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 +1,924 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::GasAcu1" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::GasAcu1::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::GasAcu1::All_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::GasAcu1::All_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::GasAcu1::All_mrna" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::GasAcu1::All_mrna.first
24
+ pp result
25
+ result.should be_true
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::GasAcu1::Author" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::GasAcu1::Author.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::GasAcu1::BlastHg18KG" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::GasAcu1::BlastHg18KG.first
44
+ pp result
45
+ result.should be_true
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::GasAcu1::Cds" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::GasAcu1::Cds.first
54
+ pp result
55
+ result.should be_true
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::GasAcu1::Cell" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::GasAcu1::Cell.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::GasAcu1::ChainAnoCar1" 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::GasAcu1::ChainAnoCar1.find_by_interval gi
75
+ pp result
76
+ result.should be_true
77
+ end
78
+ end
79
+ end
80
+
81
+ describe "Bio::Ucsc::GasAcu1::ChainAnoCar1Link" 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::GasAcu1::ChainAnoCar1Link.find_by_interval gi
86
+ pp result
87
+ result.should be_true
88
+ end
89
+ end
90
+ end
91
+
92
+ describe "Bio::Ucsc::GasAcu1::ChainDanRer7" do
93
+ context ".first" do
94
+ it 'returns the first records' do
95
+ result = Bio::Ucsc::GasAcu1::ChainDanRer7.first
96
+ pp result
97
+ result.should be_true
98
+ end
99
+ end
100
+ end
101
+
102
+ describe "Bio::Ucsc::GasAcu1::ChainDanRer7Link" do
103
+ context ".first" do
104
+ it 'returns the first records' do
105
+ result = Bio::Ucsc::GasAcu1::ChainDanRer7Link.first
106
+ pp result
107
+ result.should be_true
108
+ end
109
+ end
110
+ end
111
+
112
+ describe "Bio::Ucsc::GasAcu1::ChainFr2" do
113
+ context ".find_by_interval" do
114
+ it 'returns the first records' do
115
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
116
+ result = Bio::Ucsc::GasAcu1::ChainFr2.find_by_interval gi
117
+ pp result
118
+ result.should be_true
119
+ end
120
+ end
121
+ end
122
+
123
+ describe "Bio::Ucsc::GasAcu1::ChainFr2Link" do
124
+ context ".find_by_interval" do
125
+ it 'returns the first records' do
126
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
127
+ result = Bio::Ucsc::GasAcu1::ChainFr2Link.find_by_interval gi
128
+ pp result
129
+ result.should be_true
130
+ end
131
+ end
132
+ end
133
+
134
+ describe "Bio::Ucsc::GasAcu1::ChainGalGal3" do
135
+ context ".find_by_interval" do
136
+ it 'returns the first records' do
137
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
138
+ result = Bio::Ucsc::GasAcu1::ChainGalGal3.find_by_interval gi
139
+ pp result
140
+ result.should be_true
141
+ end
142
+ end
143
+ end
144
+
145
+ describe "Bio::Ucsc::GasAcu1::ChainGalGal3Link" do
146
+ context ".find_by_interval" do
147
+ it 'returns the first records' do
