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 +1,958 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::RheMac2" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::RheMac2::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::RheMac2::All_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::RheMac2::All_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::RheMac2::All_mrna" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::RheMac2::All_mrna.first
24
+ pp result
25
+ result.should be_true
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::RheMac2::Author" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::RheMac2::Author.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::RheMac2::Cds" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::RheMac2::Cds.first
44
+ pp result
45
+ result.should be_true
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::RheMac2::Cell" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::RheMac2::Cell.first
54
+ pp result
55
+ result.should be_true
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::RheMac2::ChainCalJac3" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::RheMac2::ChainCalJac3.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::RheMac2::ChainCalJac3Link" do
71
+ context ".first" do
72
+ it 'returns the first records' do
73
+ result = Bio::Ucsc::RheMac2::ChainCalJac3Link.first
74
+ pp result
75
+ result.should be_true
76
+ end
77
+ end
78
+ end
79
+
80
+ describe "Bio::Ucsc::RheMac2::ChainHg19" do
81
+ context ".first" do
82
+ it 'returns the first records' do
83
+ result = Bio::Ucsc::RheMac2::ChainHg19.first
84
+ pp result
85
+ result.should be_true
86
+ end
87
+ end
88
+ end
89
+
90
+ describe "Bio::Ucsc::RheMac2::ChainHg19Link" do
91
+ context ".first" do
92
+ it 'returns the first records' do
93
+ result = Bio::Ucsc::RheMac2::ChainHg19Link.first
94
+ pp result
95
+ result.should be_true
96
+ end
97
+ end
98
+ end
99
+
100
+ describe "Bio::Ucsc::RheMac2::ChainMm9" do
101
+ context ".find_by_interval" do
102
+ it 'returns the first records' do
103
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
104
+ result = Bio::Ucsc::RheMac2::ChainMm9.find_by_interval gi
105
+ pp result
106
+ result.should be_true
107
+ end
108
+ end
109
+ end
110
+
111
+ describe "Bio::Ucsc::RheMac2::ChainMm9Link" do
112
+ context ".find_by_interval" do
113
+ it 'returns the first records' do
114
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
115
+ result = Bio::Ucsc::RheMac2::ChainMm9Link.find_by_interval gi
116
+ pp result
117
+ result.should be_true
118
+ end
119
+ end
120
+ end
121
+
122
+ describe "Bio::Ucsc::RheMac2::ChainMonDom5" do
123
+ context ".first" do
124
+ it 'returns the first records' do
125
+ result = Bio::Ucsc::RheMac2::ChainMonDom5.first
126
+ pp result
127
+ result.should be_true
128
+ end
129
+ end
130
+ end
131
+
132
+ describe "Bio::Ucsc::RheMac2::ChainMonDom5Link" do
133
+ context ".first" do
134
+ it 'returns the first records' do
135
+ result = Bio::Ucsc::RheMac2::ChainMonDom5Link.first
136
+ pp result
137
+ result.should be_true
138
+ end
139
+ end
140
+ end
141
+
142
+ describe "Bio::Ucsc::RheMac2::ChainPanTro2" do
143
+ context ".find_by_interval" do
144
+ it 'returns the first records' do
145
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
146
+ result = Bio::Ucsc::RheMac2::ChainPanTro2.find_by_interval gi
147
+ pp result
148
