92
+ it 'returns the first records' do
93
+ result = Bio::Ucsc::SacCer2::BlastHg18KG.first
94
+ pp result
95
+ result.should be_true
96
+ end
97
+ end
98
+ end
99
+
100
+ describe "Bio::Ucsc::SacCer2::Cds" do
101
+ context ".first" do
102
+ it 'returns the first records' do
103
+ result = Bio::Ucsc::SacCer2::Cds.first
104
+ pp result
105
+ result.should be_true
106
+ end
107
+ end
108
+ end
109
+
110
+ describe "Bio::Ucsc::SacCer2::CeBlastTab" do
111
+ context ".first" do
112
+ it 'returns the first records' do
113
+ result = Bio::Ucsc::SacCer2::CeBlastTab.first
114
+ pp result
115
+ result.should be_true
116
+ end
117
+ end
118
+ end
119
+
120
+ describe "Bio::Ucsc::SacCer2::Cell" do
121
+ context ".first" do
122
+ it 'returns the first records' do
123
+ result = Bio::Ucsc::SacCer2::Cell.first
124
+ pp result
125
+ result.should be_true
126
+ end
127
+ end
128
+ end
129
+
130
+ describe "Bio::Ucsc::SacCer2::ChoExpDistance" do
131
+ context ".first" do
132
+ it 'returns the first records' do
133
+ result = Bio::Ucsc::SacCer2::ChoExpDistance.first
134
+ pp result
135
+ result.should be_true
136
+ end
137
+ end
138
+ end
139
+
140
+ describe "Bio::Ucsc::SacCer2::ChromInfo" do
141
+ context ".first" do
142
+ it 'returns the first records' do
143
+ result = Bio::Ucsc::SacCer2::ChromInfo.first
144
+ pp result
145
+ result.should be_true
146
+ end
147
+ end
148
+ end
149
+
150
+ describe "Bio::Ucsc::SacCer2::Description" do
151
+ context ".first" do
152
+ it 'returns the first records' do
153
+ result = Bio::Ucsc::SacCer2::Description.first
154
+ pp result
155
+ result.should be_true
156
+ end
157
+ end
158
+ end
159
+
160
+ describe "Bio::Ucsc::SacCer2::Development" do
161
+ context ".first" do
162
+ it 'returns the first records' do
163
+ result = Bio::Ucsc::SacCer2::Development.first
164
+ pp result
165
+ result.should be_true
166
+ end
167
+ end
168
+ end
169
+
170
+ describe "Bio::Ucsc::SacCer2::DmBlastTab" do
171
+ context ".first" do
172
+ it 'returns the first records' do
173
+ result = Bio::Ucsc::SacCer2::DmBlastTab.first
174
+ pp result
175
+ result.should be_true
176
+ end
177
+ end
178
+ end
179
+
180
+ describe "Bio::Ucsc::SacCer2::DrBlastTab" do
181
+ context ".first" do
182
+ it 'returns the first records' do
183
+ result = Bio::Ucsc::SacCer2::DrBlastTab.first
184
+ pp result
185
+ result.should be_true
186
+ end
187
+ end
188
+ end
189
+
190
+ describe "Bio::Ucsc::SacCer2::EnsGene" do
191
+ context ".first" do
192
+ it 'returns the first records' do
193
+ result = Bio::Ucsc::SacCer2::EnsGene.first
194
+ pp result
195
+ result.should be_true
196
+ end
197
+ end
198
+ end
199
+
200
+ describe "Bio::Ucsc::SacCer2::EnsGtp" do
201
+ context ".first" do
202
+ it 'returns the first records' do
203
+ result = Bio::Ucsc::SacCer2::EnsGtp.first
204
+ pp result
205
+ result.should be_true
206
+ end
207
+ end
208
+ end
209
+
210
+ describe "Bio::Ucsc::SacCer2::EnsPep" do
211
+ context ".first" do
212
+ it 'returns the first records' do
213
+ result = Bio::Ucsc::SacCer2::EnsPep.first