148
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
149
+ result = Bio::Ucsc::GasAcu1::ChainGalGal3Link.find_by_interval gi
150
+ pp result
151
+ result.should be_true
152
+ end
153
+ end
154
+ end
155
+
156
+ describe "Bio::Ucsc::GasAcu1::ChainHg19" do
157
+ context ".first" do
158
+ it 'returns the first records' do
159
+ result = Bio::Ucsc::GasAcu1::ChainHg19.first
160
+ pp result
161
+ result.should be_true
162
+ end
163
+ end
164
+ end
165
+
166
+ describe "Bio::Ucsc::GasAcu1::ChainHg19Link" do
167
+ context ".first" do
168
+ it 'returns the first records' do
169
+ result = Bio::Ucsc::GasAcu1::ChainHg19Link.first
170
+ pp result
171
+ result.should be_true
172
+ end
173
+ end
174
+ end
175
+
176
+ describe "Bio::Ucsc::GasAcu1::ChainMm9" do
177
+ context ".find_by_interval" do
178
+ it 'returns the first records' do
179
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
180
+ result = Bio::Ucsc::GasAcu1::ChainMm9.find_by_interval gi
181
+ pp result
182
+ result.should be_true
183
+ end
184
+ end
185
+ end
186
+
187
+ describe "Bio::Ucsc::GasAcu1::ChainMm9Link" do
188
+ context ".find_by_interval" do
189
+ it 'returns the first records' do
190
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
191
+ result = Bio::Ucsc::GasAcu1::ChainMm9Link.find_by_interval gi
192
+ pp result
193
+ result.should be_true
194
+ end
195
+ end
196
+ end
197
+
198
+ describe "Bio::Ucsc::GasAcu1::ChainOryLat2" do
199
+ context ".find_by_interval" do
200
+ it 'returns the first records' do
201
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
202
+ result = Bio::Ucsc::GasAcu1::ChainOryLat2.find_by_interval gi
203
+ pp result
204
+ result.should be_true
205
+ end
206
+ end
207
+ end
208
+
209
+ describe "Bio::Ucsc::GasAcu1::ChainOryLat2Link" 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::GasAcu1::ChainOryLat2Link.find_by_interval gi
214
+ pp result
215
+ result.should be_true
216
+ end
217
+ end
218
+ end
219
+
220
+ describe "Bio::Ucsc::GasAcu1::ChainTetNig2" do
221
+ context ".first" do
222
+ it 'returns the first records' do
223
+ result = Bio::Ucsc::GasAcu1::ChainTetNig2.first
224
+ pp result
225
+ result.should be_true
226
+ end
227
+ end
228
+ end
229
+
230
+ describe "Bio::Ucsc::GasAcu1::ChainTetNig2Link" do
231
+ context ".first" do
232
+ it 'returns the first records' do
233
+ result = Bio::Ucsc::GasAcu1::ChainTetNig2Link.first
234
+ pp result
235
+ result.should be_true
236
+ end
237
+ end
238
+ end
239
+
240
+ describe "Bio::Ucsc::GasAcu1::ChromInfo" do
241
+ context ".first" do
242
+ it 'returns the first records' do
243
+ result = Bio::Ucsc::GasAcu1::ChromInfo.first
244
+ pp result
245
+ result.should be_true
246
+ end
247
+ end
248
+ end
249
+
250
+ describe "Bio::Ucsc::GasAcu1::Description" do
251
+ context ".first" do
252
+ it 'returns the first records' do
253
+ result = Bio::Ucsc::GasAcu1::Description.first
254
+ pp result
255
+ result.should be_true
256
+ end
257
+ end
258
+ end
259
+
260
+ describe "Bio::Ucsc::GasAcu1::Development" do
261
+ context ".first" do
262
+ it 'returns the first records' do
263
+ result = Bio::Ucsc::GasAcu1::Development.first
264
+ pp result
265
+ result.should be_true
266
+ end
267
+ end
268
+ end
269
+
270
+ describe "Bio::Ucsc::GasAcu1::EnsGene" do
271
+ context ".first" do
272
