The exercise says the following:
Pairwise comparision of DNA sequences is a popular technique used in Bioinformatics. It usually involves some scoring scheme to express the degree of similarity. Write a function that compares two DNA sequences based on the following scoring scheme: +1 for a match, +3 for each consecutive match and -1 for each mismatch.
>>> print pairwiseScore("ATTCGT", "ATCTAT") ATTCGT || | ATCTAT Score: 2 >>> print pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA") GATAAATCTGGTCT || ||| | CATTCATCATGCAA Score: 4 >>>
so i wrote the following, which was continuously working until i started playing with it, now i cant find whats wrong with it! please help me by pointing out where i went wrong?
def pariwiseScore(seqA, seqB): h =  c =  for x in range(0,len(seqA)): if seqA[x] == seqB[x]: h.append('|') else: h.append(' ') if len(h) > 1: if h[x] == '|': try: if h[x] == h[x-1]: c.append(3) except IndexError: c.append(1) elif h[x] == ' ': c.append(-1) else: if h[x] == '|': c.append(1) elif h[x] == ' ': c.append(-1) a = "".join(h) return seqA, '\n', a, '\n', seqB, '\n', 'Score: %I' % sum(c)
Any help is much appreciated.