bio-ucsc-api 0.2.0 → 0.2.1

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Files changed (534) hide show
  1. data/README.rdoc +79 -47
  2. data/Rakefile +4 -2
  3. data/VERSION +1 -1
  4. data/bio-ucsc-api.gemspec +408 -3
  5. data/lib/bio-ucsc.rb +162 -8
  6. data/lib/bio-ucsc/ailmel1.rb +21 -0
  7. data/lib/bio-ucsc/ailmel1/db_connection.rb +57 -0
  8. data/lib/bio-ucsc/anocar2.rb +22 -0
  9. data/lib/bio-ucsc/anocar2/db_connection.rb +57 -0
  10. data/lib/bio-ucsc/anogam1.rb +30 -0
  11. data/lib/bio-ucsc/anogam1/chaindm3.rb +81 -0
  12. data/lib/bio-ucsc/anogam1/chaindm3link.rb +81 -0
  13. data/lib/bio-ucsc/anogam1/db_connection.rb +57 -0
  14. data/lib/bio-ucsc/anogam1/est.rb +81 -0
  15. data/lib/bio-ucsc/anogam1/gap.rb +81 -0
  16. data/lib/bio-ucsc/anogam1/gold.rb +81 -0
  17. data/lib/bio-ucsc/anogam1/intronest.rb +81 -0
  18. data/lib/bio-ucsc/anogam1/mrna.rb +81 -0
  19. data/lib/bio-ucsc/anogam1/rmsk.rb +78 -0
  20. data/lib/bio-ucsc/apimel2.rb +26 -0
  21. data/lib/bio-ucsc/apimel2/chaindm2.rb +81 -0
  22. data/lib/bio-ucsc/apimel2/chaindm2link.rb +81 -0
  23. data/lib/bio-ucsc/apimel2/db_connection.rb +57 -0
  24. data/lib/bio-ucsc/aplcal1.rb +33 -0
  25. data/lib/bio-ucsc/aplcal1/chaincaepb1.rb +81 -0
  26. data/lib/bio-ucsc/aplcal1/chaincaepb1link.rb +81 -0
  27. data/lib/bio-ucsc/aplcal1/chaincaerem2.rb +81 -0
  28. data/lib/bio-ucsc/aplcal1/chaincaerem2link.rb +81 -0
  29. data/lib/bio-ucsc/aplcal1/chaincb3.rb +81 -0
  30. data/lib/bio-ucsc/aplcal1/chaincb3link.rb +81 -0
  31. data/lib/bio-ucsc/aplcal1/chaince6.rb +81 -0
  32. data/lib/bio-ucsc/aplcal1/chaince6link.rb +81 -0
  33. data/lib/bio-ucsc/aplcal1/db_connection.rb +57 -0
  34. data/lib/bio-ucsc/aplcal1/gap.rb +81 -0
  35. data/lib/bio-ucsc/aplcal1/gold.rb +81 -0
  36. data/lib/bio-ucsc/aplcal1/rmsk.rb +78 -0
  37. data/lib/bio-ucsc/bostau4.rb +24 -0
  38. data/lib/bio-ucsc/bostau4/db_connection.rb +57 -0
  39. data/lib/bio-ucsc/braflo1.rb +32 -0
  40. data/lib/bio-ucsc/braflo1/chaingalgal3.rb +81 -0
  41. data/lib/bio-ucsc/braflo1/chaingalgal3link.rb +81 -0
  42. data/lib/bio-ucsc/braflo1/chainhg18.rb +81 -0
  43. data/lib/bio-ucsc/braflo1/chainhg18link.rb +81 -0
  44. data/lib/bio-ucsc/braflo1/chainmm9.rb +81 -0
  45. data/lib/bio-ucsc/braflo1/chainmm9link.rb +81 -0
  46. data/lib/bio-ucsc/braflo1/chainpetmar1.rb +81 -0
  47. data/lib/bio-ucsc/braflo1/chainpetmar1link.rb +81 -0
  48. data/lib/bio-ucsc/braflo1/db_connection.rb +57 -0
  49. data/lib/bio-ucsc/braflo1/gap.rb +81 -0
  50. data/lib/bio-ucsc/braflo1/gold.rb +81 -0
  51. data/lib/bio-ucsc/caejap1.rb +26 -0
  52. data/lib/bio-ucsc/caejap1/chaince6.rb +81 -0
  53. data/lib/bio-ucsc/caejap1/chaince6link.rb +81 -0
  54. data/lib/bio-ucsc/caejap1/db_connection.rb +57 -0
  55. data/lib/bio-ucsc/caejap1/gap.rb +81 -0
  56. data/lib/bio-ucsc/caejap1/gold.rb +81 -0
  57. data/lib/bio-ucsc/caepb2.rb +26 -0
  58. data/lib/bio-ucsc/caepb2/chaince6.rb +81 -0
  59. data/lib/bio-ucsc/caepb2/chaince6link.rb +81 -0
  60. data/lib/bio-ucsc/caepb2/db_connection.rb +57 -0
  61. data/lib/bio-ucsc/caepb2/gap.rb +81 -0
  62. data/lib/bio-ucsc/caepb2/gold.rb +81 -0
  63. data/lib/bio-ucsc/caerem3.rb +26 -0
  64. data/lib/bio-ucsc/caerem3/chaince6.rb +81 -0
  65. data/lib/bio-ucsc/caerem3/chaince6link.rb +81 -0
  66. data/lib/bio-ucsc/caerem3/db_connection.rb +57 -0