+ it 'returns the first records' do
273
+ result = Bio::Ucsc::GasAcu1::EnsGene.first
274
+ pp result
275
+ result.should be_true
276
+ end
277
+ end
278
+ end
279
+
280
+ describe "Bio::Ucsc::GasAcu1::EnsGtp" do
281
+ context ".first" do
282
+ it 'returns the first records' do
283
+ result = Bio::Ucsc::GasAcu1::EnsGtp.first
284
+ pp result
285
+ result.should be_true
286
+ end
287
+ end
288
+ end
289
+
290
+ describe "Bio::Ucsc::GasAcu1::EnsPep" do
291
+ context ".first" do
292
+ it 'returns the first records' do
293
+ result = Bio::Ucsc::GasAcu1::EnsPep.first
294
+ pp result
295
+ result.should be_true
296
+ end
297
+ end
298
+ end
299
+
300
+ describe "Bio::Ucsc::GasAcu1::Est" do
301
+ context ".find_by_interval" do
302
+ it 'returns the first records' do
303
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
304
+ result = Bio::Ucsc::GasAcu1::Est.find_by_interval gi
305
+ pp result
306
+ result.should be_true
307
+ end
308
+ end
309
+ end
310
+
311
+ describe "Bio::Ucsc::GasAcu1::EstOrientInfo" do
312
+ context ".first" do
313
+ it 'returns the first records' do
314
+ result = Bio::Ucsc::GasAcu1::EstOrientInfo.first
315
+ pp result
316
+ result.should be_true
317
+ end
318
+ end
319
+ end
320
+
321
+ describe "Bio::Ucsc::GasAcu1::ExtFile" do
322
+ context ".first" do
323
+ it 'returns the first records' do
324
+ result = Bio::Ucsc::GasAcu1::ExtFile.first
325
+ pp result
326
+ result.should be_true
327
+ end
328
+ end
329
+ end
330
+
331
+ describe "Bio::Ucsc::GasAcu1::Gap" do
332
+ context ".first" do
333
+ it 'returns the first records' do
334
+ result = Bio::Ucsc::GasAcu1::Gap.first
335
+ pp result
336
+ result.should be_true
337
+ end
338
+ end
339
+ end
340
+
341
+ describe "Bio::Ucsc::GasAcu1::GbCdnaInfo" do
342
+ context ".first" do
343
+ it 'returns the first records' do
344
+ result = Bio::Ucsc::GasAcu1::GbCdnaInfo.first
345
+ pp result
346
+ result.should be_true
347
+ end
348
+ end
349
+ end
350
+
351
+ describe "Bio::Ucsc::GasAcu1::GbExtFile" do
352
+ context ".first" do
353
+ it 'returns the first records' do
354
+ result = Bio::Ucsc::GasAcu1::GbExtFile.first
355
+ pp result
356
+ result.should be_true
357
+ end
358
+ end
359
+ end
360
+
361
+ describe "Bio::Ucsc::GasAcu1::GbLoaded" do
362
+ context ".first" do
363
+ it 'returns the first records' do
364
+ result = Bio::Ucsc::GasAcu1::GbLoaded.first
365
+ pp result
366
+ result.should be_true
367
+ end
368
+ end
369
+ end
370
+
371
+ describe "Bio::Ucsc::GasAcu1::GbMiscDiff" do
372
+ context ".first" do
373
+ it 'returns the first records' do
374
+ result = Bio::Ucsc::GasAcu1::GbMiscDiff.first
375
+ pp result
376
+ result.should be_true
377
+ end
378
+ end
379
+ end
380
+
381
+ describe "Bio::Ucsc::GasAcu1::GbSeq" do
382
+ context ".first" do
383
+ it 'returns the first records' do
384
+ result = Bio::Ucsc::GasAcu1::GbSeq.first
385
+ pp result
386
+ result.should be_true
387
+ end
388
+ end
389
+ end
390
+
391
+ describe "Bio::Ucsc::GasAcu1::GbStatus" do
392
+ context ".first" do
393
+ it 'returns the first records' do
394
+ result = Bio::Ucsc::GasAcu1::GbStatus.first
395
+ pp result
396
+ result.should be_true
397
+ end
398
+ end
399
+ end
400
+
401
+ describe "Bio::Ucsc::GasAcu1::GbWarn" do
402
+ context ".first" do
403
+ it 'returns the first records' do
404
