test.py

import numpy as np

import cython_align
from blosum62 import *
from numpy import argmin
from fasta import readFASTA

# this is an implementation of the needleman-wunsch algorithm
# and it should handle the affine gap situation 


def mismatch_penalty(A,B):
    if A!=B:
        return -blosum62[A+B]
    else:
        return -blosum62[A+B]
        
s=readFASTA("rosalind_laff.txt")
A=s.values()[0]
B=s.values()[1]
print A,B
score=cython_align.build_dp_array(A,B,10,1,mismatch_penalty)
print score