def test_mapping_vcf_header_parser_parse_line_sample():
p = parser.HeaderParser()
INPUT = (
"##SAMPLE="
"<ID=Sample1,Assay=WholeGenome,Ethnicity=AFR,Disease=None,"
'Description="Patient germline genome from unaffected",'
"DOI=url>\n"
)
if sys.version_info < (3, 6):
EXPECTED = (
"SampleHeaderLine('SAMPLE', '<ID=Sample1,Assay=WholeGenome,"
'Ethnicity=AFR,Disease=None,Description="Patient germline genome from '
"unaffected\",DOI=url>', OrderedDict([('ID', 'Sample1'), ('Assay', "
"'WholeGenome'), ('Ethnicity', 'AFR'), ('Disease', 'None'), "
"('Description', 'Patient germline genome from unaffected'), "
"('DOI', 'url')]))"
)
else:
EXPECTED = (
"SampleHeaderLine('SAMPLE', '<ID=Sample1,Assay=WholeGenome,"
'Ethnicity=AFR,Disease=None,Description="Patient germline genome from '
"unaffected\",DOI=url>', {'ID': 'Sample1', 'Assay': 'WholeGenome', 'Ethnicity': 'AFR', 'Disease': 'None', "
"'Description': 'Patient germline genome from unaffected', 'DOI': 'url'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_format():
p = parser.HeaderParser()
INPUT = '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n'
if sys.version_info < (3, 6):
EXPECTED = (
"FormatHeaderLine('FORMAT', '<ID=GT,Number=1,Type=String,Description=\"Genotype\">', "
"OrderedDict([('ID', 'GT'), ('Number', 1), ('Type', 'String'), ('Description', 'Genotype')]))"
)
else:
EXPECTED = (
"FormatHeaderLine('FORMAT', '<ID=GT,Number=1,Type=String,Description=\"Genotype\">', "
"{'ID': 'GT', 'Number': 1, 'Type': 'String', 'Description': 'Genotype'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_vcf_header_parser_parse_line_filter():
p = parser.HeaderParser()
INPUT = '##FILTER=<ID=q10,Description="Quality below 10">\n'
if sys.version_info < (3, 6):
EXPECTED = (
"FilterHeaderLine('FILTER', '<ID=q10,Description=\"Quality below 10\">', OrderedDict([('ID', 'q10'), "
"('Description', 'Quality below 10')]))"
)
else:
EXPECTED = (
"FilterHeaderLine('FILTER', '<ID=q10,Description=\"Quality below 10\">', "
"{'ID': 'q10', 'Description': 'Quality below 10'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_info():
p = parser.HeaderParser()
INPUT = "##INFO=" "<ID=NS,Number=1,Type=Integer,Description=" '"Number of Samples With Data">\n'
if sys.version_info < (3, 6):
EXPECTED = (
"InfoHeaderLine('INFO', '<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">', "
"OrderedDict([('ID', 'NS'), ('Number', 1), ('Type', 'Integer'), ('Description', "
"'Number of Samples With Data')]))"
)
else:
EXPECTED = (
"InfoHeaderLine('INFO', '<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">', "
"{'ID': 'NS', 'Number': 1, 'Type': 'Integer', 'Description': 'Number of Samples With Data'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_pedigree():
p = parser.HeaderParser()
INPUT = "##PEDIGREE=" "<ID=TumourSample,Original=GermlineID>\n"
if sys.version_info < (3, 6):
EXPECTED = (
"PedigreeHeaderLine('PEDIGREE', "
"'<ID=TumourSample,Original=GermlineID>',"
" OrderedDict([('ID', 'TumourSample'), "
"('Original', 'GermlineID')]))"
)
else:
EXPECTED = (
"PedigreeHeaderLine('PEDIGREE', '<ID=TumourSample,Original=GermlineID>', "
"{'ID': 'TumourSample', 'Original': 'GermlineID'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_meta():
p = parser.HeaderParser()
INPUT = "##META=" "<ID=Assay,Type=String,Number=.,Values=[WholeGenome, Exome]>\n"
if sys.version_info < (3, 6):
EXPECTED = (
"MetaHeaderLine('META', '<ID=Assay,Type=String,Number=.,"
"Values=[WholeGenome, Exome]>', OrderedDict([('ID', 'Assay'), "
"('Type', 'String'), ('Number', '.'), ('Values', ['WholeGenome', "
"'Exome'])]))"
)
else:
EXPECTED = (
"MetaHeaderLine('META', '<ID=Assay,Type=String,Number=.,Values=[WholeGenome, Exome]>', "
"{'ID': 'Assay', 'Type': 'String', 'Number': '.', 'Values': ['WholeGenome', 'Exome']})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_alt_allele():
p = parser.HeaderParser()
INPUT = "##ALT=" '<ID=R,Description="IUPAC code R = A/G">\n'
if sys.version_info < (3, 6):
EXPECTED = (
"AltAlleleHeaderLine('ALT', "
"'<ID=R,Description=\"IUPAC code R = A/G\">', "
"OrderedDict([('ID', 'R'), "
"('Description', 'IUPAC code R = A/G')]))"
)
else:
EXPECTED = (
"AltAlleleHeaderLine('ALT', "
"'<ID=R,Description=\"IUPAC code R = A/G\">', "
"{'ID': 'R', 'Description': 'IUPAC code R = A/G'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_mapping_vcf_header_parser_parse_line_contig():
p = parser.HeaderParser()
INPUT = (
"##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,"
'species="H**o sapiens",taxonomy=x>\n'
)
if sys.version_info < (3, 6):
EXPECTED = (
"ContigHeaderLine('contig', '<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,"
"species=\"H**o sapiens\",taxonomy=x>', OrderedDict([('ID', '20'), ('length', '62435964'), "
"('assembly', 'B36'), ('md5', 'f126cdf8a6e0c7f379d618ff66beb2da'), ('species', 'H**o sapiens'), "
"('taxonomy', 'x')]))"
)
else:
EXPECTED = (
"ContigHeaderLine('contig', '<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,"
"species=\"H**o sapiens\",taxonomy=x>', {'ID': '20', 'length': '62435964', 'assembly': 'B36', "
"'md5': 'f126cdf8a6e0c7f379d618ff66beb2da', 'species': 'H**o sapiens', 'taxonomy': 'x'})"
)
assert str(p.parse_line(INPUT)) == EXPECTED
def test_vcf_header_parser_file_format():
p = parser.HeaderParser()
INPUT = "##fileFormat=VCFv4.2\n"
EXPECTED = "HeaderLine('fileFormat', 'VCFv4.2')"
assert str(p.parse_line(INPUT)) == EXPECTED