+ result.should be_true
149
+ end
150
+ end
151
+ end
152
+
153
+ describe "Bio::Ucsc::RheMac2::ChainPanTro2Link" do
154
+ context ".find_by_interval" do
155
+ it 'returns the first records' do
156
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
157
+ result = Bio::Ucsc::RheMac2::ChainPanTro2Link.find_by_interval gi
158
+ pp result
159
+ result.should be_true
160
+ end
161
+ end
162
+ end
163
+
164
+ describe "Bio::Ucsc::RheMac2::ChainPanTro3" do
165
+ context ".first" do
166
+ it 'returns the first records' do
167
+ result = Bio::Ucsc::RheMac2::ChainPanTro3.first
168
+ pp result
169
+ result.should be_true
170
+ end
171
+ end
172
+ end
173
+
174
+ describe "Bio::Ucsc::RheMac2::ChainPanTro3Link" do
175
+ context ".first" do
176
+ it 'returns the first records' do
177
+ result = Bio::Ucsc::RheMac2::ChainPanTro3Link.first
178
+ pp result
179
+ result.should be_true
180
+ end
181
+ end
182
+ end
183
+
184
+ describe "Bio::Ucsc::RheMac2::ChainPonAbe2" do
185
+ context ".find_by_interval" do
186
+ it 'returns the first records' do
187
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
188
+ result = Bio::Ucsc::RheMac2::ChainPonAbe2.find_by_interval gi
189
+ pp result
190
+ result.should be_true
191
+ end
192
+ end
193
+ end
194
+
195
+ describe "Bio::Ucsc::RheMac2::ChainPonAbe2Link" do
196
+ context ".find_by_interval" do
197
+ it 'returns the first records' do
198
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
199
+ result = Bio::Ucsc::RheMac2::ChainPonAbe2Link.find_by_interval gi
200
+ pp result
201
+ result.should be_true
202
+ end
203
+ end
204
+ end
205
+
206
+ describe "Bio::Ucsc::RheMac2::ChainRn4" do
207
+ context ".find_by_interval" do
208
+ it 'returns the first records' do
209
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
210
+ result = Bio::Ucsc::RheMac2::ChainRn4.find_by_interval gi
211
+ pp result
212
+ result.should be_true
213
+ end
214
+ end
215
+ end
216
+
217
+ describe "Bio::Ucsc::RheMac2::ChainRn4Link" do
218
+ context ".find_by_interval" do
219
+ it 'returns the first records' do
220
+ gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
221
+ result = Bio::Ucsc::RheMac2::ChainRn4Link.find_by_interval gi
222
+ pp result
223
+ result.should be_true
224
+ end
225
+ end
226
+ end
227
+
228
+ describe "Bio::Ucsc::RheMac2::ChromInfo" do
229
+ context ".first" do
230
+ it 'returns the first records' do
231
+ result = Bio::Ucsc::RheMac2::ChromInfo.first
232
+ pp result
233
+ result.should be_true
234
+ end
235
+ end
236
+ end
237
+
238
+ describe "Bio::Ucsc::RheMac2::CpgIslandExt" do
239
+ context ".first" do
240
+ it 'returns the first records' do
241
+ result = Bio::Ucsc::RheMac2::CpgIslandExt.first
242
+ pp result
243
+ result.should be_true
244
+ end
245
+ end
246
+ end
247
+
248
+ describe "Bio::Ucsc::RheMac2::CtgPos" do
249
+ context ".first" do
250
+ it 'returns the first records' do
251
+ result = Bio::Ucsc::RheMac2::CtgPos.first
252
+ pp result
253
+ result.should be_true
254
+ end
255
+ end
256
+ end
257
+
258
+ describe "Bio::Ucsc::RheMac2::Description" do
259
+ context ".first" do
260
+ it 'returns the first records' do
261
+ result = Bio::Ucsc::RheMac2::Description.first
262
+ pp result
263
+ result.should be_true
264
+ end
265
+ end
266
+ end
267
+
268
+ describe "Bio::Ucsc::RheMac2::Development" do
269
+ context ".first" do
270
+ it 'returns the first records' do
271
+ result = Bio::Ucsc::RheMac2::Development.first
