Identify short sequences of matches between 2 strings

Question

I have the following code:

for k, (j,k) in enumerate (zip(line1_u,line2_u_rev_comp)):
    if j==k:
        Match1+=1 
    if j== 'N' or k == 'N':
        Unknown1+=1
    if j != k:
        Different1+=1

This takes 2 lines (line1_u and line2_u_rev_comp) and compares them character by character to identify if they match, have an N which places it in the unknown category or are different. What I want is as well as tallying up each of these is to identify if 10 characters or more in a row match. How could this be done? Explanation of code would be greatly appreciated.

Answer 1

You should look into itertools.groupby:

from collections import defaultdict
from itertools import groupby

def class_chars(chrs):
    if 'N' in chrs:
        return 'unknown'
    elif chrs[0] == chrs[1]:
        return 'match'
    else:
        return 'not_match'

s1 = 'aaaaaaaaaaN123bbbbbbbbbbQccc'
s2 = 'aaaaaaaaaaN456bbbbbbbbbbPccc'
n = 0
consec_matches = []
chars = defaultdict(int)

for k, group in groupby(zip(s1, s2), class_chars):
    elems = len(list(group))
    chars[k] += elems
    if k == 'match':
        consec_matches.append((n, n+elems-1))
    n += elems

print chars
print consec_matches
print [x for x in consec_matches if x[1]-x[0] >= 9]

Output:

defaultdict(<type 'int'>, {'not_match': 4, 'unknown': 1, 'match': 23})
[(0, 9), (14, 23), (25, 27)]
[(0, 9), (14, 23)]

Answer 2

Have a look at the difflib module in python: https://docs.python.org/2/library/difflib.html. Use find_longest_match to find the longest common subsequence.