scout/commands/export/variant.py
def get_vcf_entry(variant_obj, case_id=None):
    """
        Get vcf entry from variant object

        Args:
            variant_obj(dict)
        Returns:
            variant_string(str): string representing variant in vcf format
    """
    if variant_obj['category'] == 'snv':
        var_type = 'TYPE'
    else:
        var_type = 'SVTYPE'

    info_field = ';'.join(
            [
                'END='+str(variant_obj['end']),
                var_type+'='+variant_obj['sub_category'].upper()
            ]
        )

    variant_string = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}".format(
        variant_obj['chromosome'],
        variant_obj['position'],
        variant_obj['dbsnp_id'],
        variant_obj['reference'],
        variant_obj['alternative'],
        variant_obj['quality'],
        ';'.join(variant_obj['filters']),
        info_field
    )

    if case_id:
        variant_string += "\tGT"
        for sample in variant_obj['samples']:
            variant_string += "\t" + sample['genotype_call']

    return variant_string
def get_vcf_entry(variant_obj, case_id=None):
    if variant_obj['category'] == 'snv':
        var_type = 'TYPE'
    else:
        var_type = 'SVTYPE'

    info_field = ';'.join(
            [
                'END='+str(variant_obj['end']),
                var_type+'='+variant_obj['sub_category'].upper()
            ]
        )

    variant_string = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}".format(
        variant_obj['chromosome'],
        variant_obj['position'],
        variant_obj['dbsnp_id'],
        variant_obj['reference'],
        variant_obj['alternative'],
        variant_obj['quality'],
        ';'.join(variant_obj['filters']),
        info_field
    )

    if case_id:
        variant_string += "\tGT"
        for sample in variant_obj['samples']:
            variant_string += "\t" + sample['genotype_call']

    return variant_string
def get_vcf_entry ( variant_obj , case_id = None ) : if variant_obj [ 'category' ] == 'snv' : var_type = 'TYPE' else : var_type = 'SVTYPE' info_field = ';' . join ( [ 'END=' + str ( variant_obj [ 'end' ] ) , var_type + '=' + variant_obj [ 'sub_category' ] . upper ( ) ] ) variant_string = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}" . format ( variant_obj [ 'chromosome' ] , variant_obj [ 'position' ] , variant_obj [ 'dbsnp_id' ] , variant_obj [ 'reference' ] , variant_obj [ 'alternative' ] , variant_obj [ 'quality' ] , ';' . join ( variant_obj [ 'filters' ] ) , info_field ) if case_id : variant_string += "\tGT" for sample in variant_obj [ 'samples' ] : variant_string += "\t" + sample [ 'genotype_call' ] return variant_string
Get vcf entry from variant object

        Args:
            variant_obj(dict)
        Returns:
            variant_string(str): string representing variant in vcf format
Get vcf entry from variant object