def test_add_variant_to_dict_merge_different_values(self): variant_dict = add_variant_to_dict(self.variant_dict, self.genomic_coordinate, self.values_to_add) merged = variant_dict[self.genomic_coordinate] date_index = 16 bx_id_index = -1 self.assertIn('22/4/2016', merged[date_index]) self.assertIn('2016-09-08', merged[date_index]) self.assertIn('677', merged[bx_id_index]) self.assertIn('46', merged[bx_id_index]) self.assertIn('BIC', merged[COLUMN_SOURCE]) self.assertIn('ENIGMA', merged[COLUMN_SOURCE])
def test_add_variant_to_dict(self): genomic_coordinate = 'chr13:g.32332705:GA>G' values = ['ENIGMA', 'BRCA2', 'chr13:32332705:GA>G', '13', '32332705', 'GA', 'G', 'NM_000059.3', 'c.1231delA', '1459delA', 'I411Yfs*19', '', 'OMIM', 'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; BROVCA2 (612555)', 'Disease', 'Pathogenic', '22/4/2016', 'ENIGMA BRCA1/2 Classification Criteria (2015)', 'https://enigmaconsortium.org/wp-content/uploads/2016/06/ENIGMA_Rules_2015-03-26.pdf', '', 'Variant allele predicted to encode a truncated non-functional protein.', 'Curation', 'Germline', 'SCV000282353.1', 'p.(Ile411TyrfsTer19)', '2'] variant_dict = add_variant_to_dict(self.variant_dict, genomic_coordinate, values) self.assertIn('chr13:g.32332705:GA>G', variant_dict) self.assertEqual(variant_dict['chr13:g.32332705:GA>G'], values)
def test_add_variant_to_dict(self): genomic_coordinate = 'chr13:g.32332705:GA>G' values = [ 'ENIGMA', 'BRCA2', 'chr13:32332705:GA>G', '13', '32332705', 'GA', 'G', 'NM_000059.3', 'c.1231delA', '1459delA', 'I411Yfs*19', '', 'OMIM', 'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; BROVCA2 (612555)', 'Disease', 'Pathogenic', '22/4/2016', 'ENIGMA BRCA1/2 Classification Criteria (2015)', 'https://enigmaconsortium.org/wp-content/uploads/2016/06/ENIGMA_Rules_2015-03-26.pdf', '', 'Variant allele predicted to encode a truncated non-functional protein.', 'Curation', 'Germline', 'SCV000282353.1', 'p.(Ile411TyrfsTer19)', '2' ] variant_dict = add_variant_to_dict(self.variant_dict, genomic_coordinate, values) self.assertIn('chr13:g.32332705:GA>G', variant_dict) self.assertEqual(variant_dict['chr13:g.32332705:GA>G'], values)
def test_add_variant_to_dict_merge_adds_new_data_to_empty_fields(self): variant_dict = add_variant_to_dict(self.variant_dict, self.genomic_coordinate, self.values_to_add) merged = variant_dict[self.genomic_coordinate] self.assertEqual('5104delAA', merged[9])
def test_add_variant_to_dict_merge_ignores_trailing_spaces(self): variant_dict = add_variant_to_dict(self.variant_dict, self.genomic_coordinate, self.values_to_add) merged = variant_dict[self.genomic_coordinate] self.assertEqual('c.4876_4877delAA', merged[8])