272
+ pp result
273
+ result.should be_true
274
+ end
275
+ end
276
+ end
277
+
278
+ describe "Bio::Ucsc::RheMac2::EnsGene" do
279
+ context ".first" do
280
+ it 'returns the first records' do
281
+ result = Bio::Ucsc::RheMac2::EnsGene.first
282
+ pp result
283
+ result.should be_true
284
+ end
285
+ end
286
+ end
287
+
288
+ describe "Bio::Ucsc::RheMac2::EnsGtp" do
289
+ context ".first" do
290
+ it 'returns the first records' do
291
+ result = Bio::Ucsc::RheMac2::EnsGtp.first
292
+ pp result
293
+ result.should be_true
294
+ end
295
+ end
296
+ end
297
+
298
+ describe "Bio::Ucsc::RheMac2::EnsPep" do
299
+ context ".first" do
300
+ it 'returns the first records' do
301
+ result = Bio::Ucsc::RheMac2::EnsPep.first
302
+ pp result
303
+ result.should be_true
304
+ end
305
+ end
306
+ end
307
+
308
+ describe "Bio::Ucsc::RheMac2::EstOrientInfo" do
309
+ context ".first" do
310
+ it 'returns the first records' do
311
+ result = Bio::Ucsc::RheMac2::EstOrientInfo.first
312
+ pp result
313
+ result.should be_true
314
+ end
315
+ end
316
+ end
317
+
318
+ describe "Bio::Ucsc::RheMac2::Gap" do
319
+ context ".first" do
320
+ it 'returns the first records' do
321
+ result = Bio::Ucsc::RheMac2::Gap.first
322
+ pp result
323
+ result.should be_true
324
+ end
325
+ end
326
+ end
327
+
328
+ describe "Bio::Ucsc::RheMac2::GbCdnaInfo" do
329
+ context ".first" do
330
+ it 'returns the first records' do
331
+ result = Bio::Ucsc::RheMac2::GbCdnaInfo.first
332
+ pp result
333
+ result.should be_true
334
+ end
335
+ end
336
+ end
337
+
338
+ describe "Bio::Ucsc::RheMac2::GbExtFile" do
339
+ context ".first" do
340
+ it 'returns the first records' do
341
+ result = Bio::Ucsc::RheMac2::GbExtFile.first
342
+ pp result
343
+ result.should be_true
344
+ end
345
+ end
346
+ end
347
+
348
+ describe "Bio::Ucsc::RheMac2::GbLoaded" do
349
+ context ".first" do
350
+ it 'returns the first records' do
351
+ result = Bio::Ucsc::RheMac2::GbLoaded.first
352
+ pp result
353
+ result.should be_true
354
+ end
355
+ end
356
+ end
357
+
358
+ describe "Bio::Ucsc::RheMac2::GbMiscDiff" do
359
+ context ".first" do
360
+ it 'returns the first records' do
361
+ result = Bio::Ucsc::RheMac2::GbMiscDiff.first
362
+ pp result
363
+ result.should be_true
364
+ end
365
+ end
366
+ end
367
+
368
+ describe "Bio::Ucsc::RheMac2::GbSeq" do
369
+ context ".first" do
370
+ it 'returns the first records' do
371
+ result = Bio::Ucsc::RheMac2::GbSeq.first
372
+ pp result
373
+ result.should be_true
374
+ end
375
+ end
376
+ end
377
+
378
+ describe "Bio::Ucsc::RheMac2::GbStatus" do
379
+ context ".first" do
380
+ it 'returns the first records' do
381
+ result = Bio::Ucsc::RheMac2::GbStatus.first
382
+ pp result
383
+ result.should be_true
384
+ end
385
+ end
386
+ end
387
+
388
+ describe "Bio::Ucsc::RheMac2::GbWarn" do
389
+ context ".first" do
390
+ it 'returns the first records' do
391
+ result = Bio::Ucsc::RheMac2::GbWarn.first
392
+ pp result
393
+ result.should be_true
394
+ end
395
+ end
396
+ end
397
+
398
+ describe "Bio::Ucsc::RheMac2::GeneName" do
399
+ context ".first" do
400
+ it 'returns the first records' do
401
+ result = Bio::Ucsc::RheMac2::GeneName.first
402
+ pp result
403
+ result.should be_true
404
+ end
405
+ end
406
+ end
407
+
408
+ describe "Bio::Ucsc::RheMac2::Geneid" do
409
+ context ".first" do
410
+ it 'returns the first records' do
411