  67. data/lib/bio-ucsc/caerem3/gap.rb +81 -0
  68. data/lib/bio-ucsc/caerem3/gold.rb +81 -0
  69. data/lib/bio-ucsc/caljac3.rb +24 -0
  70. data/lib/bio-ucsc/caljac3/db_connection.rb +55 -0
  71. data/lib/bio-ucsc/canfam2.rb +39 -0
  72. data/lib/bio-ucsc/canfam2/chainbostau4.rb +81 -0
  73. data/lib/bio-ucsc/canfam2/chainbostau4link.rb +81 -0
  74. data/lib/bio-ucsc/canfam2/chainmm9.rb +81 -0
  75. data/lib/bio-ucsc/canfam2/chainmm9link.rb +81 -0
  76. data/lib/bio-ucsc/canfam2/chainrn4.rb +81 -0
  77. data/lib/bio-ucsc/canfam2/chainrn4link.rb +81 -0
  78. data/lib/bio-ucsc/canfam2/chainself.rb +81 -0
  79. data/lib/bio-ucsc/canfam2/chainselflink.rb +81 -0
  80. data/lib/bio-ucsc/canfam2/db_connection.rb +57 -0
  81. data/lib/bio-ucsc/canfam2/est.rb +81 -0
  82. data/lib/bio-ucsc/canfam2/gap.rb +81 -0
  83. data/lib/bio-ucsc/canfam2/gold.rb +81 -0
  84. data/lib/bio-ucsc/canfam2/intronest.rb +81 -0
  85. data/lib/bio-ucsc/canfam2/mrna.rb +81 -0
  86. data/lib/bio-ucsc/canfam2/rmsk.rb +78 -0
  87. data/lib/bio-ucsc/cavpor3.rb +21 -0
  88. data/lib/bio-ucsc/cavpor3/db_connection.rb +57 -0
  89. data/lib/bio-ucsc/cb3.rb +36 -0
  90. data/lib/bio-ucsc/cb3/chaincaepb1.rb +81 -0
  91. data/lib/bio-ucsc/cb3/chaincaepb1link.rb +81 -0
  92. data/lib/bio-ucsc/cb3/chaincaerem2.rb +81 -0
  93. data/lib/bio-ucsc/cb3/chaincaerem2link.rb +81 -0
  94. data/lib/bio-ucsc/cb3/chaince6.rb +81 -0
  95. data/lib/bio-ucsc/cb3/chaince6link.rb +81 -0
  96. data/lib/bio-ucsc/cb3/chainpripac1.rb +81 -0
  97. data/lib/bio-ucsc/cb3/chainpripac1link.rb +81 -0
  98. data/lib/bio-ucsc/cb3/db_connection.rb +57 -0
  99. data/lib/bio-ucsc/cb3/est.rb +81 -0
  100. data/lib/bio-ucsc/cb3/gap.rb +81 -0
  101. data/lib/bio-ucsc/cb3/gold.rb +81 -0
  102. data/lib/bio-ucsc/cb3/intronest.rb +81 -0
  103. data/lib/bio-ucsc/cb3/mrna.rb +81 -0
  104. data/lib/bio-ucsc/cb3/rmsk.rb +78 -0
  105. data/lib/bio-ucsc/ce6/chaincaejap1.rb +2 -2
  106. data/lib/bio-ucsc/ce6/chaincaejap1link.rb +2 -2
  107. data/lib/bio-ucsc/ce6/chaincaepb2.rb +2 -2
  108. data/lib/bio-ucsc/ce6/chaincaepb2link.rb +2 -2
  109. data/lib/bio-ucsc/ce6/chaincaerem3.rb +2 -2
  110. data/lib/bio-ucsc/ce6/chaincaerem3link.rb +2 -2
  111. data/lib/bio-ucsc/ce6/chaincb3.rb +2 -2
  112. data/lib/bio-ucsc/ce6/chaincb3link.rb +2 -2
  113. data/lib/bio-ucsc/ce6/chainpripac1.rb +2 -2
  114. data/lib/bio-ucsc/ce6/chainpripac1link.rb +2 -2
  115. data/lib/bio-ucsc/ce6/chainself.rb +2 -2
  116. data/lib/bio-ucsc/ce6/chainselflink.rb +2 -2
  117. data/lib/bio-ucsc/ce6/db_connection.rb +5 -6
  118. data/lib/bio-ucsc/ce6/est.rb +2 -2
  119. data/lib/bio-ucsc/ce6/gap.rb +2 -2
  120. data/lib/bio-ucsc/ce6/gold.rb +2 -2
  121. data/lib/bio-ucsc/ce6/intronest.rb +2 -2
  122. data/lib/bio-ucsc/ce6/mrna.rb +2 -2
  123. data/lib/bio-ucsc/ce6/rmsk.rb +2 -2
  124. data/lib/bio-ucsc/ce6/t25mersrepeats.rb +2 -2
  125. data/lib/bio-ucsc/ci2.rb +23 -0
  126. data/lib/bio-ucsc/ci2/db_connection.rb +55 -0
  127. data/lib/bio-ucsc/danrer7.rb +24 -0
  128. data/lib/bio-ucsc/danrer7/db_connection.rb +57 -0
  129. data/lib/bio-ucsc/dm3/chainanogam1.rb +2 -2
  130. data/lib/bio-ucsc/dm3/chainanogam1link.rb +2 -2
  131. data/lib/bio-ucsc/dm3/chainapimel3.rb +2 -2
  132. data/lib/bio-ucsc/dm3/chainapimel3link.rb +2 -2
  133. data/lib/bio-ucsc/dm3/chaindp3.rb +2 -2
  134. data/lib/bio-ucsc/dm3/chaindp3link.rb +2 -2
