Guest User

Untitled

a guest
Jul 19th, 2018
82
0
Never
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 9.02 KB | None | 0 0
  1. ```python
  2. import mygene
  3. mg = mygene.MyGeneInfo()
  4. mg.querymany("BRCA1", returnall=True)
  5. ```
  6.  
  7. querying 1-1...done.
  8. Finished.
  9. 1 input query terms found no hit:
  10. ['BRCA1']
  11.  
  12.  
  13.  
  14.  
  15.  
  16. {'out': [{'query': 'BRCA1', 'notfound': True}],
  17. 'dup': [],
  18. 'missing': ['BRCA1']}
  19.  
  20.  
  21.  
  22.  
  23. ```python
  24. mg.query("BRCA1", returnall=True)
  25. ```
  26.  
  27.  
  28.  
  29.  
  30. {'max_score': 428.93326,
  31. 'took': 33,
  32. 'total': 4778,
  33. 'hits': [{'_id': '672',
  34. '_score': 428.93326,
  35. 'entrezgene': 672,
  36. 'name': 'BRCA1, DNA repair associated',
  37. 'symbol': 'BRCA1',
  38. 'taxid': 9606},
  39. {'_id': '12189',
  40. '_score': 363.50424,
  41. 'entrezgene': 12189,
  42. 'name': 'breast cancer 1, early onset',
  43. 'symbol': 'Brca1',
  44. 'taxid': 10090},
  45. {'_id': '497672',
  46. '_score': 309.35406,
  47. 'entrezgene': 497672,
  48. 'name': 'BRCA1, DNA repair associated',
  49. 'symbol': 'Brca1',
  50. 'taxid': 10116},
  51. {'_id': '101814437',
  52. '_score': 290.66235,
  53. 'entrezgene': 101814437,
  54. 'name': 'BRCA1, DNA repair associated',
  55. 'symbol': 'BRCA1',
  56. 'taxid': 59894},
  57. {'_id': '100347269',
  58. '_score': 290.66235,
  59. 'entrezgene': 100347269,
  60. 'name': 'BRCA1, DNA repair associated',
  61. 'symbol': 'BRCA1',
  62. 'taxid': 9986},
  63. {'_id': '101429125',
  64. '_score': 290.66235,
  65. 'entrezgene': 101429125,
  66. 'name': 'BRCA1, DNA repair associated',
  67. 'symbol': 'BRCA1',
  68. 'taxid': 9361},
  69. {'_id': '110388719',
  70. '_score': 290.66235,
  71. 'entrezgene': 110388719,
  72. 'name': 'BRCA1, DNA repair associated',
  73. 'symbol': 'BRCA1',
  74. 'taxid': 8996},
  75. {'_id': '106858689',
  76. '_score': 290.66235,
  77. 'entrezgene': 106858689,
  78. 'name': 'BRCA1, DNA repair associated',
  79. 'symbol': 'BRCA1',
  80. 'taxid': 9172},
  81. {'_id': '106948321',
  82. '_score': 290.66235,
  83. 'entrezgene': 106948321,
  84. 'name': 'BRCA1, DNA repair associated',
  85. 'symbol': 'brca1',
  86. 'taxid': 48699},
  87. {'_id': '109963046',
  88. '_score': 290.66235,
  89. 'entrezgene': 109963046,
  90. 'name': 'BRCA1, DNA repair associated',
  91. 'symbol': 'brca1',
  92. 'taxid': 43700}]}
  93.  
  94.  
  95.  
  96.  
  97. ```python
  98. mg.querymany("BRCA1", species='human', fields="ensembl,symbol,hgnc,alias", scopes="symbol,alias", returnall=True)
  99. ```
  100.  
  101. querying 1-1...done.
  102. Finished.
  103. 1 input query terms found dup hits:
  104. [('BRCA1', 2)]
  105.  
  106.  
  107.  
  108.  
  109.  