214
+ pp result
215
+ result.should be_true
216
+ end
217
+ end
218
+ end
219
+
220
+ describe "Bio::Ucsc::SacCer2::EsRegGeneToModule" do
221
+ context ".first" do
222
+ it 'returns the first records' do
223
+ result = Bio::Ucsc::SacCer2::EsRegGeneToModule.first
224
+ pp result
225
+ result.should be_true
226
+ end
227
+ end
228
+ end
229
+
230
+ describe "Bio::Ucsc::SacCer2::EsRegGeneToMotif" do
231
+ context ".first" do
232
+ it 'returns the first records' do
233
+ result = Bio::Ucsc::SacCer2::EsRegGeneToMotif.first
234
+ pp result
235
+ result.should be_true
236
+ end
237
+ end
238
+ end
239
+
240
+ describe "Bio::Ucsc::SacCer2::EsRegMotif" do
241
+ context ".first" do
242
+ it 'returns the first records' do
243
+ result = Bio::Ucsc::SacCer2::EsRegMotif.first
244
+ pp result
245
+ result.should be_true
246
+ end
247
+ end
248
+ end
249
+
250
+ describe "Bio::Ucsc::SacCer2::EsRegUpstreamRegion" do
251
+ context ".first" do
252
+ it 'returns the first records' do
253
+ result = Bio::Ucsc::SacCer2::EsRegUpstreamRegion.first
254
+ pp result
255
+ result.should be_true
256
+ end
257
+ end
258
+ end
259
+
260
+ describe "Bio::Ucsc::SacCer2::Est" do
261
+ context ".find_by_interval" do
262
+ it 'returns the first records' do
263
+ gi = Bio::GenomicInterval.parse("chrIV:1-1,000,000")
264
+ result = Bio::Ucsc::SacCer2::Est.find_by_interval gi
265
+ pp result
266
+ result.should be_true
267
+ end
268
+ end
269
+ end
270
+
271
+ describe "Bio::Ucsc::SacCer2::EstOrientInfo" do
272
+ context ".first" do
273
+ it 'returns the first records' do
274
+ result = Bio::Ucsc::SacCer2::EstOrientInfo.first
275
+ pp result
276
+ result.should be_true
277
+ end
278
+ end
279
+ end
280
+
281
+ describe "Bio::Ucsc::SacCer2::ExtFile" do
282
+ context ".first" do
283
+ it 'returns the first records' do
284
+ result = Bio::Ucsc::SacCer2::ExtFile.first
285
+ pp result
286
+ result.should be_true
287
+ end
288
+ end
289
+ end
290
+
291
+ describe "Bio::Ucsc::SacCer2::Gap" do
292
+ context ".find_by_interval" do
293
+ it 'returns the first records' do
294
+ gi = Bio::GenomicInterval.parse("chrIV:1-1,000,000")
295
+ result = Bio::Ucsc::SacCer2::Gap.find_by_interval gi
296
+ pp result
297
+ result.should be_nil
298
+ end
299
+ end
300
+ end
301
+
302
+ describe "Bio::Ucsc::SacCer2::GbCdnaInfo" do
303
+ context ".first" do
304
+ it 'returns the first records' do
305
+ result = Bio::Ucsc::SacCer2::GbCdnaInfo.first
306
+ pp result
307
+ result.should be_true
308
+ end
309
+ end
310
+ end
311
+
312
+ describe "Bio::Ucsc::SacCer2::GbExtFile" do
313
+ context ".first" do
314
+ it 'returns the first records' do
315
+ result = Bio::Ucsc::SacCer2::GbExtFile.first
316
+ pp result
317
+ result.should be_true
318
+ end
319
+ end
320
+ end
321
+
322
+ describe "Bio::Ucsc::SacCer2::GbLoaded" do
323
+ context ".first" do
324
+ it 'returns the first records' do
325
+ result = Bio::Ucsc::SacCer2::GbLoaded.first
326
+ pp result
327
+ result.should be_true
328
+ end
329
+ end
330
+ end
331
