def test_vcfparser(self):
'It test the vcf arser'
vcf_path = join(TEST_DATA_DIR, 'contigs.vcf')
vcf = VcfParser(vcf_path)
assert vcf.version == '3.3'
header = vcf.header
filter_info = 'SNV is not a CAP detectable by the enzymes: cheap ones'
assert header['FILTER']['CEF'] == filter_info
vcf_ = vcf.get_snv(('CUTC000002', '79'))
assert vcf_['CHROM'] == 'CUTC000002'
assert vcf_['POS'] == '79'
vcfs = list(vcf.vcfs)
assert len(vcfs) == 15
assert vcfs[4]['samples'] == {'MU16_454_MU16': {},
'UPV196_454_UPV196': {'C': 2, 'T': 16}}
assert vcfs[14]['samples'] == {'MU16_454_MU16': {'A': 2},
'UPV196_454_UPV196': {'G': 2}}
#version 4.1
vcf_path = join(TEST_DATA_DIR, 'snvs_to_igv.vcf')
vcf = VcfParser(vcf_path)
assert vcf.version == '4.1'
assert vcf.header['FILTER'] == {'q10': 'Quality below 10'}
vcf_ = vcf.get_snv(('ctg1', '36'))
vcfs = list(vcf.vcfs)
assert len(vcfs) == 2
assert vcfs[0] == vcf_
assert 'GROUP11' in vcf_['samples']
assert vcf_['FILTER'] == ['.']
def test_vcfparser(self):
"It test the vcf arser"
vcf_path = join(TEST_DATA_DIR, "contigs.vcf")
vcf = VcfParser(vcf_path)
assert vcf.version == "3.3"
header = vcf.header
filter_info = "SNV is not a CAP detectable by the enzymes: cheap ones"
assert header["FILTER"]["CEF"] == filter_info
vcf_ = vcf.get_snv(("CUTC000002", "79"))
assert vcf_["CHROM"] == "CUTC000002"
assert vcf_["POS"] == "79"
vcfs = list(vcf.vcfs)
assert len(vcfs) == 15
assert vcfs[4]["samples"] == {"MU16_454_MU16": {}, "UPV196_454_UPV196": {"C": 2, "T": 16}}
assert vcfs[14]["samples"] == {"MU16_454_MU16": {"A": 2}, "UPV196_454_UPV196": {"G": 2}}