def test_run_cleanVCF_VEPannotations_SpAI_08():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_VEPannotation_clean.vcf',
'outputfile': 'tests/files/main_test.out',
'SpliceAI': '0.8',
'VEP': True,
'VEPrescue': None,
'VEPremove': None,
'filter_VEP': None,
'VEPtag': None,
'tag': [],
'verbose': None,
'VEPsep': None,
'SpliceAItag': None
}
# Run
main_cleanVCF(args)
# Tests
assert [row for row in open('tests/files/main_test.out')] == [
row
for row in open('tests/files/input_VEPannotation_clean_SpAI_08.out')
]
# Clean
os.remove('tests/files/main_test.out')
def test_run_cleanVCF_VEP_remove_rescue():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_cleanVCF.vcf',
'outputfile': 'tests/files/main_test.out',
'SpliceAI': None,
'VEP': True,
'VEPrescue': ['downstream_gene_variant', 'NMD_transcript_variant'],
'filter_VEP': None,
'VEPremove': ['5_prime_UTR_variant', '3_prime_UTR_variant'],
'VEPtag': 'VEP',
'tag': [],
'verbose': None,
'VEPsep': None,
'SpliceAItag': None
}
# Run
main_cleanVCF(args)
# Tests
assert [row for row in open('tests/files/main_test.out')] == [
row for row in open('tests/files/input_cleanVCF_VEP_remove_rescue.out')
]
# Clean
os.remove('tests/files/main_test.out')
def test_run_cleanVCF_VEP_SpAI_SpAItag_remove_rescue_tag_2():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_cleanVCF_SpAI_SpAItag.vcf',
'outputfile': 'tests/files/main_test.out',
'SpliceAI': 0.9,
'VEP': True,
'VEPrescue': ['downstream_gene_variant', 'NMD_transcript_variant'],
'filter_VEP': None,
'VEPremove': ['5_prime_UTR_variant', '3_prime_UTR_variant'],
'VEPtag': 'VEP',
'tag': ['BaseQRankSum', 'novoCaller'],
'verbose': None,
'VEPsep': None,
'SpliceAItag': 'VALUE_MAX'
}
# Run
main_cleanVCF(args)
# Tests
assert [row for row in open('tests/files/main_test.out')] == [
row for row in open(
'tests/files/input_cleanVCF_VEP_SpAI_SpAItag_remove_rescue_tag_2.out'
)
]
# Clean
os.remove('tests/files/main_test.out')
def test_run_cleanVCF_VEP_as_ANNOTTAG():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_cleanVCF_ANNOTTAG.vcf',
'outputfile': 'tests/files/main_test.out',
'SpliceAI': None,
'VEP': True,
'VEPrescue': None,
'VEPremove': None,
'filter_VEP': None,
'VEPtag': 'ANNOTTAG',
'tag': [],
'verbose': None,
'VEPsep': None,
'SpliceAItag': None
}
# Run
main_cleanVCF(args)
# Tests
assert [row for row in open('tests/files/main_test.out')] == [
row for row in open('tests/files/input_cleanVCF_ANNOTTAG_VEP.out')
]
# Clean
os.remove('tests/files/main_test.out')
def test_args_conflict():
''' '''
# Variables
args = {
'inputfile': 'tests/files/input_cleanVCF.vcf',
'outputfile': 'tests/files/main_test.out',
'filter_VEP': None,
'SpliceAI': None,
'VEP': None,
'VEPrescue':
['splice_region_variant', 'non_coding_transcript_variant'],
'VEPremove': None,
'VEPtag': 'VEP',
'tag': [],
'verbose': None,
'VEPsep': None,
'SpliceAItag': None
}
# Run and Tests
with pytest.raises(SystemExit) as e:
assert main_cleanVCF(args)
assert str(
e.value
) == '\nERROR in parsing arguments: specify the flag "--VEP" to filter by VEP annotations to apply rescue terms or remove additional terms\n'
# Clean
os.remove('tests/files/main_test.out')