Commit 3479a77a authored by van den Berg's avatar van den Berg
Browse files

Convert single use fixtures to regular tests

parent 9e87861b
......@@ -83,19 +83,7 @@ def test_no_call(BLANK_NA12878):
assert BLANK_NA12878['alleles_no_call'] == 8
@pytest.fixture(scope='module')
def NA12878_BLANK():
filename = 'tests/cases/gatk.vcf.gz'
call = VCF(filename, gts012=True)
positive = VCF(filename, gts012=True)
d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
positive_samples=['BLANK'],
min_gq=30, min_dp=20)
return d
@pytest.fixture(scope='module')
def NA12878_call_truncated():
def test_truncated_call_file():
""" When the call set is truncated, i.e. is missing variants which are
present in the positive vcf file """
......@@ -106,17 +94,10 @@ def NA12878_call_truncated():
d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
positive_samples=['BLANK'],
min_gq=30, min_dp=20)
return d
def test_truncated_called_no_call(NA12878_call_truncated):
""" Variants which are missing from the call vcf count towards
alleles_no_call """
assert NA12878_call_truncated['alleles_no_call'] == 12
assert d['alleles_no_call'] == 12
@pytest.fixture(scope='module')
def NA12878_positive_truncated():
def test_truncated_positive_file():
""" When the positive set is truncated, i.e. the called vcf file contains
variants which are absent from the positive vcf file """
filename = 'tests/cases/gatk.vcf.gz'
......@@ -126,16 +107,10 @@ def NA12878_positive_truncated():
d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
positive_samples=['BLANK'],
min_gq=30, min_dp=20)
return d
def test_truncated_positive_no_call(NA12878_positive_truncated):
""" Variants which are missing from the positive vcf do not count towards
alleles_no_call """
assert NA12878_positive_truncated['alleles_no_call'] == 0
assert d['alleles_no_call'] == 0
def test_phased_positive():
def test_phased_positive_file():
""" Test error message when the positive vcf contains phased variants """
filename = 'tests/cases/gatk.vcf.gz'
phased = 'tests/cases/dummy_phased_blank.vcf.gz'
......@@ -147,7 +122,7 @@ def test_phased_positive():
positive_samples=['BLANK'])
def test_phased_call():
def test_phased_call_file():
""" Test error message when the call vcf contains phased variants """
filename = 'tests/cases/gatk.vcf.gz'
phased = 'tests/cases/dummy_phased_blank.vcf.gz'
......
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