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_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_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_fail_if_sample_data_objects_have_different_sample(self):
sample_data1 = SampleData(['GT'], ['sample_name_1'])
sample_data1.add_sample_data('sample_name_1', 'GT',
GenotypeCall('0/0'))
sample_data2 = SampleData(['GT'], ['sample_name_2'])
sample_data2.add_sample_data('sample_name_2', 'GT',
GenotypeCall('0/0'))
self.assertRaises(Exception, sample_data1.merge_genotype_calls,
sample_data2.genotypes())
class TestGenotypeDataView(unittest.TestCase):
def setUp(self):
self.sample_data = SampleData(['GT', 'key'],
['sample_name1', 'sample_name2'])
self.sample_data.add_sample_data("sample_name1", "key", [1, 2])
self.sample_data.add_sample_data("sample_name2", "GT",
GenotypeCall("0/1"))
def test_contains_method_returns_expected_value_sample1(self):
genotype_data = self.sample_data.get_genotype_data("sample_name1")
self.assertNotIn("cheesecake", genotype_data)
self.assertNotIn("sample_name1", genotype_data)
self.assertIn("GT", genotype_data)
self.assertIn("key", genotype_data)
def test_contains_method_returns_expected_value_sample2(self):
genotype_data = self.sample_data.get_genotype_data("sample_name2")
self.assertIn("GT", genotype_data)
self.assertIn("key", genotype_data)
def test_getitem_method_returns_expected_value(self):
genotype_data = self.sample_data.get_genotype_data("sample_name1")
self.assertEqual(genotype_data["GT"], GenotypeCall("./."))
self.assertEqual(genotype_data["key"], [1, 2])
genotype_data = self.sample_data.get_genotype_data("sample_name2")
self.assertEqual(genotype_data["GT"], GenotypeCall("0/1"))
self.assertEqual(genotype_data["key"], [])
def test_keys_method_returns_expected_data(self):
genotype_data = self.sample_data.get_genotype_data("sample_name1")
self.assertEqual(list(genotype_data.keys()), ["GT", "key"])
genotype_data = self.sample_data.get_genotype_data("sample_name2")
self.assertEqual(list(genotype_data.keys()), ["GT", "key"])
def test_values_method_returns_expected_data(self):
genotype_data = self.sample_data.get_genotype_data("sample_name1")
self.assertEqual(list(genotype_data.values()),
[GenotypeCall("./."), [1, 2]])
genotype_data = self.sample_data.get_genotype_data("sample_name2")
self.assertEqual(list(genotype_data.values()),
[GenotypeCall("0/1"), []])
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_value_for_GQ_key(self):
sample_name = 'sample_name'
sample_data = SampleData(['GQ'], [sample_name])
sample_data.add_sample_data(sample_name, 'GQ', [2.3])
self.assertEqual(sample_data.get_genotype_quality(sample_name), [2.3])
def test_gets_exact_values_if_key_is_NV(self):
sample_name = 'sample_name'
sample_data = SampleData(['NV'], [sample_name])
sample_data.add_sample_data(sample_name, 'NV', [100])
self.assertEqual(sample_data.get_variant_support(sample_name), [100])
def test_gets_exact_values_if_key_is_NR(self):
sample_name = 'sample_name'
sample_data = SampleData(['NR'], [sample_name])
sample_data.add_sample_data(sample_name, 'NR', [100])
self.assertEqual(sample_data.get_read_depth(sample_name), [100])
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_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_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])
def test_should_write_missing_values_in_sample_data(self):
with VCFReaderContextManager(
os.path.join(self.data_dir, "vcf_example.vcf")) as vcf_handler:
first_record = next(vcf_handler.read_records())
sample_data = SampleData(['GT', 'PL', 'GQ'],
['sample1', 'sample2', 'sample3'])
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("sample2", "GT", GenotypeCall("1|1"))
sample_data.add_sample_data("sample2", "PL", [2000, 0, 1000])
sample_data.add_sample_data("sample2", "GQ", [3])
first_record.sample_info = sample_data
print((sample_data.to_vcf_columns()))
vcf_string = vcf_row_from_record(first_record)
expected_vcf_string = "20 10 . CT C 3000 PASS PP=3000;DP=250;DPR=140;DPF=110;VC=100;VCR=49;VCF=51;ABPV=0.2;SBPV=0.3;MQ=70.0;BR=31.0;QD=None GT:PL:GQ 1|0:3000,0,3000:1000 1|1:2000,0,1000:3 ./.:.:." # noqa
self.assertEqual(expected_vcf_string, vcf_string)
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])