def test_run_comHet_proband_plus_NA12878():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_comHet.vcf',
'outputfile': 'tests/files/main_test.out',
'trio': ['NA12879_sample', 'NA12878_sample'],
'VEPtag': 'VEP',
'allow_undef': None,
'filter_cmpHet': True,
'verbose': None,
'sep': None,
'impact': None,
'SpliceAItag': None
}
# Run
main_comHet(args)
# Tests
assert [row for row in open('tests/files/main_test.out')] == [
row for row in open('tests/files/input_comHet_plus_NA12878.out')
]
# Clean
os.remove('tests/files/main_test.out')
os.remove('tests/files/main_test.out.summary')
os.remove('tests/files/main_test.out.json')
def test_run_trio_error(): # NA12879
''' '''
# Variables
args = {
'inputfile':
'tests/files/input_comHet.vcf',
'outputfile':
'tests/files/main_test.out',
'trio':
['NA12879_sample', 'NA12878_sample', 'NA12877_sample', 'extra_sample'],
'VEPtag':
'VEP',
'allow_undef':
None,
'filter_cmpHet':
True,
'verbose':
None,
'sep':
None,
'impact':
None,
'SpliceAItag':
None
}
# Run and Tests
with pytest.raises(SystemExit) as e:
assert main_comHet(args)
assert str(
e.value
) == '\nERROR in parsing arguments: too many sample IDs provided for trio\n'
# Clean
os.remove('tests/files/main_test.out')