Python building 2d array getting list assignment index out of range

Question

N = len(s1)
M = len(s2)
matrix = [[0 for i in range(N+1)] for j in range(M+1)]
gap = int(raw_input('Enter gap score'))
mismatch = int(raw_input('Enter mismatch score'))
match = int(raw_input('Enter the match score'))

matrix[0][0] = 0

for i in range(1,(N+1)):
    matrix[i][0]=(matrix[(i-1)][0] + gap)

for j in range(1,(M+1)):
    matrix[0][j]=(matrix[0][(j-1)] + gap)  

for i in range(1,N+1):
    for j in range(1,M+1):
        if(s1[i-1] == s2[j-1]):
            score1 = matrix[i-1][j-1] + match

        else:
            score1 = matrix[i-1][j-1] + mismatch

        score2 = matrix[i][j-1] + gap
        score3 = matrix[i-1][j] + gap
        matrix[i][j] = max(score1, score2, score3)

I get the error code Traceback (most recent call last): File "C:\Users\Matt\workspace\ch3skills\ch3skills.py", line 67, in matrix[0][j]=(matrix[0][(j-1)] + gap)
IndexError: list assignment index out of range

It should because it's created matrix = [[0 for i in range(N+1)] for j in range(M+1)] however if I flip the N and M around in the for loops it works just fine. That throws off the rest of the program though — Matt
– Matt, Commented Jan 22, 2015 at 5:57

Arundas R · Accepted Answer · 2015-01-22 06:20:34Z

1

The error is with defining the matrix. If N and M are same you will not get an error. With different N and M values you find the error. Consider the case for N=1 and M=2 your matrix is [[0, 0], [0, 0], [0, 0]]. Now consider this bit of code: for i in range(1,(M+1)): matrix[i][0]=(matrix[(i-1)][0] + gap) In case you have i with values 1 to 3, but you don't have matrix[3][0]. This gives such an error. I cannot understand what is code is intended to do. Now changing M and N i don't get any further errors. But i am not sure whether you are looking for this. I will include the code also.

s1 = raw_input('1: ')
s2 = raw_input('2: ')
N = len(s1)
M = len(s2)
matrix = [[0 for i in range(N+1)] for j in range(M+1)]
gap = int(raw_input('Enter gap score'))
mismatch = int(raw_input('Enter mismatch score'))
match = int(raw_input('Enter the match score'))

matrix[0][0] = 0

for i in range(1,(M+1)):
    matrix[i][0]=(matrix[(i-1)][0] + gap)

for j in range(1,(N+1)):
    matrix[0][j]=(matrix[0][(j-1)] + gap)  

for i in range(1,M+1):
    for j in range(1,N+1):
        if(s1[j-1] == s2[i-1]):
            score1 = matrix[i-1][j-1] + match

        else:
            score1 = matrix[i-1][j-1] + mismatch

        score2 = matrix[i][j-1] + gap
        score3 = matrix[i-1][j] + gap
        matrix[i][j] = max(score1, score2, score3)

answered Jan 22, 2015 at 6:20

Arundas R

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1 Comment

Matt Over a year ago

Yeah I figured that I had to switch them when creating the 2d array. However the for loops do not have to be changed. But thanks for the information on why switching them when making the 2d array worked.

tom10 · Accepted Answer · 2015-01-22 06:20:04Z

0

You need to switch M and N in your for loops, like this:

for i in range(1,M+1):
    matrix[i][0] = matrix[i-1][0] + gap

for j in range(1,N+1):
    matrix[0][j] = matrix[0][j-1] + gap

Since you initially make M items, each being a list of length N, matrix[x] is the xth list (of length N).

Also: 1) all those parentheses add too much clutter; 2) numpy would make all of this much easier.

answered Jan 22, 2015 at 6:20

tom10

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