change IUPAC nucleotide code to nucleotide

iupac_change.py

#!/usr/bin/env python

usage="""
iupac_change.py <infile> <outfile>
change IUPAC nucleotide codes for tab delimited file with CHR, ID, REF, ALT columns
"""

import sys
import os

if len(sys.argv) < 3:
	print usage
	
vcf_file = sys.argv[1]
f = open(vcf_file, "r")
outfile = open(sys.argv[2], "w")

for line in f.readlines():
	delim = line.split('\t')
	alt = delim[4]
	ref = delim[3]
	if alt == "A" or alt == "T" or alt =="C" or alt == "G":
		alt = alt
	elif alt == "K" and ref == "G":
		alt = "T"
	elif alt =="K" and ref == "T":
		alt = "G"
	elif alt == "M" and ref == "A":
		alt = "C"
	elif alt == "M" and ref == "C":
		alt = "A"
	elif alt == "R" and ref == "A":
		alt = "G"
	elif alt == "R" and ref == "G":
		alt = "A"
	elif alt == "S" and ref == "G":
		alt = "C"
	elif alt == "S" and ref == "C":
		alt = "G"
	elif alt == "W" and ref == "A":
		alt = "T"
	elif alt == "W" and ref == "T":
		alt = "A"
	elif alt == "Y" and ref == "C":
		alt = "T"
	elif alt == "Y" and ref == "T":
		alt = "C"
	delim[4] = alt
	#convert delim list to string
	line = "\t".join(delim)

	outfile.write(line)

f.close()
outfile.close()