  110. {'out': [{'query': 'BRCA1',
  111. '_id': '672',
  112. '_score': 85.786644,
  113. 'alias': ['BRCAI',
  114. 'BRCC1',
  115. 'BROVCA1',
  116. 'FANCS',
  117. 'IRIS',
  118. 'PNCA4',
  119. 'PPP1R53',
  120. 'PSCP',
  121. 'RNF53'],
  122. 'ensembl': {'gene': 'ENSG00000012048',
  123. 'protein': ['ENSP00000312236',
  124. 'ENSP00000326002',
  125. 'ENSP00000350283',
  126. 'ENSP00000397145',
  127. 'ENSP00000417148',
  128. 'ENSP00000417241',
  129. 'ENSP00000417554',
  130. 'ENSP00000417988',
  131. 'ENSP00000418212',
  132. 'ENSP00000418548',
  133. 'ENSP00000418775',
  134. 'ENSP00000418819',
  135. 'ENSP00000418960',
  136. 'ENSP00000418986',
  137. 'ENSP00000419103',
  138. 'ENSP00000419274',
  139. 'ENSP00000419481',
  140. 'ENSP00000419988',
  141. 'ENSP00000420201',
  142. 'ENSP00000420253',
  143. 'ENSP00000420412',
  144. 'ENSP00000420705',
  145. 'ENSP00000420781',
  146. 'ENSP00000465347',
  147. 'ENSP00000465818',
  148. 'ENSP00000467329',
  149. 'ENSP00000478114',
  150. 'ENSP00000489431',
  151. 'ENSP00000494614',
  152. 'ENSP00000495897',
  153. 'ENSP00000496570'],
  154. 'transcript': ['ENST00000352993',
  155. 'ENST00000354071',
  156. 'ENST00000357654',
  157. 'ENST00000412061',
  158. 'ENST00000461221',
  159. 'ENST00000461574',
  160. 'ENST00000461798',
  161. 'ENST00000468300',
  162. 'ENST00000470026',
  163. 'ENST00000471181',
  164. 'ENST00000472490',
  165. 'ENST00000473961',
  166. 'ENST00000476777',
  167. 'ENST00000477152',
  168. 'ENST00000478531',
  169. 'ENST00000484087',
  170. 'ENST00000487825',
  171. 'ENST00000489037',
  172. 'ENST00000491747',
  173. 'ENST00000492859',
  174. 'ENST00000493795',
  175. 'ENST00000493919',
  176. 'ENST00000494123',
  177. 'ENST00000497488',
  178. 'ENST00000586385',
  179. 'ENST00000591534',
  180. 'ENST00000591849',
  181. 'ENST00000618469',
  182. 'ENST00000621897',
  183. 'ENST00000634433',
  184. 'ENST00000642945',
  185. 'ENST00000644379',
  186. 'ENST00000644555'],
  187. 'translation': [{'protein': 'ENSP00000312236', 'rna': 'ENST00000352993'},
  188. {'protein': 'ENSP00000350283', 'rna': 'ENST00000357654'},
  189. {'protein': 'ENSP00000418960', 'rna': 'ENST00000471181'},
  190. {'protein': 'ENSP00000417148', 'rna': 'ENST00000468300'},
  191. {'protein': 'ENSP00000496570', 'rna': 'ENST00000644379'},
  192. {'protein': 'ENSP00000465818', 'rna': 'ENST00000586385'},
  193. {'protein': 'ENSP00000467329', 'rna': 'ENST00000591534'},
  194. {'protein': 'ENSP00000465347', 'rna': 'ENST00000591849'},
  195. {'protein': 'ENSP00000418775', 'rna': 'ENST00000493795'},
  196. {'protein': 'ENSP00000418548', 'rna': 'ENST00000461221'},
  197. {'protein': 'ENSP00000420705', 'rna': 'ENST00000491747'},
  198. {'protein': 'ENSP00000419481', 'rna': 'ENST00000484087'},
  199. {'protein': 'ENSP00000420412', 'rna': 'ENST00000478531'},
  200. {'protein': 'ENSP00000418819', 'rna': 'ENST00000493919'},
  201. {'protein': 'ENSP00000418212', 'rna': 'ENST00000487825'},
  202. {'protein': 'ENSP00000417241', 'rna': 'ENST00000461574'},
  203. {'protein': 'ENSP00000326002', 'rna': 'ENST00000354071'},
  204. {'protein': 'ENSP00000489431', 'rna': 'ENST00000634433'},
  205. {'protein': 'ENSP00000397145', 'rna': 'ENST00000412061'},
  206. {'protein': 'ENSP00000419274', 'rna': 'ENST00000470026'},
  207. {'protein': 'ENSP00000419988', 'rna': 'ENST00000477152'},
  208. {'protein': 'ENSP00000420253', 'rna': 'ENST00000492859'},
  209. {'protein': 'ENSP00000418986', 'rna': 'ENST00000497488'},
  210. {'protein': 'ENSP00000419103', 'rna': 'ENST00000494123'},
  211. {'protein': 'ENSP00000420201', 'rna': 'ENST00000473961'},
  212. {'protein': 'ENSP00000495897', 'rna': 'ENST00000642945'},
  213. {'protein': 'ENSP00000417554', 'rna': 'ENST00000476777'},
  214. {'protein': 'ENSP00000417988', 'rna': 'ENST00000461798'},
  215. {'protein': 'ENSP00000420781', 'rna': 'ENST00000489037'},
  216. {'protein': 'ENSP00000494614', 'rna': 'ENST00000644555'},
  217. {'protein': 'ENSP00000478114', 'rna': 'ENST00000618469'}],
  218. 'type_of_gene': 'protein_coding'},
  219. 'symbol': 'BRCA1'},
  220. {'query': 'BRCA1',
  221. '_id': '394269',
  222. '_score': 3.1628551,
  223. 'alias': ['LBRCA1', 'PsiBRCA1', 'pseudo-BRCA1'],
  224. 'symbol': 'BRCA1P1'}],
  225. 'dup': [('BRCA1', 2)],
  226. 'missing': []}
  227.  
