def test_region_filter():
test_dir = os.path.dirname(__file__)
args = Namespace()
# prepare the args to tell filter_vcf_file how to proceed
setattr(args, "snv_only_filter", True)
input_file = open(os.path.join(test_dir, "data/test_input1.vcf"))
setattr(args, "input_file", input_file)
output_file = StringIO()
setattr(args, "output_file", output_file)
expected_content = open(os.path.join(test_dir,
"data/test_output6.vcf")).read()
expected_masked_variants_count = 10
masked_variants_count = filter_vcf_file(args)
assert (
masked_variants_count == expected_masked_variants_count
), f"expected {expected_masked_variants_count} got {masked_variants_count}"
assert output_file.getvalue() == expected_content
def test_alt_percentage_filter_multialt():
test_dir = os.path.dirname(__file__)
args = Namespace()
# prepare the args to tell filter_vcf_file how to proceed
setattr(args, "min_percentage_alt_filter", True)
setattr(args, "min_percentage_alt", 30)
input_file = open(os.path.join(test_dir, "data/test_input2.vcf"))
setattr(args, "input_file", input_file)
output_file = StringIO()
setattr(args, "output_file", output_file)
expected_content = open(os.path.join(test_dir,
"data/test_output4.vcf")).read()
expected_masked_variants_count = 2
masked_variants_count = filter_vcf_file(args)
assert (
masked_variants_count == expected_masked_variants_count
), f"expected {expected_masked_variants_count} got {masked_variants_count}"
assert output_file.getvalue() == expected_content