+ result = Bio::Ucsc::RheMac2::Geneid.first
412
+ pp result
413
+ result.should be_true
414
+ end
415
+ end
416
+ end
417
+
418
+ describe "Bio::Ucsc::RheMac2::GeneidPep" do
419
+ context ".first" do
420
+ it 'returns the first records' do
421
+ result = Bio::Ucsc::RheMac2::GeneidPep.first
422
+ pp result
423
+ result.should be_true
424
+ end
425
+ end
426
+ end
427
+
428
+ describe "Bio::Ucsc::RheMac2::GenomicSuperDups" do
429
+ context ".first" do
430
+ it 'returns the first records' do
431
+ result = Bio::Ucsc::RheMac2::GenomicSuperDups.first
432
+ pp result
433
+ result.should be_true
434
+ end
435
+ end
436
+ end
437
+
438
+ describe "Bio::Ucsc::RheMac2::Gold" do
439
+ context ".first" do
440
+ it 'returns the first records' do
441
+ result = Bio::Ucsc::RheMac2::Gold.first
442
+ pp result
443
+ result.should be_true
444
+ end
445
+ end
446
+ end
447
+
448
+ describe "Bio::Ucsc::RheMac2::Grp" do
449
+ context ".first" do
450
+ it 'returns the first records' do
451
+ result = Bio::Ucsc::RheMac2::Grp.first
452
+ pp result
453
+ result.should be_true
454
+ end
455
+ end
456
+ end
457
+
458
+ describe "Bio::Ucsc::RheMac2::HgFindSpec" do
459
+ context ".first" do
460
+ it 'returns the first records' do
461
+ result = Bio::Ucsc::RheMac2::HgFindSpec.first
462
+ pp result
463
+ result.should be_true
464
+ end
465
+ end
466
+ end
467
+
468
+ describe "Bio::Ucsc::RheMac2::History" do
469
+ context ".first" do
470
+ it 'returns the first records' do
471
+ result = Bio::Ucsc::RheMac2::History.first
472
+ pp result
473
+ result.should be_true
474
+ end
475
+ end
476
+ end
477
+
478
+ describe "Bio::Ucsc::RheMac2::ImageClone" do
479
+ context ".first" do
480
+ it 'returns the first records' do
481
+ result = Bio::Ucsc::RheMac2::ImageClone.first
482
+ pp result
483
+ result.should be_true
484
+ end
485
+ end
486
+ end
487
+
488
+ describe "Bio::Ucsc::RheMac2::IntronEst" do
489
+ context ".first" do
490
+ it 'returns the first records' do
491
+ result = Bio::Ucsc::RheMac2::IntronEst.first
492
+ pp result
493
+ result.should be_true
494
+ end
495
+ end
496
+ end
497
+
498
+ describe "Bio::Ucsc::RheMac2::Keyword" do
499
+ context ".first" do
500
+ it 'returns the first records' do
501
+ result = Bio::Ucsc::RheMac2::Keyword.first
502
+ pp result
503
+ result.should be_true
504
+ end
505
+ end
506
+ end
507
+
508
+ describe "Bio::Ucsc::RheMac2::Library" do
509
+ context ".first" do
510
+ it 'returns the first records' do
511
+ result = Bio::Ucsc::RheMac2::Library.first
512
+ pp result
513
+ result.should be_true
514
+ end
515
+ end
516
+ end
517
+
518
+ describe "Bio::Ucsc::RheMac2::MrnaClone" do
519
+ context ".first" do
520
+ it 'returns the first records' do
521
+ result = Bio::Ucsc::RheMac2::MrnaClone.first
522
+ pp result
523
+ result.should be_true
524
+ end
525
+ end
526
+ end
527
+
528
+ describe "Bio::Ucsc::RheMac2::MrnaOrientInfo" do
529
+ context ".first" do
530
+ it 'returns the first records' do
531
+ result = Bio::Ucsc::RheMac2::MrnaOrientInfo.first
532
+ pp result
533
+ result.should be_true
534
+ end
535
+ end
536
+ end
537
+
538
+ describe "Bio::Ucsc::RheMac2::NetCalJac3" do
539
+ context ".first" do
540
+ it 'returns the first records' do
541
+ result = Bio::Ucsc::RheMac2::NetCalJac3.first
542
+ pp result
543
+ result.should be_true
544
+ end
545
+ end
546
+ end
547
+
548
+ describe "Bio::Ucsc::RheMac2::NetHg19" do
549
+ context ".first" do
550