+ result = Bio::Ucsc::GasAcu1::GbWarn.first
405
+ pp result
406
+ result.should be_true
407
+ end
408
+ end
409
+ end
410
+
411
+ describe "Bio::Ucsc::GasAcu1::Gc5Base" do
412
+ context ".first" do
413
+ it 'returns the first records' do
414
+ result = Bio::Ucsc::GasAcu1::Gc5Base.first
415
+ pp result
416
+ result.should be_true
417
+ end
418
+ end
419
+ end
420
+
421
+ describe "Bio::Ucsc::GasAcu1::GeneName" do
422
+ context ".first" do
423
+ it 'returns the first records' do
424
+ result = Bio::Ucsc::GasAcu1::GeneName.first
425
+ pp result
426
+ result.should be_true
427
+ end
428
+ end
429
+ end
430
+
431
+ describe "Bio::Ucsc::GasAcu1::Gold" do
432
+ context ".first" do
433
+ it 'returns the first records' do
434
+ result = Bio::Ucsc::GasAcu1::Gold.first
435
+ pp result
436
+ result.should be_true
437
+ end
438
+ end
439
+ end
440
+
441
+ describe "Bio::Ucsc::GasAcu1::Grp" do
442
+ context ".first" do
443
+ it 'returns the first records' do
444
+ result = Bio::Ucsc::GasAcu1::Grp.first
445
+ pp result
446
+ result.should be_true
447
+ end
448
+ end
449
+ end
450
+
451
+ describe "Bio::Ucsc::GasAcu1::HgFindSpec" do
452
+ context ".first" do
453
+ it 'returns the first records' do
454
+ result = Bio::Ucsc::GasAcu1::HgFindSpec.first
455
+ pp result
456
+ result.should be_true
457
+ end
458
+ end
459
+ end
460
+
461
+ describe "Bio::Ucsc::GasAcu1::History" do
462
+ context ".first" do
463
+ it 'returns the first records' do
464
+ result = Bio::Ucsc::GasAcu1::History.first
465
+ pp result
466
+ result.should be_true
467
+ end
468
+ end
469
+ end
470
+
471
+ describe "Bio::Ucsc::GasAcu1::ImageClone" do
472
+ context ".first" do
473
+ it 'returns the first records' do
474
+ result = Bio::Ucsc::GasAcu1::ImageClone.first
475
+ pp result
476
+ result.should be_true
477
+ end
478
+ end
479
+ end
480
+
481
+ describe "Bio::Ucsc::GasAcu1::IntronEst" do
482
+ context ".find_by_interval" do
483
+ it 'returns the first records' do
484
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
485
+ result = Bio::Ucsc::GasAcu1::IntronEst.find_by_interval gi
486
+ pp result
487
+ result.should be_true
488
+ end
489
+ end
490
+ end
491
+
492
+ describe "Bio::Ucsc::GasAcu1::Keyword" do
493
+ context ".first" do
494
+ it 'returns the first records' do
495
+ result = Bio::Ucsc::GasAcu1::Keyword.first
496
+ pp result
497
+ result.should be_true
498
+ end
499
+ end
500
+ end
501
+
502
+ describe "Bio::Ucsc::GasAcu1::Library" do
503
+ context ".first" do
504
+ it 'returns the first records' do
505
+ result = Bio::Ucsc::GasAcu1::Library.first
506
+ pp result
507
+ result.should be_true
508
+ end
509
+ end
510
+ end
511
+
512
+ describe "Bio::Ucsc::GasAcu1::Mrna" do
513
+ context ".find_by_interval" do
514
+ it 'returns the first records' do
515
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
516
+ result = Bio::Ucsc::GasAcu1::Mrna.find_by_interval gi
517
+ pp result
518
+ result.should be_true
519
+ end
520
+ end
521
+ end
522
+
523
+ describe "Bio::Ucsc::GasAcu1::MrnaClone" do
524
+ context ".first" do
525
+ it 'returns the first records' do
526
+ result = Bio::Ucsc::GasAcu1::MrnaClone.first
527
+ pp result
528
+ result.should be_true
529
+ end
530
+ end
531
+ end
532
+
533
+ describe "Bio::Ucsc::GasAcu1::MrnaOrientInfo" do
534
+ context ".first" do
535
+ it 'returns the first records' do
