crispy wrote:
> Thanks, i've finally came to solution.
>
> Here it is -> http://codepad.org/Q70eGkO8
>
> def pairwiseScore(seqA, seqB):
>
> score = 0
> bars = [str(' ') for x in seqA] # ...
> length = len(seqA)
> similarity = []
>
> for x in xrange(length):
>
> if seqA[x] == seqB[x]: # ...
> if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): # ...
> score += 3
> similarity.append(x)
> else:
> score += 1
> similarity.append(x)
> else:
> score -= 1
>
> for x in similarity:
> bars[x] = '|' # ...
>
> return ''.join((seqA, '\n', ''.join(bars), '\n', seqB, '\n', 'Score:
', str(score)))
>
Python has a function zip() that lets you iterate over multiple sequences
simultaneously. Instead of
for i in xrange(len(a)):
x = a[i]
y = b[i]
...
you can write
for x, y in zip(a, b):
...
Also, you can build the bar list immediately and avoid the similarity list.
With these changes:
def pairwise_score(a, b):
score = 0
was_equal = False
bars = []
for x, y in zip(a, b):
equal = x == y
if equal:
bars.append("|")
if was_equal:
score += 3
else:
score += 1
else:
bars.append(" ")
score -= 1
was_equal = equal
print a
print "".join(bars)
print b
print "Score:", score
If you want to take this even further you can use a score matrix instead of
if ... else:
def pairwise_score(a, b):
score = 0
was_equal = False
bars = []
matrix = [[-1, 1], [-1, 3]]
for x, y in zip(a, b):
equal = x == y
score += matrix[was_equal][equal]
bars.append(" |"[equal])
was_equal = equal
print a
print "".join(bars)
print b
print "Score:", score
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