def test_write_headers(self):
header = _get_vcf_header_from_lines(self.lines)
with temp_dir.TempDir() as tempdir:
tempfile = tempdir.create_temp_file(suffix='.vcf')
header_fn = WriteVcfHeaderFn(tempfile)
header_fn.process(header)
self._assert_file_contents_equal(tempfile, self.lines)
def test_write_headers_with_vcf_version_line(self):
header = _get_vcf_header_from_lines(self.lines)
vcf_version_line = '##fileformat=VCFv4.3\n'
expected_results = [
vcf_version_line.encode('utf-8'),
b'##INFO=<ID=NS,Number=1,Type=Integer,Description="Number samples">\n',
b'##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n',
b'##INFO=<ID=HG,Number=G,Type=Integer,Description="IntInfo_G">\n',
b'##INFO=<ID=HR,Number=R,Type=String,Description="ChrInfo_R">\n',
b'##FILTER=<ID=MPCBT,Description="Mate pair count below 10">\n',
b'##ALT=<ID=INS:ME:MER,Description="Insertion of MER element">\n',
b'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n',
b'##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="GQ">\n',
b'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT\n'
]
with temp_dir.TempDir() as tempdir:
tempfile = tempdir.create_temp_file(suffix='.vcf')
header_fn = WriteVcfHeaderFn(tempfile)
header_fn.process(header, vcf_version_line)
with open(tempfile, 'rb') as f:
actual = f.readlines()
self.assertCountEqual(actual, expected_results)