  135. data/lib/bio-ucsc/dm3/chaindroana2.rb +2 -2
  136. data/lib/bio-ucsc/dm3/chaindroana2link.rb +2 -2
  137. data/lib/bio-ucsc/dm3/chaindroere1.rb +2 -2
  138. data/lib/bio-ucsc/dm3/chaindroere1link.rb +2 -2
  139. data/lib/bio-ucsc/dm3/chaindroper1.rb +2 -2
  140. data/lib/bio-ucsc/dm3/chaindroper1link.rb +2 -2
  141. data/lib/bio-ucsc/dm3/chaindrosec1.rb +2 -2
  142. data/lib/bio-ucsc/dm3/chaindrosec1link.rb +2 -2
  143. data/lib/bio-ucsc/dm3/chaindrosim1.rb +2 -2
  144. data/lib/bio-ucsc/dm3/chaindrosim1link.rb +2 -2
  145. data/lib/bio-ucsc/dm3/chaindroyak2.rb +2 -2
  146. data/lib/bio-ucsc/dm3/chaindroyak2link.rb +2 -2
  147. data/lib/bio-ucsc/dm3/db_connection.rb +5 -6
  148. data/lib/bio-ucsc/dm3/est.rb +2 -2
  149. data/lib/bio-ucsc/dm3/gap.rb +2 -2
  150. data/lib/bio-ucsc/dm3/gold.rb +2 -2
  151. data/lib/bio-ucsc/dm3/intronest.rb +2 -2
  152. data/lib/bio-ucsc/dm3/mrna.rb +2 -2
  153. data/lib/bio-ucsc/dm3/rmsk.rb +2 -2
  154. data/lib/bio-ucsc/dp3.rb +33 -0
  155. data/lib/bio-ucsc/dp3/chaindm3.rb +81 -0
  156. data/lib/bio-ucsc/dp3/chaindm3link.rb +81 -0
  157. data/lib/bio-ucsc/dp3/db_connection.rb +57 -0
  158. data/lib/bio-ucsc/dp3/est.rb +81 -0
  159. data/lib/bio-ucsc/dp3/gap.rb +81 -0
  160. data/lib/bio-ucsc/dp3/gold.rb +81 -0
  161. data/lib/bio-ucsc/dp3/intronest.rb +81 -0
  162. data/lib/bio-ucsc/dp3/mrna.rb +81 -0
  163. data/lib/bio-ucsc/dp3/rmsk.rb +78 -0
  164. data/lib/bio-ucsc/droana2.rb +22 -0
  165. data/lib/bio-ucsc/droana2/db_connection.rb +57 -0
  166. data/lib/bio-ucsc/droere1.rb +22 -0
  167. data/lib/bio-ucsc/droere1/db_connection.rb +57 -0
  168. data/lib/bio-ucsc/drogri1.rb +22 -0
  169. data/lib/bio-ucsc/drogri1/db_connection.rb +57 -0
  170. data/lib/bio-ucsc/dromoj2.rb +22 -0
  171. data/lib/bio-ucsc/dromoj2/db_connection.rb +57 -0
  172. data/lib/bio-ucsc/droper1.rb +22 -0
  173. data/lib/bio-ucsc/droper1/db_connection.rb +57 -0
  174. data/lib/bio-ucsc/drosec1.rb +22 -0
  175. data/lib/bio-ucsc/drosec1/db_connection.rb +57 -0
  176. data/lib/bio-ucsc/drosim1.rb +30 -0
  177. data/lib/bio-ucsc/drosim1/chaindm3.rb +81 -0
  178. data/lib/bio-ucsc/drosim1/chaindm3link.rb +81 -0
  179. data/lib/bio-ucsc/drosim1/db_connection.rb +57 -0
  180. data/lib/bio-ucsc/drosim1/est.rb +81 -0
  181. data/lib/bio-ucsc/drosim1/gap.rb +81 -0
  182. data/lib/bio-ucsc/drosim1/gold.rb +81 -0
  183. data/lib/bio-ucsc/drosim1/intronest.rb +81 -0
  184. data/lib/bio-ucsc/drosim1/mrna.rb +81 -0
  185. data/lib/bio-ucsc/drosim1/rmsk.rb +78 -0
  186. data/lib/bio-ucsc/drovir2.rb +22 -0
  187. data/lib/bio-ucsc/drovir2/db_connection.rb +57 -0
  188. data/lib/bio-ucsc/droyak2.rb +32 -0
  189. data/lib/bio-ucsc/droyak2/chaindm3.rb +81 -0
  190. data/lib/bio-ucsc/droyak2/chaindm3link.rb +81 -0
  191. data/lib/bio-ucsc/droyak2/db_connection.rb +57 -0
  192. data/lib/bio-ucsc/droyak2/est.rb +81 -0
  193. data/lib/bio-ucsc/droyak2/gap.rb +81 -0
  194. data/lib/bio-ucsc/droyak2/gold.rb +81 -0
  195. data/lib/bio-ucsc/droyak2/intronest.rb +81 -0
  196. data/lib/bio-ucsc/droyak2/mrna.rb +81 -0
  197. data/lib/bio-ucsc/droyak2/rmsk.rb +78 -0
  198. data/lib/bio-ucsc/equcab2.rb +31 -0
  199. data/lib/bio-ucsc/equcab2/db_connection.rb +57 -0
  200. data/lib/bio-ucsc/equcab2/est.rb +81 -0
  201. data/lib/bio-ucsc/equcab2/gap.rb +81 -0
  202. data/lib/bio-ucsc/equcab2/gold.rb +81 -0