+ it 'returns the first records' do
551
+ result = Bio::Ucsc::RheMac2::NetHg19.first
552
+ pp result
553
+ result.should be_true
554
+ end
555
+ end
556
+ end
557
+
558
+ describe "Bio::Ucsc::RheMac2::NetMm9" do
559
+ context ".first" do
560
+ it 'returns the first records' do
561
+ result = Bio::Ucsc::RheMac2::NetMm9.first
562
+ pp result
563
+ result.should be_true
564
+ end
565
+ end
566
+ end
567
+
568
+ describe "Bio::Ucsc::RheMac2::NetMonDom5" do
569
+ context ".first" do
570
+ it 'returns the first records' do
571
+ result = Bio::Ucsc::RheMac2::NetMonDom5.first
572
+ pp result
573
+ result.should be_true
574
+ end
575
+ end
576
+ end
577
+
578
+ describe "Bio::Ucsc::RheMac2::NetPanTro2" do
579
+ context ".first" do
580
+ it 'returns the first records' do
581
+ result = Bio::Ucsc::RheMac2::NetPanTro2.first
582
+ pp result
583
+ result.should be_true
584
+ end
585
+ end
586
+ end
587
+
588
+ describe "Bio::Ucsc::RheMac2::NetPanTro3" do
589
+ context ".first" do
590
+ it 'returns the first records' do
591
+ result = Bio::Ucsc::RheMac2::NetPanTro3.first
592
+ pp result
593
+ result.should be_true
594
+ end
595
+ end
596
+ end
597
+
598
+ describe "Bio::Ucsc::RheMac2::NetPonAbe2" do
599
+ context ".first" do
600
+ it 'returns the first records' do
601
+ result = Bio::Ucsc::RheMac2::NetPonAbe2.first
602
+ pp result
603
+ result.should be_true
604
+ end
605
+ end
606
+ end
607
+
608
+ describe "Bio::Ucsc::RheMac2::NetRn4" do
609
+ context ".first" do
610
+ it 'returns the first records' do
611
+ result = Bio::Ucsc::RheMac2::NetRn4.first
612
+ pp result
613
+ result.should be_true
614
+ end
615
+ end
616
+ end
617
+
618
+ describe "Bio::Ucsc::RheMac2::NscanGene" do
619
+ context ".first" do
620
+ it 'returns the first records' do
621
+ result = Bio::Ucsc::RheMac2::NscanGene.first
622
+ pp result
623
+ result.should be_true
624
+ end
625
+ end
626
+ end
627
+
628
+ describe "Bio::Ucsc::RheMac2::NscanPep" do
629
+ context ".first" do
630
+ it 'returns the first records' do
631
+ result = Bio::Ucsc::RheMac2::NscanPep.first
632
+ pp result
633
+ result.should be_true
634
+ end
635
+ end
636
+ end
637
+
638
+ describe "Bio::Ucsc::RheMac2::Organism" do
639
+ context ".first" do
640
+ it 'returns the first records' do
641
+ result = Bio::Ucsc::RheMac2::Organism.first
642
+ pp result
643
+ result.should be_true
644
+ end
645
+ end
646
+ end
647
+
648
+ describe "Bio::Ucsc::RheMac2::ProductName" do
649
+ context ".first" do
650
+ it 'returns the first records' do
651
+ result = Bio::Ucsc::RheMac2::ProductName.first
652
+ pp result
653
+ result.should be_true
654
+ end
655
+ end
656
+ end
657
+
658
+ describe "Bio::Ucsc::RheMac2::Quality" do
659
+ context ".first" do
660
+ it 'returns the first records' do
661
+ result = Bio::Ucsc::RheMac2::Quality.first
662
+ pp result
663
+ result.should be_true
664
+ end
665
+ end
666
+ end
667
+
668
+ describe "Bio::Ucsc::RheMac2::RefFlat" do
669
+ context ".first" do
670
+ it 'returns the first records' do
671
+ result = Bio::Ucsc::RheMac2::RefFlat.first
672
+ pp result
673
+ result.should be_true
674
+ end
675
+ end
676
+ end
677
+
678
+ describe "Bio::Ucsc::RheMac2::RefGene" do
679
+ context ".first" do
680
+ it 'returns the first records' do
681
+ result = Bio::Ucsc::RheMac2::RefGene.first
682
+ pp result
683
+ result.should be_true
684
+ end
685
+ end
686
+ end
687
+
688
+ describe "Bio::Ucsc::RheMac2::RefLink" do
689
