python_ver.py

yup = 0
b = 'AATTCCGGAATT'
p = set([b])
for x in range(0,len(b)):
    for x_val in ['A','C','G','T']:
        for y in range(0,len(b)):
            for y_val in ['A','C','G','T']:
                temp = list(b)
                temp[x],temp[y] = x_val,y_val
                p.add( ''.join(temp) )
try:
    with open("/Users/John/Desktop/ENCFF001LCU.fq",'r') as f:
        next(f); new_line = next(f)
        while True:
            yup += any([frag in p for frag in [new_line[s:e] for s,e in enumerate(xrange(len(b),len(new_line)+1))]])
            next(f);next(f);next(f); new_line = next(f)
except StopIteration:
    print 'Final Result:',yup