  203. data/lib/bio-ucsc/equcab2/intronest.rb +81 -0
  204. data/lib/bio-ucsc/equcab2/mrna.rb +81 -0
  205. data/lib/bio-ucsc/equcab2/rmsk.rb +78 -0
  206. data/lib/bio-ucsc/felcat4.rb +23 -0
  207. data/lib/bio-ucsc/felcat4/db_connection.rb +57 -0
  208. data/lib/bio-ucsc/fr2.rb +35 -0
  209. data/lib/bio-ucsc/fr2/chaingalgal3.rb +81 -0
  210. data/lib/bio-ucsc/fr2/chaingalgal3link.rb +81 -0
  211. data/lib/bio-ucsc/fr2/chaingasacu1.rb +81 -0
  212. data/lib/bio-ucsc/fr2/chaingasacu1link.rb +81 -0
  213. data/lib/bio-ucsc/fr2/chainmm9.rb +81 -0
  214. data/lib/bio-ucsc/fr2/chainmm9link.rb +81 -0
  215. data/lib/bio-ucsc/fr2/chainorylat2.rb +81 -0
  216. data/lib/bio-ucsc/fr2/chainorylat2link.rb +81 -0
  217. data/lib/bio-ucsc/fr2/db_connection.rb +57 -0
  218. data/lib/bio-ucsc/fr2/est.rb +81 -0
  219. data/lib/bio-ucsc/fr2/gap.rb +81 -0
  220. data/lib/bio-ucsc/fr2/gold.rb +81 -0
  221. data/lib/bio-ucsc/fr2/intronest.rb +81 -0
  222. data/lib/bio-ucsc/fr2/mrna.rb +81 -0
  223. data/lib/bio-ucsc/fr2/rmsk.rb +78 -0
  224. data/lib/bio-ucsc/galgal3.rb +54 -0
  225. data/lib/bio-ucsc/galgal3/chainanocar1.rb +81 -0
  226. data/lib/bio-ucsc/galgal3/chainanocar1link.rb +81 -0
  227. data/lib/bio-ucsc/galgal3/chainbraflo1.rb +81 -0
  228. data/lib/bio-ucsc/galgal3/chainbraflo1link.rb +81 -0
  229. data/lib/bio-ucsc/galgal3/chaincavpor3.rb +81 -0
  230. data/lib/bio-ucsc/galgal3/chaincavpor3link.rb +81 -0
  231. data/lib/bio-ucsc/galgal3/chaindanrer4.rb +81 -0
  232. data/lib/bio-ucsc/galgal3/chaindanrer4link.rb +81 -0
  233. data/lib/bio-ucsc/galgal3/chainfr2.rb +81 -0
  234. data/lib/bio-ucsc/galgal3/chainfr2link.rb +81 -0
  235. data/lib/bio-ucsc/galgal3/chaingasacu1.rb +81 -0
  236. data/lib/bio-ucsc/galgal3/chaingasacu1link.rb +81 -0
  237. data/lib/bio-ucsc/galgal3/chainmm9.rb +81 -0
  238. data/lib/bio-ucsc/galgal3/chainmm9link.rb +81 -0
  239. data/lib/bio-ucsc/galgal3/chainornana1.rb +81 -0
  240. data/lib/bio-ucsc/galgal3/chainornana1link.rb +81 -0
  241. data/lib/bio-ucsc/galgal3/chainpetmar1.rb +81 -0
  242. data/lib/bio-ucsc/galgal3/chainpetmar1link.rb +81 -0
  243. data/lib/bio-ucsc/galgal3/chainrn4.rb +81 -0
  244. data/lib/bio-ucsc/galgal3/chainrn4link.rb +81 -0
  245. data/lib/bio-ucsc/galgal3/chaintaegut1.rb +81 -0
  246. data/lib/bio-ucsc/galgal3/chaintaegut1link.rb +81 -0
  247. data/lib/bio-ucsc/galgal3/chainxentro2.rb +81 -0
  248. data/lib/bio-ucsc/galgal3/chainxentro2link.rb +81 -0
  249. data/lib/bio-ucsc/galgal3/db_connection.rb +57 -0
  250. data/lib/bio-ucsc/galgal3/est.rb +81 -0
  251. data/lib/bio-ucsc/galgal3/gap.rb +81 -0
  252. data/lib/bio-ucsc/galgal3/gold.rb +81 -0
  253. data/lib/bio-ucsc/galgal3/intronest.rb +81 -0
  254. data/lib/bio-ucsc/galgal3/mrna.rb +81 -0
  255. data/lib/bio-ucsc/galgal3/rmsk.rb +78 -0
  256. data/lib/bio-ucsc/gasacu1.rb +39 -0
  257. data/lib/bio-ucsc/gasacu1/chainanocar1.rb +81 -0
  258. data/lib/bio-ucsc/gasacu1/chainanocar1link.rb +81 -0
  259. data/lib/bio-ucsc/gasacu1/chainfr2.rb +81 -0
  260. data/lib/bio-ucsc/gasacu1/chainfr2link.rb +81 -0
  261. data/lib/bio-ucsc/gasacu1/chaingalgal3.rb +81 -0
  262. data/lib/bio-ucsc/gasacu1/chaingalgal3link.rb +81 -0
  263. data/lib/bio-ucsc/gasacu1/chainmm9.rb +81 -0
  264. data/lib/bio-ucsc/gasacu1/chainmm9link.rb +81 -0
  265. data/lib/bio-ucsc/gasacu1/chainorylat2.rb +81 -0
