def test_to_csv():
filter_dict = {'freebayes_score': 200, 'frequency': 0.85, 'min_depth': 10,
'forward_depth': 3, 'reverse_depth': 3, 'strand_ratio': 0.3}
v = VCF_freebayes(sequana_data('JB409847.expected.vcf'))
filter_v = v.filter_vcf(filter_dict)
with TempFile(suffix='.csv') as ft:
filter_v.to_csv(ft.name)
def test_vcf_filter():
vcf_output_expected = sequana_data('JB409847.expected.vcf')
v = VCF_freebayes(sequana_data('JB409847.vcf'))
filter_dict = {'freebayes_score': 200, 'frequency': 0.85, 'min_depth': 10,
'forward_depth': 3, 'reverse_depth': 3, 'strand_ratio': 0.3}
filter_v = v.filter_vcf(filter_dict)
with TempFile(suffix='.vcf') as ft:
filter_v.to_vcf(ft.name)
compare_file = filecmp.cmp(ft.name, vcf_output_expected)
assert compare_file
def test_to_csv():
filter_dict = {
'freebayes_score': 200,
'frequency': 0.85,
'min_depth': 10,
'forward_depth': 3,
'reverse_depth': 3,
'strand_ratio': 0.3
}
v = VCF_freebayes(sequana_data('JB409847.expected.vcf'))
filter_v = v.filter_vcf(filter_dict)
with TempFile(suffix='.csv') as ft:
filter_v.to_csv(ft.name)
def test_vcf_filter():
vcf_output_expected = sequana_data('JB409847.expected.vcf')
v = VCF_freebayes(sequana_data('JB409847.vcf'))
filter_dict = {
'freebayes_score': 200,
'frequency': 0.85,
'min_depth': 10,
'forward_depth': 3,
'reverse_depth': 3,
'strand_ratio': 0.3
}
filter_v = v.filter_vcf(filter_dict)
with TempFile(suffix='.vcf') as ft:
filter_v.to_vcf(ft.name)
compare_file = filecmp.cmp(ft.name, vcf_output_expected)
assert compare_file