compare 2 23andMe plaintext files to get the number of SNPs which have the identical genotype over both files

23andme-compare.py

# usage: just run "./compare_snps.py 23andme_file_1.txt 23andme_file_2.txt"

import sys

def read_23andme(filename):
	handle = open(filename,"r")
	snps = {}
	for line in handle:
		if line[0] != "#":
			line_array = line.split("\t")
			snps[line_array[0]] = line_array[3].rstrip()
	return snps

def compare_genotypes(first_snps,second_snps):
	total_snps = 0
	total_in_both = 0
	same_snps = 0
	different_snps = 0

	if len(first_snps) > len(second_snps):
		longer = "first"
		longer_snps = first_snps
		shorter_snps = second_snps
	else:
		longer = "second"
		longer_snps = second_snps
		shorter_snps = first_snps

	for snp in longer_snps:
		if shorter_snps.has_key(snp):

			if len(longer_snps[snp]) > 1:
				reverse_longer = longer_snps[snp][1]+longer_snps[snp][0]
			else:
				reverse_longer = longer_snps[snp]

			if longer_snps[snp] == shorter_snps[snp]:
				same_snps += 1
			elif reverse_longer == shorter_snps[snp]:
				same_snps += 1
			else:
				different_snps += 1
			total_in_both += 1	
		else:
				print snp + " is missing from the shorter file"
		total_snps += 1

	print "The "+longer+" file includes more SNPS"
	print "In total "+str(total_snps)+" SNPs were tested of which "+str(total_in_both)+" can be found in both files"
	print str(same_snps) +" of those SNPs have the same genotype between both files."
	print str(different_snps) + " of those SNPs have different genotypes between both files"


first_snps = read_23andme(sys.argv[1])
second_snps = read_23andme(sys.argv[2])
compare_genotypes(first_snps,second_snps)