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plink_prune_vcf.py
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plink_prune_vcf.py
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#!/usr/bin/env python3
##########################
# Author: B.M. Anderson
# Date: September 2023
# Description: use a PLINK *.prune.out file to remove SNPs from a VCF
##########################
import argparse
import os
import sys
# instantiate the parser
parser = argparse.ArgumentParser(description = 'A script to use the output of PLINK "--indep" to remove SNPs from a VCF')
# add arguments to parse
parser.add_argument('-p', type = str, dest = 'plink_file', help = 'The PLINK *.prune.out file with SNP IDs in the format CHROM:POS, one per line')
parser.add_argument('-v', type = str, dest = 'vcf_file', help = 'The VCF file to remove SNPs from; output will prefix the name with "mod_"')
# parse the command line
if len(sys.argv[1:]) == 0: # if there are no arguments
parser.print_help(sys.stderr)
sys.exit(1)
args = parser.parse_args()
plink_file = args.plink_file
vcf_file = args.vcf_file
if any([not plink_file, not vcf_file]):
parser.print_help(sys.stderr)
sys.exit(1)
# read in the SNPs to remove
snp_list = []
with open(plink_file, 'r') as pfile:
for line in pfile:
chrom = line.rstrip().split(':')[0]
pos = line.rstrip().split(':')[1]
snp_list.append(str(chrom) + '_' + str(pos))
# filter the VCF
dropped = 0
kept = 0
with open(vcf_file, 'r') as vcf, open('mod_' + os.path.basename(vcf_file), 'w') as outvcf:
for line in vcf:
if line.startswith('#'): # a header INFO line
outvcf.write(line)
else:
line_fields = line.rstrip().split()
chrom = line_fields[0]
pos = line_fields[1]
search_str = str(chrom) + '_' + str(pos)
if search_str in snp_list:
dropped = dropped + 1
continue
else:
kept = kept + 1
outvcf.write(line)
print('Removed ' + str(dropped) + ' SNPs and kept ' + str(kept) + ' SNPs in file mod_' + os.path.basename(vcf_file))