  266. data/lib/bio-ucsc/gasacu1/chainorylat2link.rb +81 -0
  267. data/lib/bio-ucsc/gasacu1/db_connection.rb +57 -0
  268. data/lib/bio-ucsc/gasacu1/est.rb +81 -0
  269. data/lib/bio-ucsc/gasacu1/intronest.rb +81 -0
  270. data/lib/bio-ucsc/gasacu1/mrna.rb +81 -0
  271. data/lib/bio-ucsc/gasacu1/rmsk.rb +78 -0
  272. data/lib/bio-ucsc/go/db_connection.rb +5 -6
  273. data/lib/bio-ucsc/hg18/chainanocar1.rb +2 -2
  274. data/lib/bio-ucsc/hg18/chainbostau4.rb +2 -2
  275. data/lib/bio-ucsc/hg18/chainbraflo1.rb +2 -2
  276. data/lib/bio-ucsc/hg18/chaincaljac1.rb +2 -2
  277. data/lib/bio-ucsc/hg18/chaincanfam2.rb +2 -2
  278. data/lib/bio-ucsc/hg18/chaincavpor3.rb +2 -2
  279. data/lib/bio-ucsc/hg18/chaindanrer5.rb +2 -2
  280. data/lib/bio-ucsc/hg18/chainequcab1.rb +2 -2
  281. data/lib/bio-ucsc/hg18/chainfelcat3.rb +2 -2
  282. data/lib/bio-ucsc/hg18/chainfr2.rb +2 -2
  283. data/lib/bio-ucsc/hg18/chaingalgal3.rb +2 -2
  284. data/lib/bio-ucsc/hg18/chaingasacu1.rb +2 -2
  285. data/lib/bio-ucsc/hg18/chainmm9.rb +2 -2
  286. data/lib/bio-ucsc/hg18/chainmondom4.rb +2 -2
  287. data/lib/bio-ucsc/hg18/chainornana1.rb +2 -2
  288. data/lib/bio-ucsc/hg18/chainorylat2.rb +2 -2
  289. data/lib/bio-ucsc/hg18/chainpantro2.rb +2 -2
  290. data/lib/bio-ucsc/hg18/chainpetmar1.rb +2 -2
  291. data/lib/bio-ucsc/hg18/chainponabe2.rb +2 -2
  292. data/lib/bio-ucsc/hg18/chainrhemac2.rb +2 -2
  293. data/lib/bio-ucsc/hg18/chainrn4.rb +2 -2
  294. data/lib/bio-ucsc/hg18/chainself.rb +2 -2
  295. data/lib/bio-ucsc/hg18/chainstrpur2.rb +2 -2
  296. data/lib/bio-ucsc/hg18/chaintaegut1.rb +2 -2
  297. data/lib/bio-ucsc/hg18/chaintetnig2.rb +2 -2
  298. data/lib/bio-ucsc/hg18/chainxentro2.rb +2 -2
  299. data/lib/bio-ucsc/hg18/db_connection.rb +5 -7
  300. data/lib/bio-ucsc/hg18/gap.rb +2 -2
  301. data/lib/bio-ucsc/hg18/gold.rb +2 -2
  302. data/lib/bio-ucsc/hg18/intronest.rb +2 -2
  303. data/lib/bio-ucsc/hg18/rmsk.rb +2 -2
  304. data/lib/bio-ucsc/hg18/rmskrm327.rb +2 -2
  305. data/lib/bio-ucsc/hgfixed/db_connection.rb +5 -6
  306. data/lib/bio-ucsc/loxafr3.rb +20 -0
  307. data/lib/bio-ucsc/loxafr3/db_connection.rb +57 -0
  308. data/lib/bio-ucsc/mm9/chainanocar1.rb +2 -2
  309. data/lib/bio-ucsc/mm9/chainanocar1link.rb +2 -2
  310. data/lib/bio-ucsc/mm9/chainbostau4.rb +2 -2
  311. data/lib/bio-ucsc/mm9/chainbostau4link.rb +3 -3
  312. data/lib/bio-ucsc/mm9/chainbraflo1.rb +2 -2
  313. data/lib/bio-ucsc/mm9/chainbraflo1link.rb +2 -2
  314. data/lib/bio-ucsc/mm9/chaincanfam2.rb +2 -2
  315. data/lib/bio-ucsc/mm9/chaincanfam2link.rb +2 -2
  316. data/lib/bio-ucsc/mm9/chaincavpor3.rb +2 -2
  317. data/lib/bio-ucsc/mm9/chaincavpor3link.rb +2 -2
  318. data/lib/bio-ucsc/mm9/chainfr2.rb +2 -2
  319. data/lib/bio-ucsc/mm9/chainfr2link.rb +2 -2
  320. data/lib/bio-ucsc/mm9/chaingalgal3.rb +2 -2
  321. data/lib/bio-ucsc/mm9/chaingalgal3link.rb +2 -2
  322. data/lib/bio-ucsc/mm9/chaingasacu1.rb +2 -2
  323. data/lib/bio-ucsc/mm9/chaingasacu1link.rb +2 -2
  324. data/lib/bio-ucsc/mm9/chainornana1.rb +2 -2
  325. data/lib/bio-ucsc/mm9/chainornana1link.rb +2 -2
  326. data/lib/bio-ucsc/mm9/chainorylat2.rb +2 -2
  327. data/lib/bio-ucsc/mm9/chainorylat2link.rb +2 -2
  328. data/lib/bio-ucsc/mm9/chainpantro2.rb +2 -2
  329. data/lib/bio-ucsc/mm9/chainpantro2link.rb +2 -2
  330. data/lib/bio-ucsc/mm9/chainpetmar1.rb +2 -2