+
332
+ describe "Bio::Ucsc::SacCer2::GbMiscDiff" do
333
+ context ".first" do
334
+ it 'returns the first records' do
335
+ result = Bio::Ucsc::SacCer2::GbMiscDiff.first
336
+ pp result
337
+ result.should be_true
338
+ end
339
+ end
340
+ end
341
+
342
+ describe "Bio::Ucsc::SacCer2::GbSeq" do
343
+ context ".first" do
344
+ it 'returns the first records' do
345
+ result = Bio::Ucsc::SacCer2::GbSeq.first
346
+ pp result
347
+ result.should be_true
348
+ end
349
+ end
350
+ end
351
+
352
+ describe "Bio::Ucsc::SacCer2::GbStatus" do
353
+ context ".first" do
354
+ it 'returns the first records' do
355
+ result = Bio::Ucsc::SacCer2::GbStatus.first
356
+ pp result
357
+ result.should be_true
358
+ end
359
+ end
360
+ end
361
+
362
+ describe "Bio::Ucsc::SacCer2::GbWarn" do
363
+ context ".find_by_interval" do
364
+ it 'returns the first records' do
365
+ result = Bio::Ucsc::SacCer2::GbWarn.first
366
+ pp result
367
+ result.should be_nil
368
+ end
369
+ end
370
+ end
371
+
372
+ describe "Bio::Ucsc::SacCer2::Gc5Base" do
373
+ context ".first" do
374
+ it 'returns the first records' do
375
+ result = Bio::Ucsc::SacCer2::Gc5Base.first
376
+ pp result
377
+ result.should be_true
378
+ end
379
+ end
380
+ end
381
+
382
+ describe "Bio::Ucsc::SacCer2::GeneName" do
383
+ context ".first" do
384
+ it 'returns the first records' do
385
+ result = Bio::Ucsc::SacCer2::GeneName.first
386
+ pp result
387
+ result.should be_true
388
+ end
389
+ end
390
+ end
391
+
392
+ describe "Bio::Ucsc::SacCer2::Gold" do
393
+ context ".find_by_interval" do
394
+ it 'returns the first records' do
395
+ gi = Bio::GenomicInterval.parse("chrIV:1-1,000,000")
396
+ result = Bio::Ucsc::SacCer2::Gold.find_by_interval gi
397
+ pp result
398
+ result.should be_true
399
+ end
400
+ end
401
+ end
402
+
403
+ describe "Bio::Ucsc::SacCer2::GrowthCondition" do
404
+ context ".first" do
405
+ it 'returns the first records' do
406
+ result = Bio::Ucsc::SacCer2::GrowthCondition.first
407
+ pp result
408
+ result.should be_true
409
+ end
410
+ end
411
+ end
412
+
413
+ describe "Bio::Ucsc::SacCer2::Grp" do
414
+ context ".first" do
415
+ it 'returns the first records' do
416
+ result = Bio::Ucsc::SacCer2::Grp.first
417
+ pp result
418
+ result.should be_true
419
+ end
420
+ end
421
+ end
422
+
423
+ describe "Bio::Ucsc::SacCer2::HgBlastTab" do
424
+ context ".first" do
425
+ it 'returns the first records' do
426
+ result = Bio::Ucsc::SacCer2::HgBlastTab.first
427
+ pp result
428
+ result.should be_true
429
+ end
430
+ end
431
+ end
432
+
433
+ describe "Bio::Ucsc::SacCer2::HgFindSpec" do
434
+ context ".first" do
435
+ it 'returns the first records' do
436
+ result = Bio::Ucsc::SacCer2::HgFindSpec.first
437
+ pp result
438
+ result.should be_true
439
+ end
440
+ end
441
+ end
442
+
443
+ describe "Bio::Ucsc::SacCer2::History" do
444
+ context ".first" do
445
+ it 'returns the first records' do
446
+ result = Bio::Ucsc::SacCer2::History.first
447
+ pp result
448
+ result.should be_true
449
+ end
450
+ end
