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_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])
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])