536
+ result = Bio::Ucsc::GasAcu1::MrnaOrientInfo.first
537
+ pp result
538
+ result.should be_true
539
+ end
540
+ end
541
+ end
542
+
543
+ describe "Bio::Ucsc::GasAcu1::Multiz8way" do
544
+ context ".first" do
545
+ it 'returns the first records' do
546
+ result = Bio::Ucsc::GasAcu1::Multiz8way.first
547
+ pp result
548
+ result.should be_true
549
+ end
550
+ end
551
+ end
552
+
553
+ describe "Bio::Ucsc::GasAcu1::Multiz8wayFrames" do
554
+ context ".first" do
555
+ it 'returns the first records' do
556
+ result = Bio::Ucsc::GasAcu1::Multiz8wayFrames.first
557
+ pp result
558
+ result.should be_true
559
+ end
560
+ end
561
+ end
562
+
563
+ describe "Bio::Ucsc::GasAcu1::Multiz8waySummary" do
564
+ context ".first" do
565
+ it 'returns the first records' do
566
+ result = Bio::Ucsc::GasAcu1::Multiz8waySummary.first
567
+ pp result
568
+ result.should be_true
569
+ end
570
+ end
571
+ end
572
+
573
+ describe "Bio::Ucsc::GasAcu1::NetAnoCar1" do
574
+ context ".first" do
575
+ it 'returns the first records' do
576
+ result = Bio::Ucsc::GasAcu1::NetAnoCar1.first
577
+ pp result
578
+ result.should be_true
579
+ end
580
+ end
581
+ end
582
+
583
+ describe "Bio::Ucsc::GasAcu1::NetDanRer7" do
584
+ context ".first" do
585
+ it 'returns the first records' do
586
+ result = Bio::Ucsc::GasAcu1::NetDanRer7.first
587
+ pp result
588
+ result.should be_true
589
+ end
590
+ end
591
+ end
592
+
593
+ describe "Bio::Ucsc::GasAcu1::NetFr2" do
594
+ context ".first" do
595
+ it 'returns the first records' do
596
+ result = Bio::Ucsc::GasAcu1::NetFr2.first
597
+ pp result
598
+ result.should be_true
599
+ end
600
+ end
601
+ end
602
+
603
+ describe "Bio::Ucsc::GasAcu1::NetGalGal3" do
604
+ context ".first" do
605
+ it 'returns the first records' do
606
+ result = Bio::Ucsc::GasAcu1::NetGalGal3.first
607
+ pp result
608
+ result.should be_true
609
+ end
610
+ end
611
+ end
612
+
613
+ describe "Bio::Ucsc::GasAcu1::NetHg19" do
614
+ context ".first" do
615
+ it 'returns the first records' do
616
+ result = Bio::Ucsc::GasAcu1::NetHg19.first
617
+ pp result
618
+ result.should be_true
619
+ end
620
+ end
621
+ end
622
+
623
+ describe "Bio::Ucsc::GasAcu1::NetMm9" do
624
+ context ".first" do
625
+ it 'returns the first records' do
626
+ result = Bio::Ucsc::GasAcu1::NetMm9.first
627
+ pp result
628
+ result.should be_true
629
+ end
630
+ end
631
+ end
632
+
633
+ describe "Bio::Ucsc::GasAcu1::NetOryLat2" do
634
+ context ".first" do
635
+ it 'returns the first records' do
636
+ result = Bio::Ucsc::GasAcu1::NetOryLat2.first
637
+ pp result
638
+ result.should be_true
639
+ end
640
+ end
641
+ end
642
+
643
+ describe "Bio::Ucsc::GasAcu1::NetTetNig2" do
644
+ context ".first" do
645
+ it 'returns the first records' do
646
+ result = Bio::Ucsc::GasAcu1::NetTetNig2.first
647
+ pp result
648
+ result.should be_true
649
+ end
650
+ end
651
+ end
652
+
653
+ describe "Bio::Ucsc::GasAcu1::NscanGene" do
654
+ context ".first" do
655
+ it 'returns the first records' do
656
+ result = Bio::Ucsc::GasAcu1::NscanGene.first
657
+ pp result
658
+ result.should be_true
659
+ end
660
+ end
661
+ end
662
+
663
+ describe "Bio::Ucsc::GasAcu1::NscanPep" do
664
+ context ".first" do
665
+ it 'returns the first records' do
666
+ result = Bio::Ucsc::GasAcu1::NscanPep.first
