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 +1,588 @@
1
+ require "bio-ucsc"
2
+ require "pp"
3
+
4
+ describe "Bio::Ucsc::DroSim1" do
5
+
6
+ before(:all) do
7
+ Bio::Ucsc::DroSim1::DBConnection.connect
8
+ end
9
+
10
+ describe "Bio::Ucsc::DroSim1::All_est" do
11
+ context ".first" do
12
+ it 'returns the first records' do
13
+ result = Bio::Ucsc::DroSim1::All_est.first
14
+ pp result
15
+ result.should be_true
16
+ end
17
+ end
18
+ end
19
+
20
+ describe "Bio::Ucsc::DroSim1::All_mrna" do
21
+ context ".first" do
22
+ it 'returns the first records' do
23
+ result = Bio::Ucsc::DroSim1::All_mrna.first
24
+ pp result
25
+ result.should be_true
26
+ end
27
+ end
28
+ end
29
+
30
+ describe "Bio::Ucsc::DroSim1::Author" do
31
+ context ".first" do
32
+ it 'returns the first records' do
33
+ result = Bio::Ucsc::DroSim1::Author.first
34
+ pp result
35
+ result.should be_true
36
+ end
37
+ end
38
+ end
39
+
40
+ describe "Bio::Ucsc::DroSim1::BlastDm2FB" do
41
+ context ".first" do
42
+ it 'returns the first records' do
43
+ result = Bio::Ucsc::DroSim1::BlastDm2FB.first
44
+ pp result
45
+ result.should be_true
46
+ end
47
+ end
48
+ end
49
+
50
+ describe "Bio::Ucsc::DroSim1::Cds" do
51
+ context ".first" do
52
+ it 'returns the first records' do
53
+ result = Bio::Ucsc::DroSim1::Cds.first
54
+ pp result
55
+ result.should be_true
56
+ end
57
+ end
58
+ end
59
+
60
+ describe "Bio::Ucsc::DroSim1::Cell" do
61
+ context ".first" do
62
+ it 'returns the first records' do
63
+ result = Bio::Ucsc::DroSim1::Cell.first
64
+ pp result
65
+ result.should be_true
66
+ end
67
+ end
68
+ end
69
+
70
+ describe "Bio::Ucsc::DroSim1::ChainDm3" do
71
+ context ".find_by_interval" do
72
+ it 'returns the first records' do
73
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
74
+ result = Bio::Ucsc::DroSim1::ChainDm3.find_by_interval gi
75
+ pp result
76
+ result.should be_true
77
+ end
78
+ end
79
+ end
80
+
81
+ describe "Bio::Ucsc::DroSim1::ChainDm3Link" do
82
+ context ".find_by_interval" do
83
+ it 'returns the first records' do
84
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
85
+ result = Bio::Ucsc::DroSim1::ChainDm3Link.find_by_interval gi
86
+ pp result
87
+ result.should be_true
88
+ end
89
+ end
90
+ end
91
+
92
+ describe "Bio::Ucsc::DroSim1::ChromInfo" do
93
+ context ".first" do
94
+ it 'returns the first records' do
95
+ result = Bio::Ucsc::DroSim1::ChromInfo.first
96
+ pp result
97
+ result.should be_true
98
+ end
99
+ end
100
+ end
101
+
102
+ describe "Bio::Ucsc::DroSim1::Description" do
103
+ context ".first" do
104
+ it 'returns the first records' do
105
+ result = Bio::Ucsc::DroSim1::Description.first
106
+ pp result
107
+ result.should be_true
108
+ end
109
+ end
110
+ end
111
+
112
+ describe "Bio::Ucsc::DroSim1::Development" do
113
+ context ".first" do
114
+ it 'returns the first records' do
115
+ result = Bio::Ucsc::DroSim1::Development.first
116
+ pp result
117
+ result.should be_true
118
+ end
119
+ end
120
+ end
121
+
122
+ describe "Bio::Ucsc::DroSim1::DmRefGene" do
123
+ context ".first" do
124
+ it 'returns the first records' do
125
+ result = Bio::Ucsc::DroSim1::DmRefGene.first
126
+ pp result
127
+ result.should be_true
128
+ end
129
+ end
130
+ end
131
+
132
+ describe "Bio::Ucsc::DroSim1::Est" do
133
+ context ".find_by_interval" do
134
+ it 'returns the first records' do
135
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
136
+ result = Bio::Ucsc::DroSim1::Est.find_by_interval gi
137
+ pp result
138
+ result.should be_true
139
+ end
140
+ end
141
+ end
142
+
143
+ describe "Bio::Ucsc::DroSim1::EstOrientInfo" do
144
+ context ".first" do
145
+ it 'returns the first records' do
146
