Question

I have two strings in python that I have converted to lists:

Seq1 = [x1,x2,x3,x4]

Seq2 = [y1,y2,y3,y4]

The strings are the same length and are composed of only the letters 'a', 'c', 'g', and 'u'.

Then I created an empty matrix len(Seq1) by len(Seq2):

a = numpy.zeros(shape=len(Seq1),len(Seq2))

Next, I want to compare the list values and place a 1 if the values match and 0 if they don’t. The value should be placed in the relevant array element
i.e.

if seq1[0] == seq[0]:
    a[0,0] = [1]
else:
    a[0,0] = [0]

# repeat for all the values.
print a

I had a loop that was working but it only filled in the first row and column. I can see that it’s a problem with a range function like Seq1[i] == Seq2[j] but I can’t figure it out.

Answer 1

A compact way to write the loop is:

import itertools

for i1,i2 in itertools.product(xrange(len(Seq1)), xrange(len(Seq2))):
    a[i1,i2] = Seq1[i1] == Seq2[i2]