451
+ end
452
+
453
+ describe "Bio::Ucsc::SacCer2::ImageClone" do
454
+ context ".first" do
455
+ it 'returns the first records' do
456
+ result = Bio::Ucsc::SacCer2::ImageClone.first
457
+ pp result
458
+ result.should be_nil
459
+ end
460
+ end
461
+ end
462
+
463
+ describe "Bio::Ucsc::SacCer2::IntronEst" do
464
+ context ".find_by_interval" do
465
+ it 'returns the first records' do
466
+ gi = Bio::GenomicInterval.parse("chrIV:1-1,000,000")
467
+ result = Bio::Ucsc::SacCer2::IntronEst.find_by_interval gi
468
+ pp result
469
+ result.should be_true
470
+ end
471
+ end
472
+ end
473
+
474
+ describe "Bio::Ucsc::SacCer2::Keyword" do
475
+ context ".first" do
476
+ it 'returns the first records' do
477
+ result = Bio::Ucsc::SacCer2::Keyword.first
478
+ pp result
479
+ result.should be_true
480
+ end
481
+ end
482
+ end
483
+
484
+ describe "Bio::Ucsc::SacCer2::Library" do
485
+ context ".first" do
486
+ it 'returns the first records' do
487
+ result = Bio::Ucsc::SacCer2::Library.first
488
+ pp result
489
+ result.should be_true
490
+ end
491
+ end
492
+ end
493
+
494
+ describe "Bio::Ucsc::SacCer2::MmBlastTab" do
495
+ context ".first" do
496
+ it 'returns the first records' do
497
+ result = Bio::Ucsc::SacCer2::MmBlastTab.first
498
+ pp result
499
+ result.should be_true
500
+ end
501
+ end
502
+ end
503
+
504
+ describe "Bio::Ucsc::SacCer2::Mrna" do
505
+ context ".find_by_interval" do
506
+ it 'returns the first records' do
507
+ gi = Bio::GenomicInterval.parse("chrIV:1-1,000,000")
508
+ result = Bio::Ucsc::SacCer2::Mrna.find_by_interval gi
509
+ pp result
510
+ result.should be_true
511
+ end
512
+ end
513
+ end
514
+
515
+ describe "Bio::Ucsc::SacCer2::MrnaClone" do
516
+ context ".first" do
517
+ it 'returns the first records' do
518
+ result = Bio::Ucsc::SacCer2::MrnaClone.first
519
+ pp result
520
+ result.should be_true
521
+ end
522
+ end
523
+ end
524
+
525
+ describe "Bio::Ucsc::SacCer2::MrnaOrientInfo" do
526
+ context ".first" do
527
+ it 'returns the first records' do
528
+ result = Bio::Ucsc::SacCer2::MrnaOrientInfo.first
529
+ pp result
530
+ result.should be_true
531
+ end
532
+ end
533
+ end
534
+
535
+ describe "Bio::Ucsc::SacCer2::Multiz7way" do
536
+ context ".first" do
537
+ it 'returns the first records' do
538
+ result = Bio::Ucsc::SacCer2::Multiz7way.first
539
+ pp result
540
+ result.should be_true
541
+ end
542
+ end
543
+ end
544
+
545
+ describe "Bio::Ucsc::SacCer2::Multiz7wayFrames" do
546
+ context ".first" do
547
+ it 'returns the first records' do
548
+ result = Bio::Ucsc::SacCer2::Multiz7wayFrames.first
549
+ pp result
550
+ result.should be_true
551
+ end
552
+ end
553
+ end
554
+
555
+ describe "Bio::Ucsc::SacCer2::Multiz7waySummary" do
556
+ context ".first" do
557
+ it 'returns the first records' do
558
+ result = Bio::Ucsc::SacCer2::Multiz7waySummary.first
559
+ pp result
560
+ result.should be_true
561
+ end
562
+ end
563
+ end
564
+
565
+ describe "Bio::Ucsc::SacCer2::Oreganno" do
566
+ context ".first" do
567
