def bedpeToVcf(bedpe_file, vcf_out):
myvcf = Vcf()
converter = BedpeToVcfConverter(myvcf)
in_header = True
# parse the bedpe data
header = list()
for line in bedpe_file:
if in_header:
if line[0:2] == '##':
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list_str = line.rstrip().split('\t', 20)[-1]
header.append('\t'.join([
'#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER',
'INFO', sample_list_str
]))
continue
else:
in_header = False
myvcf.add_header(header)
myvcf.file_format = 'VCFv4.2'
vcf_out.write(myvcf.get_header() + '\n')
#
bedpe = Bedpe(line.rstrip().split('\t'))
variants = converter.convert(bedpe)
for v in variants:
vcf_out.write(v.get_var_string() + '\n')
# close the VCF output file
vcf_out.close()
return
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
