def test_sample_data_copes_with_mixed_missing_values_in_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.add_sample_data(sample_name, 'PL',
[-0.1, '.', -0.2, None, -0.3])
self.assertEqual(sample_data.get_genotype_likelihoods(sample_name),
[0.01, None, 0.02, None, 0.03])
def test_gets_list_of_none_if_key_is_GL(self):
sample_name = 'sample_name'
sample_data = SampleData(['GL'], [sample_name])
sample_data.add_sample_data(sample_name, 'GL', [None, None, None])
self.assertEqual(sample_data.get_genotype_likelihoods(sample_name),
[None, None, None])
def test_gets_dot_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.add_sample_data(sample_name, 'PL', '.')
self.assertEqual(sample_data.get_genotype_likelihoods(sample_name),
'.')
def test_gets_exact_values_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.add_sample_data(sample_name, 'PL', [1, 2, 3])
self.assertEqual(sample_data.get_genotype_likelihoods(sample_name),
[-0.1, -0.2, -0.3])