667
+ pp result
668
+ result.should be_true
669
+ end
670
+ end
671
+ end
672
+
673
+ describe "Bio::Ucsc::GasAcu1::Organism" do
674
+ context ".first" do
675
+ it 'returns the first records' do
676
+ result = Bio::Ucsc::GasAcu1::Organism.first
677
+ pp result
678
+ result.should be_true
679
+ end
680
+ end
681
+ end
682
+
683
+ describe "Bio::Ucsc::GasAcu1::PhastCons8" do
684
+ context ".first" do
685
+ it 'returns the first records' do
686
+ result = Bio::Ucsc::GasAcu1::PhastCons8.first
687
+ pp result
688
+ result.should be_true
689
+ end
690
+ end
691
+ end
692
+
693
+ describe "Bio::Ucsc::GasAcu1::PhastConsElements8way" do
694
+ context ".first" do
695
+ it 'returns the first records' do
696
+ result = Bio::Ucsc::GasAcu1::PhastConsElements8way.first
697
+ pp result
698
+ result.should be_true
699
+ end
700
+ end
701
+ end
702
+
703
+ describe "Bio::Ucsc::GasAcu1::ProductName" do
704
+ context ".first" do
705
+ it 'returns the first records' do
706
+ result = Bio::Ucsc::GasAcu1::ProductName.first
707
+ pp result
708
+ result.should be_true
709
+ end
710
+ end
711
+ end
712
+
713
+ describe "Bio::Ucsc::GasAcu1::Quality" do
714
+ context ".first" do
715
+ it 'returns the first records' do
716
+ result = Bio::Ucsc::GasAcu1::Quality.first
717
+ pp result
718
+ result.should be_true
719
+ end
720
+ end
721
+ end
722
+
723
+ describe "Bio::Ucsc::GasAcu1::RefLink" do
724
+ context ".first" do
725
+ it 'returns nil (empty table)' do
726
+ result = Bio::Ucsc::GasAcu1::RefLink.first
727
+ pp result
728
+ result.should be_nil # empty table
729
+ end
730
+ end
731
+ end
732
+
733
+ describe "Bio::Ucsc::GasAcu1::RefSeqStatus" do
734
+ context ".first" do
735
+ it 'returns nil (empty table)' do
736
+ result = Bio::Ucsc::GasAcu1::RefSeqStatus.first
737
+ pp result
738
+ result.should be_nil # empyty table
739
+ end
740
+ end
741
+ end
742
+
743
+ describe "Bio::Ucsc::GasAcu1::RefSeqSummary" do
744
+ context "returns nil (empty table)" do
745
+ it 'returns the first records' do
746
+ result = Bio::Ucsc::GasAcu1::RefSeqSummary.first
747
+ pp result
748
+ result.should be_nil # empyty table
749
+ end
750
+ end
751
+ end
752
+
753
+ describe "Bio::Ucsc::GasAcu1::Rmsk" do
754
+ context ".find_by_interval" do
755
+ it 'returns the first records' do
756
+ gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
757
+ result = Bio::Ucsc::GasAcu1::Rmsk.find_by_interval gi
758
+ pp result
759
+ result.should be_true
760
+ end
761
+ end
762
+ end
763
+
764
+ describe "Bio::Ucsc::GasAcu1::Sex" do
765
+ context ".first" do
766
+ it 'returns the first records' do
767
+ result = Bio::Ucsc::GasAcu1::Sex.first
768
+ pp result
769
+ result.should be_true
770
+ end
771
+ end
772
+ end
773
+
774
+ describe "Bio::Ucsc::GasAcu1::SimpleRepeat" do
775
+ context ".first" do
776
+ it 'returns the first records' do
777
+ result = Bio::Ucsc::GasAcu1::SimpleRepeat.first
778
+ pp result
779
+ result.should be_true
780
+ end
781
+ end
782
+ end
783
+
784
+ describe "Bio::Ucsc::GasAcu1::Source" do
785
+ context ".first" do
786
+ it 'returns the first records' do
787
+ result = Bio::Ucsc::GasAcu1::Source.first
788
+ pp result
789
+ result.should be_true
790
+ end
791
+ end
792
+ end
793
+
794
+ describe "Bio::Ucsc::GasAcu1::TableDescriptions" do
795
+ context ".first" do
796