+ context ".first" do
690
+ it 'returns the first records' do
691
+ result = Bio::Ucsc::RheMac2::RefLink.first
692
+ pp result
693
+ result.should be_true
694
+ end
695
+ end
696
+ end
697
+
698
+ describe "Bio::Ucsc::RheMac2::RefSeqAli" do
699
+ context ".first" do
700
+ it 'returns the first records' do
701
+ result = Bio::Ucsc::RheMac2::RefSeqAli.first
702
+ pp result
703
+ result.should be_true
704
+ end
705
+ end
706
+ end
707
+
708
+ describe "Bio::Ucsc::RheMac2::RefSeqAnno" do
709
+ context ".first" do
710
+ it 'returns the first records' do
711
+ result = Bio::Ucsc::RheMac2::RefSeqAnno.first
712
+ pp result
713
+ result.should be_true
714
+ end
715
+ end
716
+ end
717
+
718
+ describe "Bio::Ucsc::RheMac2::RefSeqStatus" do
719
+ context ".first" do
720
+ it 'returns the first records' do
721
+ result = Bio::Ucsc::RheMac2::RefSeqStatus.first
722
+ pp result
723
+ result.should be_true
724
+ end
725
+ end
726
+ end
727
+
728
+ describe "Bio::Ucsc::RheMac2::RefSeqSummary" do
729
+ context ".first" do
730
+ it 'returns the first records' do
731
+ result = Bio::Ucsc::RheMac2::RefSeqSummary.first
732
+ pp result
733
+ result.should be_true
734
+ end
735
+ end
736
+ end
737
+
738
+ describe "Bio::Ucsc::RheMac2::Rmsk" do
739
+ context ".first" do
740
+ it 'returns the first records' do
741
+ result = Bio::Ucsc::RheMac2::Rmsk.first
742
+ pp result
743
+ result.should be_true
744
+ end
745
+ end
746
+ end
747
+
748
+ describe "Bio::Ucsc::RheMac2::ScaffoldCoords" do
749
+ context ".first" do
750
+ it 'returns the first records' do
751
+ result = Bio::Ucsc::RheMac2::ScaffoldCoords.first
752
+ pp result
753
+ result.should be_true
754
+ end
755
+ end
756
+ end
757
+
758
+ describe "Bio::Ucsc::RheMac2::Sex" do
759
+ context ".first" do
760
+ it 'returns the first records' do
761
+ result = Bio::Ucsc::RheMac2::Sex.first
762
+ pp result
763
+ result.should be_true
764
+ end
765
+ end
766
+ end
767
+
768
+ describe "Bio::Ucsc::RheMac2::SgpGene" do
769
+ context ".first" do
770
+ it 'returns the first records' do
771
+ result = Bio::Ucsc::RheMac2::SgpGene.first
772
+ pp result
773
+ result.should be_true
774
+ end
775
+ end
776
+ end
777
+
778
+ describe "Bio::Ucsc::RheMac2::SimpleRepeat" do
779
+ context ".first" do
780
+ it 'returns the first records' do
781
+ result = Bio::Ucsc::RheMac2::SimpleRepeat.first
782
+ pp result
783
+ result.should be_true
784
+ end
785
+ end
786
+ end
787
+
788
+ describe "Bio::Ucsc::RheMac2::Source" do
789
+ context ".first" do
790
+ it 'returns the first records' do
791
+ result = Bio::Ucsc::RheMac2::Source.first
792
+ pp result
793
+ result.should be_true
794
+ end
795
+ end
796
+ end
797
+
798
+ describe "Bio::Ucsc::RheMac2::TableDescriptions" do
799
+ context ".first" do
800
+ it 'returns the first records' do
801
+ result = Bio::Ucsc::RheMac2::TableDescriptions.first
802
+ pp result
803
+ result.should be_true
804
+ end
805
+ end
806
+ end
807
+
808
+ describe "Bio::Ucsc::RheMac2::Tissue" do
809
+ context ".first" do
810
+ it 'returns the first records' do
811
+ result = Bio::Ucsc::RheMac2::Tissue.first
812
+ pp result
813
+ result.should be_true
814
+ end
815
+ end
816
+ end
817
+
818
+ describe "Bio::Ucsc::RheMac2::TrackDb" do
819
+ context ".first" do
820
+ it 'returns the first records' do
821
+ result = Bio::Ucsc::RheMac2::TrackDb.first
822
+ pp result
823
+ result.should be_true
824
+ end
825
+ end
826
+ end
827
+