+ result = Bio::Ucsc::DroSim1::EstOrientInfo.first
147
+ pp result
148
+ result.should be_true
149
+ end
150
+ end
151
+ end
152
+
153
+ describe "Bio::Ucsc::DroSim1::ExtFile" do
154
+ context ".first" do
155
+ it 'returns the first records' do
156
+ result = Bio::Ucsc::DroSim1::ExtFile.first
157
+ pp result
158
+ result.should be_true
159
+ end
160
+ end
161
+ end
162
+
163
+ describe "Bio::Ucsc::DroSim1::Gap" do
164
+ context ".find_by_interval" do
165
+ it 'returns the first records' do
166
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
167
+ result = Bio::Ucsc::DroSim1::Gap.find_by_interval gi
168
+ pp result
169
+ result.should be_true
170
+ end
171
+ end
172
+ end
173
+
174
+ describe "Bio::Ucsc::DroSim1::GbCdnaInfo" do
175
+ context ".first" do
176
+ it 'returns the first records' do
177
+ result = Bio::Ucsc::DroSim1::GbCdnaInfo.first
178
+ pp result
179
+ result.should be_true
180
+ end
181
+ end
182
+ end
183
+
184
+ describe "Bio::Ucsc::DroSim1::GbDelete_tmp" do
185
+ context ".first" do
186
+ it 'returns the first records' do
187
+ result = Bio::Ucsc::DroSim1::GbDelete_tmp.first
188
+ pp result
189
+ result.should be_true
190
+ end
191
+ end
192
+ end
193
+
194
+ describe "Bio::Ucsc::DroSim1::GbExtFile" do
195
+ context ".first" do
196
+ it 'returns the first records' do
197
+ result = Bio::Ucsc::DroSim1::GbExtFile.first
198
+ pp result
199
+ result.should be_true
200
+ end
201
+ end
202
+ end
203
+
204
+ describe "Bio::Ucsc::DroSim1::GbLoaded" do
205
+ context ".first" do
206
+ it 'returns the first records' do
207
+ result = Bio::Ucsc::DroSim1::GbLoaded.first
208
+ pp result
209
+ result.should be_true
210
+ end
211
+ end
212
+ end
213
+
214
+ describe "Bio::Ucsc::DroSim1::GbMiscDiff" do
215
+ context ".first" do
216
+ it 'returns the first records' do
217
+ result = Bio::Ucsc::DroSim1::GbMiscDiff.first
218
+ pp result
219
+ result.should be_true
220
+ end
221
+ end
222
+ end
223
+
224
+ describe "Bio::Ucsc::DroSim1::GbSeq" do
225
+ context ".first" do
226
+ it 'returns the first records' do
227
+ result = Bio::Ucsc::DroSim1::GbSeq.first
228
+ pp result
229
+ result.should be_true
230
+ end
231
+ end
232
+ end
233
+
234
+ describe "Bio::Ucsc::DroSim1::GbStatus" do
235
+ context ".first" do
236
+ it 'returns the first records' do
237
+ result = Bio::Ucsc::DroSim1::GbStatus.first
238
+ pp result
239
+ result.should be_true
240
+ end
241
+ end
242
+ end
243
+
244
+ describe "Bio::Ucsc::DroSim1::GbWarn" do
245
+ context ".first" do
246
+ it 'returns the first records' do
247
+ result = Bio::Ucsc::DroSim1::GbWarn.first
248
+ pp result
249
+ result.should be_true
250
+ end
251
+ end
252
+ end
253
+
254
+ describe "Bio::Ucsc::DroSim1::GcPercent" do
255
+ context ".first" do
256
+ it 'returns the first records' do
257
+ result = Bio::Ucsc::DroSim1::GcPercent.first
258
+ pp result
259
+ result.should be_true
260
+ end
261
+ end
262
+ end
263
+
264
+ describe "Bio::Ucsc::DroSim1::GeneName" do
265
+ context ".first" do
266
+ it 'returns the first records' do
267
+ result = Bio::Ucsc::DroSim1::GeneName.first
268
+ pp result
269
+ result.should be_true
270
+ end
271
+ end
272
+ end
273
+
274
+ describe "Bio::Ucsc::DroSim1::Geneid" do
275
+ context ".first" do
276
+ it 'returns the first records' do
277
+ result = Bio::Ucsc::DroSim1::Geneid.first
278
+ pp result
279
+ result.should be_true
280
+ end
281
+ end
282
+ end
283
+
284
+ describe "Bio::Ucsc::DroSim1::Genscan" do
285
+ context ".first" do
286
+ it 'returns the first records' do
287
+ result = Bio::Ucsc::DroSim1::Genscan.first
288
+ pp result
289
+ result.should be_true
290
+ end
291
+ end
292
+ end
293
+
294
+ describe "Bio::Ucsc::DroSim1::GenscanPep" do
295
+ context ".first" do
