nucleotideMap = { 'a':0, 'c':1, 'g':2, 't':3 }
reverseMap = { 0:'a', 1:'c', 2:'g', 3:'t' }

ScoreCount = 0

def getAndClearScoreCount():
    global ScoreCount
    rval = ScoreCount
    ScoreCount = 0
    return rval

def Score(s, DNA, l):
    # s = list of starting indices, 1-based, 0 means ignore
    # DNA = list of nucleotide strings
    # l = Target Motif length
    global ScoreCount
    ScoreCount += 1
    score = 0
    for i in xrange(l):
       # loop over string positions
       cnt = [0 for x in xrange(4)]
       for j in xrange(len(s)):
           # loop over DNA strands
           sval = s[j]
           if (sval != 0):
               cnt[nucleotideMap[DNA[j][sval-1+i]]] += 1
       score += max(cnt)
    return score


def Consensus(s, DNA, l):
    # s = list of starting indices, 1-based, 0 means ignore
    # DNA = list of nucleotide strings
    # l = Target Motif length
    cstring = ''
    for i in xrange(l):
       # loop over string positions
       cnt = [0 for x in xrange(4)]
       for j in xrange(len(s)):
           # loop over DNA strands
           sval = s[j]
           if (sval != 0):
               cnt[nucleotideMap[DNA[j][sval-1+i]]] += 1
       cstring += reverseMap[cnt.index(max(cnt))]
    return cstring


if __name__ == "__main__":
    DNA = ["acatatag",
           "acatatag",
           "acatatag",
           "acatatag",
           "acatatag"]

    for s in DNA:
        print s

    print Score([1,1,1,1,1], DNA, 8), Consensus([1,1,1,1,1], DNA, 8)
    print Score([2,2,2,2,2], DNA, 6), Consensus([2,2,2,2,2], DNA, 6)
    print Score([2,2,0,2,2], DNA, 6), Consensus([2,2,0,2,2], DNA, 6)
    print Score([1,3,1,3,1], DNA, 4), Consensus([1,3,1,3,1], DNA, 4)
    print Score([1,2,3,4,5], DNA, 4), Consensus([1,2,3,4,5], DNA, 4)
    raw_input("Press [Enter] to quit")