def test_parse_genotypes(self):
genotype_field_strings = ['0/1:20', '0/0:15']
parsed_dict = self.variant._parse_genotypes(genotype_field_strings)
na12878_gt = Genotype(self.variant,
genotype_field_strings[0].split(':'))
na0001_gt = Genotype(self.variant,
genotype_field_strings[1].split(':'))
expected_genotype_dict = {'NA12878': na12878_gt, 'NA0001': na0001_gt}
self.assertEqual(parsed_dict, expected_genotype_dict)
def _parse_genotypes(self, genotype_array):
'''
Parse the genotype strings
'''
gts = dict()
for index, sample_string in enumerate(genotype_array):
sample_name = self.sample_list[index]
sample_field = sample_string.split(':')
g = Genotype(self, sample_field)
gts[sample_name] = g
return gts
def test_get_gt_string(self):
g = Genotype(self.variant, '0/1')
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_gt_string(), '0/1:.:10')
def test_set_format(self):
g = Genotype(self.variant, '0/1')
self.assertFalse('INACTIVE' in self.variant.active_formats)
g.set_format('INACTIVE', 10)
self.assertEqual(g.format['INACTIVE'], 10)
self.assertTrue('INACTIVE' in self.variant.active_formats)
def test_get_format(self):
g = Genotype(self.variant, '0/1')
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_format('INACTIVE'), 10)
def test_get_gt_string(self):
g = Genotype(self.variant, ['0/1'])
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_gt_string(), '0/1:.:10')
def test_set_genotype(self):
new_genotype = Genotype(self.variant, ['0/1', '9'])
self.variant.set_genotype('NA12878', new_genotype)
self.assertEqual(
self.variant.genotype('NA12878').get_gt_string(), '0/1:9')
def test_get_format(self):
g = Genotype(self.variant, ['0/1'])
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_format('INACTIVE'), 10)
def test_set_format(self):
g = Genotype(self.variant, ['0/1'])
self.assertFalse('INACTIVE' in self.variant.format_dict)
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_format('INACTIVE'), 10)
self.assertTrue('INACTIVE' in self.variant.format_dict)
def test_equal(self):
g1 = Genotype(self.variant, ['0/1'])
g1.set_format('INACTIVE', 10)
g2 = Genotype(self.variant, ['0/1'])
g2.set_format('INACTIVE', 10)
self.assertEqual(g1, g2)
def test_set_format(self):
g = Genotype(self.variant, ['0/1'])
self.assertFalse('INACTIVE' in self.variant.format_dict)
g.set_format('INACTIVE', 10)
self.assertEqual(g.get_format('INACTIVE'), 10)
self.assertTrue('INACTIVE' in self.variant.format_dict)
def test_equal(self):
g1 = Genotype(self.variant, ['0/1'])
g1.set_format('INACTIVE', 10)
g2 = Genotype(self.variant, ['0/1'])
g2.set_format('INACTIVE', 10)
self.assertEqual(g1, g2)