  331. data/lib/bio-ucsc/mm9/chainpetmar1link.rb +2 -2
  332. data/lib/bio-ucsc/mm9/chainponabe2.rb +2 -2
  333. data/lib/bio-ucsc/mm9/chainponabe2link.rb +2 -2
  334. data/lib/bio-ucsc/mm9/chainrhemac2.rb +2 -2
  335. data/lib/bio-ucsc/mm9/chainrhemac2link.rb +2 -2
  336. data/lib/bio-ucsc/mm9/chainrn4.rb +2 -2
  337. data/lib/bio-ucsc/mm9/chainrn4link.rb +2 -2
  338. data/lib/bio-ucsc/mm9/chainxentro2.rb +2 -2
  339. data/lib/bio-ucsc/mm9/chainxentro2link.rb +2 -2
  340. data/lib/bio-ucsc/mm9/db_connection.rb +6 -7
  341. data/lib/bio-ucsc/mm9/est.rb +2 -2
  342. data/lib/bio-ucsc/mm9/gap.rb +2 -2
  343. data/lib/bio-ucsc/mm9/gold.rb +2 -2
  344. data/lib/bio-ucsc/mm9/intronest.rb +2 -2
  345. data/lib/bio-ucsc/mm9/mrna.rb +2 -2
  346. data/lib/bio-ucsc/mm9/rmsk.rb +2 -2
  347. data/lib/bio-ucsc/mondom5.rb +21 -0
  348. data/lib/bio-ucsc/mondom5/db_connection.rb +57 -0
  349. data/lib/bio-ucsc/ornana1.rb +20 -0
  350. data/lib/bio-ucsc/ornana1/db_connection.rb +57 -0
  351. data/lib/bio-ucsc/orycun2.rb +24 -0
  352. data/lib/bio-ucsc/orycun2/db_connection.rb +57 -0
  353. data/lib/bio-ucsc/orylat2.rb +24 -0
  354. data/lib/bio-ucsc/orylat2/db_connection.rb +55 -0
  355. data/lib/bio-ucsc/oviari1.rb +24 -0
  356. data/lib/bio-ucsc/oviari1/db_connection.rb +57 -0
  357. data/lib/bio-ucsc/pantro3.rb +24 -0
  358. data/lib/bio-ucsc/pantro3/db_connection.rb +55 -0
  359. data/lib/bio-ucsc/petmar1.rb +22 -0
  360. data/lib/bio-ucsc/petmar1/db_connection.rb +57 -0
  361. data/lib/bio-ucsc/ponabe2.rb +36 -0
  362. data/lib/bio-ucsc/ponabe2/chainmm9.rb +81 -0
  363. data/lib/bio-ucsc/ponabe2/chainmm9link.rb +81 -0
  364. data/lib/bio-ucsc/ponabe2/chainornana1.rb +81 -0
  365. data/lib/bio-ucsc/ponabe2/chainornana1link.rb +81 -0
  366. data/lib/bio-ucsc/ponabe2/chainrhemac2.rb +81 -0
  367. data/lib/bio-ucsc/ponabe2/chainrhemac2link.rb +81 -0
  368. data/lib/bio-ucsc/ponabe2/db_connection.rb +55 -0
  369. data/lib/bio-ucsc/ponabe2/est.rb +81 -0
  370. data/lib/bio-ucsc/ponabe2/gap.rb +81 -0
  371. data/lib/bio-ucsc/ponabe2/gold.rb +81 -0
  372. data/lib/bio-ucsc/ponabe2/intronest.rb +81 -0
  373. data/lib/bio-ucsc/ponabe2/mrna.rb +81 -0
  374. data/lib/bio-ucsc/ponabe2/rmsk.rb +78 -0
  375. data/lib/bio-ucsc/pripac1.rb +33 -0
  376. data/lib/bio-ucsc/pripac1/chaincaepb1.rb +81 -0
  377. data/lib/bio-ucsc/pripac1/chaincaepb1link.rb +81 -0
  378. data/lib/bio-ucsc/pripac1/chaincaerem2.rb +81 -0
  379. data/lib/bio-ucsc/pripac1/chaincaerem2link.rb +81 -0
  380. data/lib/bio-ucsc/pripac1/chaincb3.rb +81 -0
  381. data/lib/bio-ucsc/pripac1/chaincb3link.rb +81 -0
  382. data/lib/bio-ucsc/pripac1/chaince6.rb +81 -0
  383. data/lib/bio-ucsc/pripac1/chaince6link.rb +81 -0
  384. data/lib/bio-ucsc/pripac1/db_connection.rb +57 -0
  385. data/lib/bio-ucsc/pripac1/gap.rb +81 -0
  386. data/lib/bio-ucsc/pripac1/gold.rb +81 -0
  387. data/lib/bio-ucsc/pripac1/rmsk.rb +78 -0
  388. data/lib/bio-ucsc/proteome/db_connection.rb +5 -7
  389. data/lib/bio-ucsc/rhemac2.rb +32 -0
  390. data/lib/bio-ucsc/rhemac2/chainmm9.rb +81 -0
  391. data/lib/bio-ucsc/rhemac2/chainmm9link.rb +81 -0
  392. data/lib/bio-ucsc/rhemac2/chainpantro2.rb +81 -0
  393. data/lib/bio-ucsc/rhemac2/chainpantro2link.rb +81 -0
  394. data/lib/bio-ucsc/rhemac2/chainponabe2.rb +81 -0
  395. data/lib/bio-ucsc/rhemac2/chainponabe2link.rb +81 -0