+ it 'returns the first records' do
568
+ result = Bio::Ucsc::SacCer2::Oreganno.first
569
+ pp result
570
+ result.should be_true
571
+ end
572
+ end
573
+ end
574
+
575
+ describe "Bio::Ucsc::SacCer2::OregannoAttr" do
576
+ context ".first" do
577
+ it 'returns the first records' do
578
+ result = Bio::Ucsc::SacCer2::OregannoAttr.first
579
+ pp result
580
+ result.should be_true
581
+ end
582
+ end
583
+ end
584
+
585
+ describe "Bio::Ucsc::SacCer2::OregannoLink" do
586
+ context ".first" do
587
+ it 'returns the first records' do
588
+ result = Bio::Ucsc::SacCer2::OregannoLink.first
589
+ pp result
590
+ result.should be_true
591
+ end
592
+ end
593
+ end
594
+
595
+ describe "Bio::Ucsc::SacCer2::Organism" do
596
+ context ".first" do
597
+ it 'returns the first records' do
598
+ result = Bio::Ucsc::SacCer2::Organism.first
599
+ pp result
600
+ result.should be_true
601
+ end
602
+ end
603
+ end
604
+
605
+ describe "Bio::Ucsc::SacCer2::PhastCons7way" do
606
+ context ".first" do
607
+ it 'returns the first records' do
608
+ result = Bio::Ucsc::SacCer2::PhastCons7way.first
609
+ pp result
610
+ result.should be_true
611
+ end
612
+ end
613
+ end
614
+
615
+ describe "Bio::Ucsc::SacCer2::PhastConsElements7way" do
616
+ context ".first" do
617
+ it 'returns the first records' do
618
+ result = Bio::Ucsc::SacCer2::PhastConsElements7way.first
619
+ pp result
620
+ result.should be_true
621
+ end
622
+ end
623
+ end
624
+
625
+ describe "Bio::Ucsc::SacCer2::ProductName" do
626
+ context ".first" do
627
+ it 'returns the first records' do
628
+ result = Bio::Ucsc::SacCer2::ProductName.first
629
+ pp result
630
+ result.should be_true
631
+ end
632
+ end
633
+ end
634
+
635
+ describe "Bio::Ucsc::SacCer2::RnBlastTab" do
636
+ context ".first" do
637
+ it 'returns the first records' do
638
+ result = Bio::Ucsc::SacCer2::RnBlastTab.first
639
+ pp result
640
+ result.should be_true
641
+ end
642
+ end
643
+ end
644
+
645
+ describe "Bio::Ucsc::SacCer2::Sex" do
646
+ context ".first" do
647
+ it 'returns the first records' do
648
+ result = Bio::Ucsc::SacCer2::Sex.first
649
+ pp result
650
+ result.should be_true
651
+ end
652
+ end
653
+ end
654
+
655
+ describe "Bio::Ucsc::SacCer2::SgdAbundance" do
656
+ context ".first" do
657
+ it 'returns the first records' do
658
+ result = Bio::Ucsc::SacCer2::SgdAbundance.first
659
+ pp result
660
+ result.should be_true
661
+ end
662
+ end
663
+ end
664
+
665
+ describe "Bio::Ucsc::SacCer2::SgdBlastTab" do
666
+ context ".first" do
667
+ it 'returns the first records' do
668
+ result = Bio::Ucsc::SacCer2::SgdBlastTab.first
669
+ pp result
670
+ result.should be_true
671
+ end
672
+ end
673
+ end
674
+
675
+ describe "Bio::Ucsc::SacCer2::SgdCanonical" do
676
+ context ".first" do
677
+ it 'returns the first records' do
678
+ result = Bio::Ucsc::SacCer2::SgdCanonical.first
679
+ pp result
680
+ result.should be_true
681
+ end
682
+ end
683
+ end
684
+
685
+ describe "Bio::Ucsc::SacCer2::SgdClone" do
686
+ context ".first" do
687
