Table

import numpy
import scipy
from string import *

#return value of each variation
def Diagonal(n1, n2, pt):
    if (n1 == n2):
        return pt['MATCH']
    else:
        return pt['MISMATCH']
#the function gets the optional elements of the alignment matrix and returns pointer's elements
def Pointers( di, ho, ve):
    pointer = max(di, ho, ve)
    if (di == pointer):
        return 'D'
    elif (ho == pointer):
        return 'H'
    else:
        return 'V'

def NW(s1, s2, match = 1, mismatch = -1, gap = -2):
    penalty = { 'MATCH': match, 'MISMATCH' : mismatch, 'GAP': gap}
    n = len(s1) + 1 #dimension of the matrix columns
    m = len(s2) + 1  #dimension of the matrix rows
    al_mat = numpy.zeros((m, n), dtype = int) # alignments matrix with zeros
    p_mat = numpy.zeros((m, n), dtype = str) # alignments matrix with zeros
# checking on gaps
    for i in range(m):
        al_mat[i][0] = penalty['GAP'] * i
        p_mat[i][0] = 'V'
    for j in range(n):
        al_mat[0][j] = penalty['GAP'] * j
        p_mat[0][j] = 'H'
    p_mat[0][0] = 0 #return the first element of pointer matrix back to 0
    for i in range(1, m):
        for j in range(1, n):
            di = al_mat[i - 1][j - 1] + Diagonal(s1[j - 1], s2[i - 1], penalty)
#value of matching on diagonal
            ho = al_mat[i][j - 1] + penalty['GAP']
            #horizontal
            ve = al_mat[i - 1][j] + penalty['GAP']
            #vertical
            al_mat[i][j] = max(di, ho, ve)
            p_mat[i][j] = Pointers(di, ho, ve)
    f1 = open('output1.txt', 'w')
    f2 = open('output2.txt', 'w')

    f1.write(numpy.matrix(al_mat))
    f2.write(numpy.matrix(p_mat))

NW('TCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAATCGATCGATCGAGGATCGA', 'TCGGAGAGAGGGAGAGCGGCAGCAGCGAGCAGTTTTTTT')