def test_tso_no_one_related_unexpected_related_duplicate(self):
# relatedness a duplicate sample - 18M01316 21M10702
result, comment = relatedness_test(
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ.ped',
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ_duplicate.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_multiple_trios_fail(self):
# should fail as 19M06442 is not related to its dad 20M11003
result, comment = relatedness_test(
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX_2.ped',
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX_2.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_duplicate_sample1(self):
# test correct wings run with same sample repeated
result, comment = relatedness_test(
'qc_database/tests/test_data/210604_A00748_0108_AHWVTGDMXX.ped',
'qc_database/tests/test_data/210604_A00748_0108_AHWVTGDMXX.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_tso_no_one_related(self):
# should not fail as no one related
result, comment = relatedness_test(
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ.ped',
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, True)
def test_tso_no_one_related_unexpected_related(self):
# relatedness between 18M01316 21M11357 is 0.2
result, comment = relatedness_test(
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ.ped',
'qc_database/tests/test_data/210709_NB551319_0232_AHF2JFBGXJ_2.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_no_parent_in_relatedness_file(self):
# should fail as 20M08216 (FAM001) is not in same family as mum (20M11351)
result, comment = relatedness_test(
'qc_database/tests/test_data/wrong_ped_no_parents.ped',
'qc_database/tests/test_data/wrong_ped_no_parents.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_siblings(self):
# should fail as 20M08216 (FAM001) is not in same family as mum (20M11351)
result, comment = relatedness_test(
'qc_database/tests/test_data/siblings.ped',
'qc_database/tests/test_data/siblings.relatedness2', 0.2, 0.06,
0.06, 0.4)
self.assertEqual(result, True)
def test_mixed_up_relatedness_mum_not_in_same_family(self):
# should fail as 20M08216 (FAM001) is not in same family as mum (20M11351)
result, comment = relatedness_test(
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX_4.ped',
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_big_genome_run(self):
# Test run with 5 correct trios
result, comment = relatedness_test(
'qc_database/tests/test_data/K00150_0149_AHG7YKBBXX.ped',
'qc_database/tests/test_data/K00150_0149_AHG7YKBBXX.relatedness2',
0.2, 0.06, 0.06, 0.4)
print(result, comment)
self.assertEqual(result, True, msg=[result, comment])
def get_relatedness_metrics(self, min_relatedness_parents,
max_relatedness_unrelated,
max_relatedness_between_parents,
max_child_parent_relatedness):
results_path = Path(self.results_dir)
ped_file = results_path.glob(
f'post_processing/results/ped/{self.run_id}.ped')
ped_file = list(ped_file)[0]
relatedness_file = results_path.glob(
f'post_processing/results/relatedness/{self.run_id}.relatedness2')
relatedness_file = list(relatedness_file)[0]
parsed_relatedness, parsed_relatedness_comment = relatedness2.relatedness_test(
ped_file, relatedness_file, min_relatedness_parents,
max_relatedness_unrelated, max_relatedness_between_parents,
max_child_parent_relatedness)
return parsed_relatedness, parsed_relatedness_comment
def test_function_with_one_family(self):
result, comment = relatedness_test(
'qc_database/tests/test_data/210622_A00748_0110_AH5T3CDRXY.ped',
'qc_database/tests/test_data/210622_A00748_0110_AH5T3CDRXY.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, True)
def test_either_ped_or_relatedness_file_not_found(self):
result, comment = relatedness_test(
'this_file_does_not_exist.ped',
'this_file_also_does_not_exist.relatedness2', 0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)
def test_function_with_multiple_families(self):
result, comment = relatedness_test(
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX.ped',
'qc_database/tests/test_data/201215_A00748_0068_AHT3FCDMXX.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, True)
def test_parents_related(self):
result, comment = relatedness_test(
'qc_database/tests/test_data/210622_A00748_0110_AH5T3CDRXY.ped',
'qc_database/tests/test_data/210622_A00748_0110_AH5T3CDRXYPR.relatedness2',
0.2, 0.06, 0.06, 0.4)
self.assertEqual(result, False)