def test_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual((1515, 1529), ma.get_transcript_position('ENST00000361221', '17953929', '17953943', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(self.NP_001005353, ma.get_product_sequence("NP_001005353", type=EIdentifierTypes.REFSEQ))
self.assertEqual(self.ENSP00000369497, ma.get_product_sequence("ENSP00000369497", type=EIdentifierTypes.ENSEMBL))
self.assertEqual(self.ENST00000361221[2], ma.get_transcript_sequence('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_sequence("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(self.ENST00000361221, ma.get_transcript_information('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_information("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
self.assertEqual(str(ma.get_ensembl_ids_from_id('TP53', type=EIdentifierTypes.GENENAME)), "[{0: 'ENSG00000141510', 1: '-', 3: 'ENST00000413465', 4: 'ENSP00000410739'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000359597', 4: 'ENSP00000352610'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504290', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000510385', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504937', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000269305', 4: 'ENSP00000269305'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000455263', 4: 'ENSP00000398846'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000420246', 4: 'ENSP00000391127'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000445888', 4: 'ENSP00000391478'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000576024', 4: 'ENSP00000458393'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000509690', 4: 'ENSP00000425104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000514944', 4: 'ENSP00000423862'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000574684', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000505014', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000508793', 4: 'ENSP00000424104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000604348', 4: 'ENSP00000473895'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000503591', 4: 'ENSP00000426252'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t8', 4: 'LRG_321p8'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t7', 4: 'LRG_321p13'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t6', 4: 'LRG_321p12'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t5', 4: 'LRG_321p11'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t4', 4: 'LRG_321p10'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t3', 4: 'LRG_321p3'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t2', 4: 'LRG_321p2'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t1', 4: 'LRG_321p1'}]")
def test_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual(
(1515, 1529),
ma.get_transcript_position('ENST00000361221',
'17953929',
'17953943',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_position("ENST00000614237",
7566927,
7566927,
type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(
ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(
self.NP_001005353,
ma.get_product_sequence("NP_001005353",
type=EIdentifierTypes.REFSEQ))
self.assertEqual(
self.ENSP00000369497,
ma.get_product_sequence("ENSP00000369497",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
self.ENST00000361221[2],
ma.get_transcript_sequence('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_sequence("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(
self.ENST00000361221,
ma.get_transcript_information('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_information("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
str(
ma.get_ensembl_ids_from_id('TP53',
type=EIdentifierTypes.GENENAME)),
"[{0: 'ENSG00000141510', 1: '-', 3: 'ENST00000413465', 4: 'ENSP00000410739'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000359597', 4: 'ENSP00000352610'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504290', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000510385', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504937', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000269305', 4: 'ENSP00000269305'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000455263', 4: 'ENSP00000398846'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000420246', 4: 'ENSP00000391127'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000445888', 4: 'ENSP00000391478'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000576024', 4: 'ENSP00000458393'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000509690', 4: 'ENSP00000425104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000514944', 4: 'ENSP00000423862'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000574684', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000505014', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000508793', 4: 'ENSP00000424104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000604348', 4: 'ENSP00000473895'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000503591', 4: 'ENSP00000426252'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t8', 4: 'LRG_321p8'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t7', 4: 'LRG_321p13'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t6', 4: 'LRG_321p12'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t5', 4: 'LRG_321p11'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t4', 4: 'LRG_321p10'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t3', 4: 'LRG_321p3'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t2', 4: 'LRG_321p2'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t1', 4: 'LRG_321p1'}]"
)
def test_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual(
(1515, 1529),
ma.get_transcript_position('ENST00000361221',
'17953929',
'17953943',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_position("ENST00000614237",
7566927,
7566927,
type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(
ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(
self.NP_001005353,
ma.get_product_sequence("NP_001005353",
type=EIdentifierTypes.REFSEQ))
self.assertEqual(
self.ENSP00000369497,
ma.get_product_sequence("ENSP00000369497",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
self.ENST00000361221[2],
ma.get_transcript_sequence('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_sequence("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(
self.ENST00000361221,
ma.get_transcript_information('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_information("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertListEqual(
ma.get_ensembl_ids_from_id('TP53', type=EIdentifierTypes.GENENAME),
self.tp53_ensembl_biomart)
