VCF_dip2hap.py

# -*- coding: utf-8 -*-
"""
Created on 2021-12-21

@author: Yudongcai

@Email: yudong_cai@163.com
"""

import typer
import gzip



def main(in_vcf: str = typer.Argument(..., help="输入的二倍体vcf(.vcf.gz)"),
         out_vcf: str = typer.Argument(..., help="输出的单倍体vcf(.vcf)")
         ):
    """
    把二倍体的vcf拆分为单倍体。
    """
    with gzip.open(in_vcf, 'rb') as f1, open(out_vcf, 'w') as f2:
        for line in f1:
            tline = line.decode()
            if tline[:2] == '##':
                f2.write(tline)
            elif tline[:2] == '#C':
                tline = tline.strip().split()
                f2.write('\t'.join(tline[:9]))
                for sample in tline[9:]:
                    f2.write(f'\t{sample}-1\t{sample}-2')
                f2.write('\n')
            else:
                tline = tline.strip().split()
                f2.write('\t'.join(tline[:9]))
                for gt in tline[9:]:
                    f2.write(f'\t{gt[0]}\t{gt[2]}')
                f2.write('\n')


if __name__ == '__main__':
    typer.run(main)