296
+ it 'returns the first records' do
297
+ result = Bio::Ucsc::DroSim1::GenscanPep.first
298
+ pp result
299
+ result.should be_true
300
+ end
301
+ end
302
+ end
303
+
304
+ describe "Bio::Ucsc::DroSim1::Gold" do
305
+ context ".find_by_interval" do
306
+ it 'returns the first records' do
307
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
308
+ result = Bio::Ucsc::DroSim1::Gold.find_by_interval gi
309
+ pp result
310
+ result.should be_true
311
+ end
312
+ end
313
+ end
314
+
315
+ describe "Bio::Ucsc::DroSim1::Grp" do
316
+ context ".first" do
317
+ it 'returns the first records' do
318
+ result = Bio::Ucsc::DroSim1::Grp.first
319
+ pp result
320
+ result.should be_true
321
+ end
322
+ end
323
+ end
324
+
325
+ describe "Bio::Ucsc::DroSim1::HgFindSpec" do
326
+ context ".first" do
327
+ it 'returns the first records' do
328
+ result = Bio::Ucsc::DroSim1::HgFindSpec.first
329
+ pp result
330
+ result.should be_true
331
+ end
332
+ end
333
+ end
334
+
335
+ describe "Bio::Ucsc::DroSim1::History" do
336
+ context ".first" do
337
+ it 'returns the first records' do
338
+ result = Bio::Ucsc::DroSim1::History.first
339
+ pp result
340
+ result.should be_true
341
+ end
342
+ end
343
+ end
344
+
345
+ describe "Bio::Ucsc::DroSim1::ImageClone" do
346
+ context ".first" do
347
+ it 'returns the first records' do
348
+ result = Bio::Ucsc::DroSim1::ImageClone.first
349
+ pp result
350
+ result.should be_true
351
+ end
352
+ end
353
+ end
354
+
355
+ describe "Bio::Ucsc::DroSim1::IntronEst" do
356
+ context ".find_by_interval" do
357
+ it 'returns the first records' do
358
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
359
+ result = Bio::Ucsc::DroSim1::IntronEst.find_by_interval gi
360
+ pp result
361
+ result.should be_true
362
+ end
363
+ end
364
+ end
365
+
366
+ describe "Bio::Ucsc::DroSim1::Keyword" do
367
+ context ".first" do
368
+ it 'returns the first records' do
369
+ result = Bio::Ucsc::DroSim1::Keyword.first
370
+ pp result
371
+ result.should be_true
372
+ end
373
+ end
374
+ end
375
+
376
+ describe "Bio::Ucsc::DroSim1::Library" do
377
+ context ".first" do
378
+ it 'returns the first records' do
379
+ result = Bio::Ucsc::DroSim1::Library.first
380
+ pp result
381
+ result.should be_true
382
+ end
383
+ end
384
+ end
385
+
386
+ describe "Bio::Ucsc::DroSim1::Mrna" do
387
+ context ".find_by_interval" do
388
+ it 'returns the first records' do
389
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
390
+ result = Bio::Ucsc::DroSim1::Mrna.find_by_interval gi
391
+ pp result
392
+ result.should be_true
393
+ end
394
+ end
395
+ end
396
+
397
+ describe "Bio::Ucsc::DroSim1::MrnaClone" do
398
+ context ".first" do
399
+ it 'returns the first records' do
400
+ result = Bio::Ucsc::DroSim1::MrnaClone.first
401
+ pp result
402
+ result.should be_true
403
+ end
404
+ end
405
+ end
406
+
407
+ describe "Bio::Ucsc::DroSim1::MrnaOrientInfo" do
408
+ context ".first" do
409
+ it 'returns the first records' do
410
+ result = Bio::Ucsc::DroSim1::MrnaOrientInfo.first
411
+ pp result
412
+ result.should be_true
413
+ end
414
+ end
415
+ end
416
+
417
+ describe "Bio::Ucsc::DroSim1::NetDm3" do
418
+ context ".first" do
419
+ it 'returns the first records' do
420
+ result = Bio::Ucsc::DroSim1::NetDm3.first
421
+ pp result
422
+ result.should be_true
423
+ end
424
+ end
425
+ end
426
+
427
+ describe "Bio::Ucsc::DroSim1::Organism" do
428
+ context ".first" do
429
+ it 'returns the first records' do
430
+ result = Bio::Ucsc::DroSim1::Organism.first
431
+ pp result
432
+ result.should be_true
433
+ end
434
+ end
435
+ end
436
+
437
+ describe "Bio::Ucsc::DroSim1::ProductName" do
438
+ context ".first" do
439
+ it 'returns the first records' do
