import numpy as np
import string
ifile = open('/home/scottn/mouse-data-no-repeats.csv')
data = np.genfromtxt(ifile, names = None, dtype = None, delimiter = ',')
beta = []
for row in data:
	beta.append(list(row))
data = np.array(beta)
sfile = open('/home/scottn/sixmerlist.csv')
sixmers = np.genfromtxt(sfile, names=None, delimiter=',', dtype=None)[:,0]
n = len(data)
m = len(sixmers)
output = np.zeros((n,m))
for i in range(0,n):
	for k in range(0,m):
		output[i,k] = string.count(data[i,4], sixmers[k])
ofile = open('/home/scottn/sixmercountinantisense.txt', 'w+')
for row in output:
	ofile.write('\t'.join([str(x) for x in row])+'\n')
ofile.close()
ifile.close()
sfile.close()