828
+ describe "Bio::Ucsc::RheMac2::TransMapAlnMRna" do
829
+ context ".first" do
830
+ it 'returns the first records' do
831
+ result = Bio::Ucsc::RheMac2::TransMapAlnMRna.first
832
+ pp result
833
+ result.should be_true
834
+ end
835
+ end
836
+ end
837
+
838
+ describe "Bio::Ucsc::RheMac2::TransMapAlnRefSeq" do
839
+ context ".first" do
840
+ it 'returns the first records' do
841
+ result = Bio::Ucsc::RheMac2::TransMapAlnRefSeq.first
842
+ pp result
843
+ result.should be_true
844
+ end
845
+ end
846
+ end
847
+
848
+ describe "Bio::Ucsc::RheMac2::TransMapAlnSplicedEst" do
849
+ context ".first" do
850
+ it 'returns the first records' do
851
+ result = Bio::Ucsc::RheMac2::TransMapAlnSplicedEst.first
852
+ pp result
853
+ result.should be_true
854
+ end
855
+ end
856
+ end
857
+
858
+ describe "Bio::Ucsc::RheMac2::TransMapAlnUcscGenes" do
859
+ context ".first" do
860
+ it 'returns the first records' do
861
+ result = Bio::Ucsc::RheMac2::TransMapAlnUcscGenes.first
862
+ pp result
863
+ result.should be_true
864
+ end
865
+ end
866
+ end
867
+
868
+ describe "Bio::Ucsc::RheMac2::TransMapInfoMRna" do
869
+ context ".first" do
870
+ it 'returns the first records' do
871
+ result = Bio::Ucsc::RheMac2::TransMapInfoMRna.first
872
+ pp result
873
+ result.should be_true
874
+ end
875
+ end
876
+ end
877
+
878
+ describe "Bio::Ucsc::RheMac2::TransMapInfoRefSeq" do
879
+ context ".first" do
880
+ it 'returns the first records' do
881
+ result = Bio::Ucsc::RheMac2::TransMapInfoRefSeq.first
882
+ pp result
883
+ result.should be_true
884
+ end
885
+ end
886
+ end
887
+
888
+ describe "Bio::Ucsc::RheMac2::TransMapInfoSplicedEst" do
889
+ context ".first" do
890
+ it 'returns the first records' do
891
+ result = Bio::Ucsc::RheMac2::TransMapInfoSplicedEst.first
892
+ pp result
893
+ result.should be_true
894
+ end
895
+ end
896
+ end
897
+
898
+ describe "Bio::Ucsc::RheMac2::TransMapInfoUcscGenes" do
899
+ context ".first" do
900
+ it 'returns the first records' do
901
+ result = Bio::Ucsc::RheMac2::TransMapInfoUcscGenes.first
902
+ pp result
903
+ result.should be_true
904
+ end
905
+ end
906
+ end
907
+
908
+ describe "Bio::Ucsc::RheMac2::WgEncodeNhgriBip" do
909
+ context ".first" do
910
+ it 'returns the first records' do
911
+ result = Bio::Ucsc::RheMac2::WgEncodeNhgriBip.first
912
+ pp result
913
+ result.should be_true
914
+ end
915
+ end
916
+ end
917
+
918
+ describe "Bio::Ucsc::RheMac2::XenoMrna" do
919
+ context ".first" do
920
+ it 'returns the first records' do
921
+ result = Bio::Ucsc::RheMac2::XenoMrna.first
922
+ pp result
923
+ result.should be_true
924
+ end
925
+ end
926
+ end
927
+
928
+ describe "Bio::Ucsc::RheMac2::XenoRefFlat" do
929
+ context ".first" do
930
+ it 'returns the first records' do
931
+ result = Bio::Ucsc::RheMac2::XenoRefFlat.first
932
+ pp result
933
+ result.should be_true
934
+ end
935
+ end
936
+ end
937
+
938
+ describe "Bio::Ucsc::RheMac2::XenoRefGene" do
939
+ context ".first" do
940
+ it 'returns the first records' do
941
+ result = Bio::Ucsc::RheMac2::XenoRefGene.first
942
+ pp result
943
+ result.should be_true
944
+ end
945
+ end
946
+ end
947
+
948
+ describe "Bio::Ucsc::RheMac2::XenoRefSeqAli" do
949
+ context ".first" do
950
+ it 'returns the first records' do
951
+ result = Bio::Ucsc::RheMac2::XenoRefSeqAli.first
952
+ pp result
953
+ result.should be_true
954
+ end
955
+ end
956
+ end
957
+
958
+ end