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from fasta import readFASTA
from scores import *
import numpy as np
import cython_local_align
s=readFASTA("rosalind_smgb.txt")
def pam250_penalty(x,y):
return -pam250_score(x,y)
def blosum62_penalty(x,y):
return -blosum62_score(x,y)
def edit_distance(x,y):
if x==y:
return -1
else:
return 1
def lgap(j):
return j
def agap(j):
return 10+j
A=s.values()[0]
B=s.values()[1]
cython_local_align.build_dp_array(A,B,0,1,edit_distance)
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