modify_geno_with_snp_mummer.py

#!/usr/bin/python
import sys


def modify_geno(in_geno, in_snp, col, out_geno):
	snp_db = {}
	with open(in_snp, 'r') as f_in:
		for line in f_in:
			data = line.strip().split()
			if data == []:
				continue
			if data[0].isdigit() == False:
				continue
			chrn = data[-1]
			if chrn not in snp_db:
				snp_db[chrn] = {}
			pos = int(data[3])
			snp_db[chrn][pos] = data[1].replace('.', 'N') + '/'+data[1].replace('.', 'N')
	
	cnt_ovlp_snp = 0
	with open(in_geno, 'r') as f_in:
		with open(out_geno, 'w') as f_out:
			for line in f_in:
				if line[0] == "#":
					f_out.write(line)
					continue
				data = line.strip().split()
				for i in range(0, len(data)):
					if i == col:
						if int(data[1]) in snp_db[data[0]]:
							cnt_ovlp_snp += 1
							f_out.write(snp_db[data[0]][int(data[1])])
						else:
							f_out.write(data[i])
					else:
						f_out.write(data[i])
					if i < len(data)-1:
						f_out.write('\t')
				f_out.write('\n')
	print(cnt_ovlp_snp)


if __name__ == "__main__":
	if len(sys.argv) < 4:
		print("Notice: modify column in geno file with snp result generated by show-snps of mummer")
		print("Usage: python "+sys.argv[0]+" <in_geno> <in_snp> <col> <out_geno>")
	else:
		in_geno = sys.argv[1]
		in_snp = sys.argv[2]
		col = int(sys.argv[3])
		out_geno = sys.argv[4]
		modify_geno(in_geno, in_snp, col, out_geno)