  228.  
  229.  
  230.  
  231. ```python
  232. mg.querymany("BRCA1", scopes="symbol,alias", returnall=True)
  233. ```
  234.  
  235. querying 1-1...done.
  236. Finished.
  237. 1 input query terms found dup hits:
  238. [('BRCA1', 10)]
  239.  
  240.  
  241.  
  242.  
  243.  
  244. {'out': [{'query': 'BRCA1',
  245. '_id': '672',
  246. '_score': 85.42936,
  247. 'entrezgene': 672,
  248. 'name': 'BRCA1, DNA repair associated',
  249. 'symbol': 'BRCA1',
  250. 'taxid': 9606},
  251. {'query': 'BRCA1',
  252. '_id': '12189',
  253. '_score': 73.24706,
  254. 'entrezgene': 12189,
  255. 'name': 'breast cancer 1, early onset',
  256. 'symbol': 'Brca1',
  257. 'taxid': 10090},
  258. {'query': 'BRCA1',
  259. '_id': '497672',
  260. '_score': 61.91373,
  261. 'entrezgene': 497672,
  262. 'name': 'BRCA1, DNA repair associated',
  263. 'symbol': 'Brca1',
  264. 'taxid': 10116},
  265. {'query': 'BRCA1',
  266. '_id': '101814437',
  267. '_score': 58.15771,
  268. 'entrezgene': 101814437,
  269. 'name': 'BRCA1, DNA repair associated',
  270. 'symbol': 'BRCA1',
  271. 'taxid': 59894},
  272. {'query': 'BRCA1',
  273. '_id': '109626726',
  274. '_score': 58.15771,
  275. 'entrezgene': 109626726,
  276. 'name': 'BRCA1, DNA repair associated',
  277. 'symbol': 'brca1',
  278. 'taxid': 8255},
  279. {'query': 'BRCA1',
  280. '_id': '100347269',
  281. '_score': 58.15771,
  282. 'entrezgene': 100347269,
  283. 'name': 'BRCA1, DNA repair associated',
  284. 'symbol': 'BRCA1',
  285. 'taxid': 9986},
  286. {'query': 'BRCA1',
  287. '_id': '101429125',
  288. '_score': 58.15771,
  289. 'entrezgene': 101429125,
  290. 'name': 'BRCA1, DNA repair associated',
  291. 'symbol': 'BRCA1',
  292. 'taxid': 9361},
  293. {'query': 'BRCA1',
  294. '_id': '106858689',
  295. '_score': 58.15771,
  296. 'entrezgene': 106858689,
  297. 'name': 'BRCA1, DNA repair associated',
  298. 'symbol': 'BRCA1',
  299. 'taxid': 9172},
  300. {'query': 'BRCA1',
  301. '_id': '110388719',
  302. '_score': 58.15771,
  303. 'entrezgene': 110388719,
  304. 'name': 'BRCA1, DNA repair associated',
  305. 'symbol': 'BRCA1',
  306. 'taxid': 8996},
  307. {'query': 'BRCA1',
  308. '_id': '102289404',
  309. '_score': 58.15771,
  310. 'entrezgene': 102289404,
  311. 'name': 'BRCA1, DNA repair associated',
  312. 'symbol': 'brca1',
  313. 'taxid': 8153}],
  314. 'dup': [('BRCA1', 10)],
  315. 'missing': []}
Add Comment
Please, Sign In to add comment