+ it 'returns the first records' do
688
+ result = Bio::Ucsc::SacCer2::SgdClone.first
689
+ pp result
690
+ result.should be_true
691
+ end
692
+ end
693
+ end
694
+
695
+ describe "Bio::Ucsc::SacCer2::SgdDescription" do
696
+ context ".first" do
697
+ it 'returns the first records' do
698
+ result = Bio::Ucsc::SacCer2::SgdDescription.first
699
+ pp result
700
+ result.should be_true
701
+ end
702
+ end
703
+ end
704
+
705
+ describe "Bio::Ucsc::SacCer2::SgdGene" do
706
+ context ".first" do
707
+ it 'returns the first records' do
708
+ result = Bio::Ucsc::SacCer2::SgdGene.first
709
+ pp result
710
+ result.should be_true
711
+ end
712
+ end
713
+ end
714
+
715
+ describe "Bio::Ucsc::SacCer2::SgdIsoforms" do
716
+ context ".first" do
717
+ it 'returns the first records' do
718
+ result = Bio::Ucsc::SacCer2::SgdIsoforms.first
719
+ pp result
720
+ result.should be_true
721
+ end
722
+ end
723
+ end
724
+
725
+ describe "Bio::Ucsc::SacCer2::SgdLocalization" do
726
+ context ".first" do
727
+ it 'returns the first records' do
728
+ result = Bio::Ucsc::SacCer2::SgdLocalization.first
729
+ pp result
730
+ result.should be_true
731
+ end
732
+ end
733
+ end
734
+
735
+ describe "Bio::Ucsc::SacCer2::SgdOther" do
736
+ context ".first" do
737
+ it 'returns the first records' do
738
+ result = Bio::Ucsc::SacCer2::SgdOther.first
739
+ pp result
740
+ result.should be_true
741
+ end
742
+ end
743
+ end
744
+
745
+ describe "Bio::Ucsc::SacCer2::SgdOtherDescription" do
746
+ context ".first" do
747
+ it 'returns the first records' do
748
+ result = Bio::Ucsc::SacCer2::SgdOtherDescription.first
749
+ pp result
750
+ result.should be_true
751
+ end
752
+ end
753
+ end
754
+
755
+ describe "Bio::Ucsc::SacCer2::SgdPep" do
756
+ context ".first" do
757
+ it 'returns the first records' do
758
+ result = Bio::Ucsc::SacCer2::SgdPep.first
759
+ pp result
760
+ result.should be_true
761
+ end
762
+ end
763
+ end
764
+
765
+ describe "Bio::Ucsc::SacCer2::SgdToName" do
766
+ context ".first" do
767
+ it 'returns the first records' do
768
+ result = Bio::Ucsc::SacCer2::SgdToName.first
769
+ pp result
770
+ result.should be_true
771
+ end
772
+ end
773
+ end
774
+
775
+ describe "Bio::Ucsc::SacCer2::SgdToPfam" do
776
+ context ".first" do
777
+ it 'returns the first records' do
778
+ result = Bio::Ucsc::SacCer2::SgdToPfam.first
779
+ pp result
780
+ result.should be_true
781
+ end
782
+ end
783
+ end
784
+
785
+ describe "Bio::Ucsc::SacCer2::SgdToSwissProt" do
786
+ context ".first" do
787
+ it 'returns the first records' do
788
+ result = Bio::Ucsc::SacCer2::SgdToSwissProt.first
789
+ pp result
790
+ result.should be_true
791
+ end
792
+ end
793
+ end
794
+
795
+ describe "Bio::Ucsc::SacCer2::SimpleRepeat" do
796
+ context ".first" do
797
+ it 'returns the first records' do
798
+ result = Bio::Ucsc::SacCer2::SimpleRepeat.first
799
+ pp result
800
+ result.should be_true
801
+ end
802
+ end
803
+ end
804
+
805
+ describe "Bio::Ucsc::SacCer2::Source" do
806
+ context ".first" do
807
