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gcon.py
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gcon.py
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# http://rosalind.info/problems/gcon/
from itertools import product
from Bio.SubsMat.MatrixInfo import blosum62
def get_score(s, t):
sl, tl = len(s), len(t)
m = {(0, 0): (0, None)}
f, g, h = {}, {}, {}
m.update({((i, 0), (-5, (i - 1, 0))) for i in range(1, sl + 1)})
m.update({((0, i), (-5, (0, i - 1))) for i in range(1, tl + 1)})
for i, j in product(range(1, sl + 1), range(1, tl + 1)):
cost = blosum62.get((s[i - 1], t[j - 1]))
if cost == None:
cost = blosum62.get((t[j - 1], s[i - 1]))
f[(i, j)] = m[(i - 1, j - 1)][0] + cost
g[(i, j)] = max(m[(i - 1, j)][0] - 5, g.get((i - 1, j)))
h[(i, j)] = max(m[(i, j - 1)][0] - 5, h.get((i, j - 1)))
v = max(f[(i, j)], g[(i, j)], h[(i, j)])
if v == f[(i, j)]:
m[(i, j)] = (v, (i-1, j - 1))
elif v == g[(i, j)]:
m[(i, j)] = (v, (i - 1, j))
elif v == h[(i, j)]:
m[(i, j)] = (v, (i, j - 1))
return m[(i,j)][0]
if __name__ == '__main__':
dataset = open('rosalind_gcon.txt').read().strip().split('\n')
print get_score(dataset[1], dataset[3])