local_align.py

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)