+ it 'returns the first records' do
797
+ result = Bio::Ucsc::GasAcu1::TableDescriptions.first
798
+ pp result
799
+ result.should be_true
800
+ end
801
+ end
802
+ end
803
+
804
+ describe "Bio::Ucsc::GasAcu1::Tissue" do
805
+ context ".first" do
806
+ it 'returns the first records' do
807
+ result = Bio::Ucsc::GasAcu1::Tissue.first
808
+ pp result
809
+ result.should be_true
810
+ end
811
+ end
812
+ end
813
+
814
+ describe "Bio::Ucsc::GasAcu1::TrackDb" do
815
+ context ".first" do
816
+ it 'returns the first records' do
817
+ result = Bio::Ucsc::GasAcu1::TrackDb.first
818
+ pp result
819
+ result.should be_true
820
+ end
821
+ end
822
+ end
823
+
824
+ describe "Bio::Ucsc::GasAcu1::TransMapAlnMRna" do
825
+ context ".first" do
826
+ it 'returns the first records' do
827
+ result = Bio::Ucsc::GasAcu1::TransMapAlnMRna.first
828
+ pp result
829
+ result.should be_true
830
+ end
831
+ end
832
+ end
833
+
834
+ describe "Bio::Ucsc::GasAcu1::TransMapAlnRefSeq" do
835
+ context ".first" do
836
+ it 'returns the first records' do
837
+ result = Bio::Ucsc::GasAcu1::TransMapAlnRefSeq.first
838
+ pp result
839
+ result.should be_true
840
+ end
841
+ end
842
+ end
843
+
844
+ describe "Bio::Ucsc::GasAcu1::TransMapAlnSplicedEst" do
845
+ context ".first" do
846
+ it 'returns the first records' do
847
+ result = Bio::Ucsc::GasAcu1::TransMapAlnSplicedEst.first
848
+ pp result
849
+ result.should be_true
850
+ end
851
+ end
852
+ end
853
+
854
+ describe "Bio::Ucsc::GasAcu1::TransMapAlnUcscGenes" do
855
+ context ".first" do
856
+ it 'returns the first records' do
857
+ result = Bio::Ucsc::GasAcu1::TransMapAlnUcscGenes.first
858
+ pp result
859
+ result.should be_true
860
+ end
861
+ end
862
+ end
863
+
864
+ describe "Bio::Ucsc::GasAcu1::TransMapInfoMRna" do
865
+ context ".first" do
866
+ it 'returns the first records' do
867
+ result = Bio::Ucsc::GasAcu1::TransMapInfoMRna.first
868
+ pp result
869
+ result.should be_true
870
+ end
871
+ end
872
+ end
873
+
874
+ describe "Bio::Ucsc::GasAcu1::TransMapInfoRefSeq" do
875
+ context ".first" do
876
+ it 'returns the first records' do
877
+ result = Bio::Ucsc::GasAcu1::TransMapInfoRefSeq.first
878
+ pp result
879
+ result.should be_true
880
+ end
881
+ end
882
+ end
883
+
884
+ describe "Bio::Ucsc::GasAcu1::TransMapInfoSplicedEst" do
885
+ context ".first" do
886
+ it 'returns the first records' do
887
+ result = Bio::Ucsc::GasAcu1::TransMapInfoSplicedEst.first
888
+ pp result
889
+ result.should be_true
890
+ end
891
+ end
892
+ end
893
+
894
+ describe "Bio::Ucsc::GasAcu1::TransMapInfoUcscGenes" do
895
+ context ".first" do
896
+ it 'returns the first records' do
897
+ result = Bio::Ucsc::GasAcu1::TransMapInfoUcscGenes.first
898
+ pp result
899
+ result.should be_true
900
+ end
901
+ end
902
+ end
903
+
904
+ describe "Bio::Ucsc::GasAcu1::WindowmaskerSdust" do
905
+ context ".first" do
906
+ it 'returns the first records' do
907
+ result = Bio::Ucsc::GasAcu1::WindowmaskerSdust.first
908
+ pp result
909
+ result.should be_true
910
+ end
911
+ end
912
+ end
913
+
914
+ describe "Bio::Ucsc::GasAcu1::XenoMrna" do
915
+ context ".first" do
916
+ it 'returns the first records' do
917
+ result = Bio::Ucsc::GasAcu1::XenoMrna.first
918
+ pp result
919
+ result.should be_true
920
+ end
921
+ end
922
+ end
923
+
924
+ end