SNP_number_count.py.txt

import os
import gzip

def count_snps_in_vcf(vcf_file):
    snp_count = 0

    with gzip.open(vcf_file, 'rt') as f:
        for line in f:
            if not line.startswith('#'):  # 
                snp_count += 1

    return snp_count

def batch_count_snps(vcf_directory):
    for filename in os.listdir(vcf_directory):
        if filename.endswith('1018-121sample.chr1-39_20230306.Galgal7b.SNP.filtered.PASS.geno02.vcf.recode.vcf.gz'):  # 仅处理以 '.vcf.gz' 结尾的文件
            vcf_file = os.path.join(vcf_directory, filename)
            snp_count = count_snps_in_vcf(vcf_file)
            print(f"文件名: {filename}, SNP 数量: {snp_count}")


vcf_directory = './'


batch_count_snps(vcf_directory)