import numpy as np
ifile = open('/home/scottn/mouse.ped.csv')
data = np.genfromtxt(ifile, delimiter=',', dtype=None, names=None).tolist()
sixmerid = open('/home/scottn/sixmerbininantisense.txt')
sixmergeno = np.genfromtxt(sixmerid, delimiter='\t', dtype=None, names=None).tolist()
sixmers = []
i = 0
for row in sixmergeno:
	temprow = list(data[i])
	for item in row:
		if item == 2:
			temprow = temprow + ['G','G']
		else:
			temprow = temprow + ['A','A']
	while len(temprow) != 6 + 2 * 18090:
		temprow = temprow + [0, 0]
	sixmers.append(temprow)
	i = i + 1
ofile = open('/home/scottn/plink/mouse.antisense.ped', 'w+')
for row in sixmers:
	ofile.write('\t'.join([str(x) for x in row])+'\n')
ofile.close()