  396. data/lib/bio-ucsc/rhemac2/chainrn4.rb +81 -0
  397. data/lib/bio-ucsc/rhemac2/chainrn4link.rb +81 -0
  398. data/lib/bio-ucsc/rhemac2/db_connection.rb +55 -0
  399. data/lib/bio-ucsc/rn4.rb +52 -0
  400. data/lib/bio-ucsc/rn4/chainbostau3.rb +79 -0
  401. data/lib/bio-ucsc/rn4/chainbostau3link.rb +79 -0
  402. data/lib/bio-ucsc/rn4/chaincanfam2.rb +82 -0
  403. data/lib/bio-ucsc/rn4/chaincanfam2link.rb +82 -0
  404. data/lib/bio-ucsc/rn4/chaincavpor3.rb +81 -0
  405. data/lib/bio-ucsc/rn4/chaincavpor3link.rb +81 -0
  406. data/lib/bio-ucsc/rn4/chaindanrer4.rb +81 -0
  407. data/lib/bio-ucsc/rn4/chaindanrer4link.rb +81 -0
  408. data/lib/bio-ucsc/rn4/chainequcab1.rb +81 -0
  409. data/lib/bio-ucsc/rn4/chainequcab1link.rb +81 -0
  410. data/lib/bio-ucsc/rn4/chaingalgal3.rb +81 -0
  411. data/lib/bio-ucsc/rn4/chaingalgal3link.rb +81 -0
  412. data/lib/bio-ucsc/rn4/chainmm9.rb +81 -0
  413. data/lib/bio-ucsc/rn4/chainmm9link.rb +81 -0
  414. data/lib/bio-ucsc/rn4/chainmondom4.rb +81 -0
  415. data/lib/bio-ucsc/rn4/chainmondom4link.rb +81 -0
  416. data/lib/bio-ucsc/rn4/chainpantro2.rb +81 -0
  417. data/lib/bio-ucsc/rn4/chainpantro2link.rb +82 -0
  418. data/lib/bio-ucsc/rn4/chainrhemac2.rb +81 -0
  419. data/lib/bio-ucsc/rn4/chainrhemac2link.rb +81 -0
  420. data/lib/bio-ucsc/rn4/chainxentro2.rb +81 -0
  421. data/lib/bio-ucsc/rn4/chainxentro2link.rb +81 -0
  422. data/lib/bio-ucsc/rn4/db_connection.rb +55 -0
  423. data/lib/bio-ucsc/rn4/est.rb +81 -0
  424. data/lib/bio-ucsc/rn4/gap.rb +81 -0
  425. data/lib/bio-ucsc/rn4/gold.rb +81 -0
  426. data/lib/bio-ucsc/rn4/intronest.rb +81 -0
  427. data/lib/bio-ucsc/rn4/mrna.rb +81 -0
  428. data/lib/bio-ucsc/rn4/rmsk.rb +78 -0
  429. data/lib/bio-ucsc/saccer2.rb +33 -0
  430. data/lib/bio-ucsc/saccer2/db_connection.rb +55 -0
  431. data/lib/bio-ucsc/saccer2/est.rb +83 -0
  432. data/lib/bio-ucsc/saccer2/gap.rb +83 -0
  433. data/lib/bio-ucsc/saccer2/gold.rb +83 -0
  434. data/lib/bio-ucsc/saccer2/intronest.rb +83 -0
  435. data/lib/bio-ucsc/saccer2/mrna.rb +83 -0
  436. data/lib/bio-ucsc/saccer2/t2micron_est.rb +57 -0
  437. data/lib/bio-ucsc/saccer2/t2micron_gap.rb +57 -0
  438. data/lib/bio-ucsc/saccer2/t2micron_gold.rb +58 -0
  439. data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb +57 -0
  440. data/lib/bio-ucsc/saccer2/t2micron_mrna.rb +57 -0
  441. data/lib/bio-ucsc/strpur2.rb +32 -0
  442. data/lib/bio-ucsc/strpur2/chaingalgal3.rb +81 -0
  443. data/lib/bio-ucsc/strpur2/chaingalgal3link.rb +81 -0
  444. data/lib/bio-ucsc/strpur2/chainhg18.rb +81 -0
  445. data/lib/bio-ucsc/strpur2/chainhg18link.rb +81 -0
  446. data/lib/bio-ucsc/strpur2/chainmm9.rb +81 -0
  447. data/lib/bio-ucsc/strpur2/chainmm9link.rb +81 -0
  448. data/lib/bio-ucsc/strpur2/chainpetmar1.rb +81 -0
  449. data/lib/bio-ucsc/strpur2/chainpetmar1link.rb +81 -0
  450. data/lib/bio-ucsc/strpur2/db_connection.rb +57 -0
  451. data/lib/bio-ucsc/strpur2/gap.rb +81 -0
  452. data/lib/bio-ucsc/strpur2/gold.rb +81 -0
  453. data/lib/bio-ucsc/susscr2.rb +26 -0
  454. data/lib/bio-ucsc/susscr2/db_connection.rb +57 -0
  455. data/lib/bio-ucsc/susscr2/est.rb +81 -0
  456. data/lib/bio-ucsc/susscr2/intronest.rb +81 -0
  457. data/lib/bio-ucsc/susscr2/mrna.rb +81 -0
  458. data/lib/bio-ucsc/table_class_detector.rb +18 -22
  459. data/lib/bio-ucsc/taegut1.rb +33 -0
