'''
============================================================
http://rosalind.info/problems/hamm
Given: Two DNA strings s and t of equal length (not exceeding 1 kbp).
Return: The Hamming distance dH(s,t).
============================================================
'''
import rosalind.rosutil as ro
if __name__ == "__main__":
# import doctest
# doctest.testmod()
print ro.hamm(*ro.read_lines('rosalind_hamm_sample.dat'))
print ro.hamm(*ro.read_lines('rosalind_hamm.dat'))
def apm(s, p, d):
'''Return a list of all positions where p appears in s with at most d mismatches.'''
m = len(p)
return [i for i in xrange(len(s) - m) if ro.hamm(s[i:i + m], p) <= d]