vcf2clinvar/genome.py
def _parse_genotype(self, vcf_fields):
        """Parse genotype from VCF line data"""
        format_col = vcf_fields[8].split(':')
        genome_data = vcf_fields[9].split(':')
        try:
            gt_idx = format_col.index('GT')
        except ValueError:
            return []
        return [int(x) for x in re.split(r'[\|/]', genome_data[gt_idx]) if
                x != '.']
def _parse_genotype(self, vcf_fields):
        """Parse genotype from VCF line data"""
        format_col = vcf_fields[8].split(':')
        genome_data = vcf_fields[9].split(':')
        try:
            gt_idx = format_col.index('GT')
        except ValueError:
            return []
        return [int(x) for x in re.split(r'[\|/]', genome_data[gt_idx]) if
                x != '.']
def _parse_genotype ( self , vcf_fields ) : format_col = vcf_fields [ 8 ] . split ( ':' ) genome_data = vcf_fields [ 9 ] . split ( ':' ) try : gt_idx = format_col . index ( 'GT' ) except ValueError : return [ ] return [ int ( x ) for x in re . split ( r'[\|/]' , genome_data [ gt_idx ] ) if x != '.' ]
Parse genotype from VCF line data
Parse genotype from VCF line data