  460. data/lib/bio-ucsc/taegut1/chaingalgal3.rb +81 -0
  461. data/lib/bio-ucsc/taegut1/chaingalgal3link.rb +81 -0
  462. data/lib/bio-ucsc/taegut1/db_connection.rb +57 -0
  463. data/lib/bio-ucsc/taegut1/est.rb +81 -0
  464. data/lib/bio-ucsc/taegut1/gap.rb +81 -0
  465. data/lib/bio-ucsc/taegut1/gold.rb +81 -0
  466. data/lib/bio-ucsc/taegut1/intronest.rb +81 -0
  467. data/lib/bio-ucsc/taegut1/mrna.rb +81 -0
  468. data/lib/bio-ucsc/taegut1/rmsk.rb +78 -0
  469. data/lib/bio-ucsc/tetnig2.rb +25 -0
  470. data/lib/bio-ucsc/tetnig2/db_connection.rb +57 -0
  471. data/lib/bio-ucsc/tetnig2/mrna.rb +81 -0
  472. data/lib/bio-ucsc/uniprot/db_connection.rb +5 -7
  473. data/lib/bio-ucsc/visigene/db_connection.rb +5 -6
  474. data/lib/bio-ucsc/xentro2.rb +30 -0
  475. data/lib/bio-ucsc/xentro2/chaingalgal3.rb +81 -0
  476. data/lib/bio-ucsc/xentro2/chaingalgal3link.rb +81 -0
  477. data/lib/bio-ucsc/xentro2/db_connection.rb +57 -0
  478. data/lib/bio-ucsc/xentro2/est.rb +81 -0
  479. data/lib/bio-ucsc/xentro2/gap.rb +81 -0
  480. data/lib/bio-ucsc/xentro2/gold.rb +81 -0
  481. data/lib/bio-ucsc/xentro2/intronest.rb +81 -0
  482. data/lib/bio-ucsc/xentro2/mrna.rb +81 -0
  483. data/lib/bio-ucsc/xentro2/rmsk.rb +78 -0
  484. data/samples/hg19-2bit-retrieve.rb +5 -2
  485. data/spec/ailmel1_spec.rb +770 -0
  486. data/spec/anocar2_spec.rb +750 -0
  487. data/spec/anogam1_spec.rb +568 -0
  488. data/spec/apimel2_spec.rb +542 -0
  489. data/spec/aplcal1_spec.rb +530 -0
  490. data/spec/bostau4_spec.rb +920 -0
  491. data/spec/braflo1_spec.rb +660 -0
  492. data/spec/caejap1_spec.rb +524 -0
  493. data/spec/caepb2_spec.rb +515 -0
  494. data/spec/caerem3_spec.rb +524 -0
  495. data/spec/caljac3_spec.rb +860 -0
  496. data/spec/canfam2_spec.rb +1145 -0
  497. data/spec/cavpor3_spec.rb +880 -0
  498. data/spec/cb3_spec.rb +634 -0
  499. data/spec/ci2_spec.rb +520 -0
  500. data/spec/danrer7_spec.rb +810 -0
  501. data/spec/dp3_spec.rb +617 -0
  502. data/spec/droana2_spec.rb +500 -0
  503. data/spec/droere1_spec.rb +510 -0
  504. data/spec/drogri1_spec.rb +470 -0
  505. data/spec/dromoj2_spec.rb +510 -0
  506. data/spec/droper1_spec.rb +470 -0
  507. data/spec/drosec1_spec.rb +470 -0
  508. data/spec/drosim1_spec.rb +588 -0
  509. data/spec/drovir2_spec.rb +540 -0
  510. data/spec/droyak2_spec.rb +558 -0
  511. data/spec/equcab2_spec.rb +936 -0
  512. data/spec/felcat4_spec.rb +770 -0
  513. data/spec/fr2_spec.rb +835 -0
  514. data/spec/galgal3_spec.rb +1351 -0
  515. data/spec/gasacu1_spec.rb +924 -0
  516. data/spec/loxafr3_spec.rb +550 -0
  517. data/spec/mondom5_spec.rb +1230 -0
  518. data/spec/ornana1_spec.rb +980 -0
  519. data/spec/orycun2_spec.rb +770 -0
  520. data/spec/orylat2_spec.rb +930 -0
  521. data/spec/oviari1_spec.rb +670 -0
  522. data/spec/pantro3_spec.rb +810 -0
  523. data/spec/petmar1_spec.rb +770 -0
  524. data/spec/ponabe2_spec.rb +962 -0
  525. data/spec/pripac1_spec.rb +621 -0
  526. data/spec/rhemac2_spec.rb +958 -0
  527. data/spec/rn4_spec.rb +2038 -0
  528. data/spec/saccer2_spec.rb +925 -0
  529. data/spec/strpur2_spec.rb +600 -0
  530. data/spec/susscr2_spec.rb +623 -0
  531. data/spec/taegut1_spec.rb +768 -0
  532. data/spec/tetnig2_spec.rb +721 -0
  533. data/spec/xentro2_spec.rb +900 -0
  534. metadata +477 -23
@@ -0,0 +1,924 @@
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