def test_read_sample_data(self):
schema = self.__get_example_schema("vcf_example.vcf")
sample_schema = [key for key, _ in schema.iter_sample_data()]
sample_data = SampleData(sample_schema, ['sample1'])
sample_data.add_sample_data("sample1", "GT", GenotypeCall("1|0"))
sample_data.add_sample_data("sample1", "PL", [3000, 0, 3000])
sample_data.add_sample_data("sample1", "GQ", [1000])
sample_data.add_sample_data("sample1", "PQ", [2000])
sample_data.add_sample_data("sample1", "PS", [60000])
sample_data.add_sample_data("sample1", "AD", [140, 110])
sample_data.add_sample_data("sample1", "DP", [250])
sample_data.add_sample_data("sample1", "VAF", [0.4])
self.assertTrue(sample_data.has_sample("sample1"))
self.assertEqual(sample_data.genotypes(),
{"sample1": GenotypeCall("1|0")})
self.assertEqual(sample_data.get_field("sample1", 'GT'),
GenotypeCall("1|0"))
self.assertEqual(sample_data.get_field("sample1", 'PL'),
[3000, 0, 3000])
genotype_data = sample_data.get_genotype_data("sample1")
self.assertEqual(genotype_data.genotype(), GenotypeCall("1|0"))
self.assertEqual(genotype_data['GT'], GenotypeCall("1|0"))
self.assertEqual(genotype_data['PL'], [3000, 0, 3000])
def test_should_allow_multiple_samples_for_add_sample_data(self):
sample_data = SampleData(['genotype_key1'],
['sample_name1', 'sample_name2'])
sample_data.add_sample_data('sample_name1', 'genotype_key1', [1])
sample_data.add_sample_data('sample_name2', 'genotype_key1', [3, 4])
self.assertEqual(
sample_data.get_field('sample_name1', 'genotype_key1'), [1])
self.assertEqual(
sample_data.get_field('sample_name2', 'genotype_key1'), [3, 4])
def test_default_values_are_assigned_when_sample_data_is_constructed(self):
sample_data = SampleData(['GT', 'key1', 'key2'],
['sample_name1', 'sample_name2'])
self.assertEqual(sample_data.get_field('sample_name1', 'GT'),
GenotypeCall("./."))
self.assertEqual(sample_data.get_field('sample_name2', 'GT'),
GenotypeCall("./."))
self.assertEqual(sample_data.get_field('sample_name1', 'key1'), [])
self.assertEqual(sample_data.get_field('sample_name2', 'key1'), [])
self.assertEqual(sample_data.get_field('sample_name1', 'key2'), [])
self.assertEqual(sample_data.get_field('sample_name2', 'key2'), [])
def test_sample_data_copes_with_mixed_missing_values_in_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name,
[-0.1, '.', -0.2, None, -0.3])
self.assertEqual(sample_data.get_field(sample_name, 'PL'),
[1.0, None, 2.0, None, 3.0])
def test_should_return_default_diploid_genotype(self):
sample_data = SampleData(['GT', 'GL'], ["NA12878"])
self.assertEqual(GenotypeCall("./."), GenotypeCall("./."))
self.assertTrue(sample_data.has_sample("NA12878"))
self.assertEqual(sample_data.genotypes(),
{"NA12878": GenotypeCall("./.")})
self.assertEqual(sample_data.get_field("NA12878", 'GT'),
GenotypeCall("./."))
self.assertEqual(sample_data.get_field("NA12878", 'GL'), [])
genotype_data = sample_data.get_genotype_data("NA12878")
self.assertEqual(genotype_data.genotype(), GenotypeCall("./."))
self.assertEqual(genotype_data['GT'], GenotypeCall("./."))
self.assertEqual(genotype_data['GL'], [])
def test_should_merge_genotype_call_object_in_sample_data(self):
sample_data1 = SampleData(['GT'], ['sample_name'])
sample_data1.add_sample_data('sample_name', 'GT', GenotypeCall('0/1'))
sample_data2 = SampleData(['GT'], ['sample_name'])
sample_data2.add_sample_data('sample_name', 'GT', GenotypeCall('0/1'))
sample_data1.merge_genotype_calls(sample_data2.genotypes())
self.assertEqual(sample_data1.get_field("sample_name", "GT"),
GenotypeCall("1/1"))
def test_should_add_sample_data(self):
sample_data = SampleData(['genotype_key1'], ['sample_name'])
sample_data.add_sample_data('sample_name', 'genotype_key1', [1])
self.assertEqual(sample_data.get_field('sample_name', 'genotype_key1'),
[1])
def test_gets_dot_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name, '.')
self.assertEqual(sample_data.get_field(sample_name, 'PL'), '.')
def test_gets_exact_values_if_key_is_PL(self):
sample_name = 'sample_name'
sample_data = SampleData(['PL'], [sample_name])
sample_data.set_genotype_likelihoods(sample_name, [-0.1, -0.2, -0.3])
self.assertEqual(sample_data.get_field(sample_name, 'PL'), [1, 2, 3])
def test_genotype_field_default_value_is_assigned_when_sample_data_is_constructed(
self):
sample_data = SampleData(['GT'], ['sample_name'])
self.assertEqual(sample_data.get_field('sample_name', 'GT'),
GenotypeCall("./."))
def test_default_field_value_is_assigned_when_sample_data_is_constructed(
self):
sample_data = SampleData(['key1'], ['sample_name'])
self.assertEqual(sample_data.get_field('sample_name', 'key1'), [])