+ it 'returns the first records' do
808
+ result = Bio::Ucsc::SacCer2::Source.first
809
+ pp result
810
+ result.should be_true
811
+ end
812
+ end
813
+ end
814
+
815
+ describe "Bio::Ucsc::SacCer2::TableDescriptions" do
816
+ context ".first" do
817
+ it 'returns the first records' do
818
+ result = Bio::Ucsc::SacCer2::TableDescriptions.first
819
+ pp result
820
+ result.should be_true
821
+ end
822
+ end
823
+ end
824
+
825
+ describe "Bio::Ucsc::SacCer2::Tissue" do
826
+ context ".first" do
827
+ it 'returns the first records' do
828
+ result = Bio::Ucsc::SacCer2::Tissue.first
829
+ pp result
830
+ result.should be_true
831
+ end
832
+ end
833
+ end
834
+
835
+ describe "Bio::Ucsc::SacCer2::TrackDb" do
836
+ context ".first" do
837
+ it 'returns the first records' do
838
+ result = Bio::Ucsc::SacCer2::TrackDb.first
839
+ pp result
840
+ result.should be_true
841
+ end
842
+ end
843
+ end
844
+
845
+ describe "Bio::Ucsc::SacCer2::TransRegCode" do
846
+ context ".first" do
847
+ it 'returns the first records' do
848
+ result = Bio::Ucsc::SacCer2::TransRegCode.first
849
+ pp result
850
+ result.should be_true
851
+ end
852
+ end
853
+ end
854
+
855
+ describe "Bio::Ucsc::SacCer2::TransRegCodeCondition" do
856
+ context ".first" do
857
+ it 'returns the first records' do
858
+ result = Bio::Ucsc::SacCer2::TransRegCodeCondition.first
859
+ pp result
860
+ result.should be_true
861
+ end
862
+ end
863
+ end
864
+
865
+ describe "Bio::Ucsc::SacCer2::TransRegCodeMotif" do
866
+ context ".first" do
867
+ it 'returns the first records' do
868
+ result = Bio::Ucsc::SacCer2::TransRegCodeMotif.first
869
+ pp result
870
+ result.should be_true
871
+ end
872
+ end
873
+ end
874
+
875
+ describe "Bio::Ucsc::SacCer2::TransRegCodeProbe" do
876
+ context ".first" do
877
+ it 'returns the first records' do
878
+ result = Bio::Ucsc::SacCer2::TransRegCodeProbe.first
879
+ pp result
880
+ result.should be_true
881
+ end
882
+ end
883
+ end
884
+
885
+ describe "Bio::Ucsc::SacCer2::UwFootprintsMappability" do
886
+ context ".first" do
887
+ it 'returns the first records' do
888
+ result = Bio::Ucsc::SacCer2::UwFootprintsMappability.first
889
+ pp result
890
+ result.should be_true
891
+ end
892
+ end
893
+ end
894
+
895
+ describe "Bio::Ucsc::SacCer2::UwFootprintsPrints" do
896
+ context ".first" do
897
+ it 'returns the first records' do
898
+ result = Bio::Ucsc::SacCer2::UwFootprintsPrints.first
899
+ pp result
900
+ result.should be_true
901
+ end
902
+ end
903
+ end
904
+
905
+ describe "Bio::Ucsc::SacCer2::UwFootprintsTagCounts" do
906
+ context ".first" do
907
+ it 'returns the first records' do
908
+ result = Bio::Ucsc::SacCer2::UwFootprintsTagCounts.first
909
+ pp result
910
+ result.should be_true
911
+ end
912
+ end
913
+ end
914
+
915
+ describe "Bio::Ucsc::SacCer2::YeastP2P" do
916
+ context ".first" do
917
+ it 'returns the first records' do
918
+ result = Bio::Ucsc::SacCer2::YeastP2P.first
919
+ pp result
920
+ result.should be_true
921
+ end
922
+ end
923
+ end
924
+
925
+ end