440
+ result = Bio::Ucsc::DroSim1::ProductName.first
441
+ pp result
442
+ result.should be_true
443
+ end
444
+ end
445
+ end
446
+
447
+ describe "Bio::Ucsc::DroSim1::RefLink" do
448
+ context ".first" do
449
+ it 'returns the first records' do
450
+ result = Bio::Ucsc::DroSim1::RefLink.first
451
+ pp result
452
+ result.should be_true
453
+ end
454
+ end
455
+ end
456
+
457
+ describe "Bio::Ucsc::DroSim1::RefSeqStatus" do
458
+ context ".first" do
459
+ it 'returns the first records' do
460
+ result = Bio::Ucsc::DroSim1::RefSeqStatus.first
461
+ pp result
462
+ result.should be_true
463
+ end
464
+ end
465
+ end
466
+
467
+ describe "Bio::Ucsc::DroSim1::RefSeqSummary" do
468
+ context ".first" do
469
+ it 'returns the first records' do
470
+ result = Bio::Ucsc::DroSim1::RefSeqSummary.first
471
+ pp result
472
+ result.should be_true
473
+ end
474
+ end
475
+ end
476
+
477
+ describe "Bio::Ucsc::DroSim1::Rmsk" do
478
+ context ".find_by_interva" do
479
+ it 'returns the first records' do
480
+ gi = Bio::GenomicInterval.parse("chr2L:1-10,000,000")
481
+ result = Bio::Ucsc::DroSim1::Rmsk.find_by_interval gi
482
+ pp result
483
+ result.should be_true
484
+ end
485
+ end
486
+ end
487
+
488
+ describe "Bio::Ucsc::DroSim1::Sex" do
489
+ context ".first" do
490
+ it 'returns the first records' do
491
+ result = Bio::Ucsc::DroSim1::Sex.first
492
+ pp result
493
+ result.should be_true
494
+ end
495
+ end
496
+ end
497
+
498
+ describe "Bio::Ucsc::DroSim1::SimpleRepeat" do
499
+ context ".first" do
500
+ it 'returns the first records' do
501
+ result = Bio::Ucsc::DroSim1::SimpleRepeat.first
502
+ pp result
503
+ result.should be_true
504
+ end
505
+ end
506
+ end
507
+
508
+ describe "Bio::Ucsc::DroSim1::Source" do
509
+ context ".first" do
510
+ it 'returns the first records' do
511
+ result = Bio::Ucsc::DroSim1::Source.first
512
+ pp result
513
+ result.should be_true
514
+ end
515
+ end
516
+ end
517
+
518
+ describe "Bio::Ucsc::DroSim1::TableDescriptions" do
519
+ context ".first" do
520
+ it 'returns the first records' do
521
+ result = Bio::Ucsc::DroSim1::TableDescriptions.first
522
+ pp result
523
+ result.should be_true
524
+ end
525
+ end
526
+ end
527
+
528
+ describe "Bio::Ucsc::DroSim1::Tissue" do
529
+ context ".first" do
530
+ it 'returns the first records' do
531
+ result = Bio::Ucsc::DroSim1::Tissue.first
532
+ pp result
533
+ result.should be_true
534
+ end
535
+ end
536
+ end
537
+
538
+ describe "Bio::Ucsc::DroSim1::TrackDb" do
539
+ context ".first" do
540
+ it 'returns the first records' do
541
+ result = Bio::Ucsc::DroSim1::TrackDb.first
542
+ pp result
543
+ result.should be_true
544
+ end
545
+ end
546
+ end
547
+
548
+ describe "Bio::Ucsc::DroSim1::XenoMrna" do
549
+ context ".first" do
550
+ it 'returns the first records' do
551
+ result = Bio::Ucsc::DroSim1::XenoMrna.first
552
+ pp result
553
+ result.should be_true
554
+ end
555
+ end
556
+ end
557
+
558
+ describe "Bio::Ucsc::DroSim1::XenoRefFlat" do
559
+ context ".first" do
560
+ it 'returns the first records' do
561
+ result = Bio::Ucsc::DroSim1::XenoRefFlat.first
562
+ pp result
563
+ result.should be_true
564
+ end
565
+ end
566
+ end
567
+
568
+ describe "Bio::Ucsc::DroSim1::XenoRefGene" do
569
+ context ".first" do
570
+ it 'returns the first records' do
571
+ result = Bio::Ucsc::DroSim1::XenoRefGene.first
572
+ pp result
573
+ result.should be_true
574
+ end
575
+ end
576
+ end
577
+
578
+ describe "Bio::Ucsc::DroSim1::XenoRefSeqAli" do
579
+ context ".first" do
580
+ it 'returns the first records' do
581
+ result = Bio::Ucsc::DroSim1::XenoRefSeqAli.first
582
+ pp result
583
+ result.should be_true
584
+ end
585
+ end
586
+ end
587
+
588
+ end