def test_multiple_case_genotypes():
''' Filter on multiple case genotypes '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2', 'Case3'], output=out, quiet=True)
expected_indices = [
True, True, True, True, True, True, False, True, True, True
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
assert_equal(results, expected_records)
if os.path.exists(out):
os.remove(out)
def test_one_case_control_genotypes():
''' Filter on single case/control pair genotypes '''
out = get_tmp_out()
kwargs = dict(case=['Case1'], control=['Control1'], output=out, quiet=True)
expected_indices = [
False, True, False, True, False, True, False, True, False, True
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
assert_equal(results, expected_records)
if os.path.exists(out):
os.remove(out)
def test_max_control_vaf_filtering():
''' Filter on genotypes, expressions and maximum control VAF '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2', 'Case3'],
case_expressions=["DP > 20"],
control=['Control1', 'Control2', 'Control3'],
max_control_vaf=0.05,
output=out,
quiet=True)
expected_indices = [
False, False, False, False, True, True, False, True, True, False
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
def test_case_control_vaf():
''' Filter on minimum case and maximum control VAF '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2'],
control=['Control1', 'Control2'],
min_case_vaf=0.2,
max_control_vaf=0.05,
ignore_genotypes=True,
output=out,
quiet=True)
expected_indices = [
False, False, False, True, True, False, False, True, False, False
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
def test_expression_plus_genotypes():
''' Filter cases using both genotypes and an expression '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2', 'Case3'],
case_expressions=["AD > 5"],
output=out,
quiet=True)
expected_indices = [
True, True, True, False, True, True, False, True, False, True
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
assert_equal(results, expected_records)
if os.path.exists(out):
os.remove(out)
def test_expressions_with_summed_values():
''' Filter cases using a summed values '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2', 'Case3'],
case_expressions=["sum(AD) >= 30"],
ignore_genotypes=True,
output=out,
quiet=True)
expected_indices = [
True, False, True, False, True, True, True, True, True, True
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
assert_equal(results, expected_records)
if os.path.exists(out):
os.remove(out)
def test_vaf_ratio_multi():
''' Filter on multiple case/control VAF ratio '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2'],
control=['Control1', 'Control2'],
vaf_ratio=10.0,
ignore_genotypes=True,
output=out,
quiet=True)
expected_indices = [
False, False, False, True, True, True, False, True, True, False
]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
assert_equal(results, expected_records)
if os.path.exists(out):
os.remove(out)
def test_add_info_tag():
''' Test filtering and adding bitwise filter tag '''
out = get_tmp_out()
kwargs = dict(case=['Case1', 'Case2', 'Case3'],
control=['Control1', 'Control2', 'Control3'],
output=out,
info_tag="TEST_TAG",
quiet=True)
expected_indices = [
False, True, True, False, True, True, False, True, True, True
]
expected_flags = [1, 1, 1, 3, 1, 1, 1]
expected_records = [x for x, y in zip(ad_records, expected_indices) if y]
main(ad_vcf, **kwargs)
results = get_variants(out)
for res, exp, flag in zip(results, expected_records, expected_flags):
for attr in ('pos', 'ref', 'alts'):
assert_equal(getattr(res, attr), getattr(exp, attr))
assert_equal(res.info['TEST_TAG'], flag)
if os.path.exists(out):
os.remove(out)
