Hi, Please have a look at the code below:

import string
from collections import defaultdict



first_complex=open( "residue_a_chain_a_b_backup.txt", "r" )
first_complex_lines=first_complex.readlines()
first_complex_lines=map( string.strip, first_complex_lines )
first_complex.close()

second_complex=open( "residue_a_chain_a_c_backup.txt", "r" )
second_complex_lines=second_complex.readlines()
second_complex_lines=map( string.strip, second_complex_lines )
second_complex.close()
list_1=[]
list_2=[]
for x in first_complex_lines:
    if x[0]!="d":
        list_1.append( x )
for y in second_complex_lines:
    if y[0]!="d":
        list_2.append( y ) 
j=0
list_3=[]      
list_4=[]
for a in list_1:
    pass
    for b in list_2:
        pass
        if a==b:
            list_3.append( a )    

kvmap=defaultdict( int )
for k in list_3:
    kvmap[k]+=1 
print kvmap

Normally I use izip or izip_longest to club two for loops, but this time the length of the files are different. I don't want a None entry. If I use the above method, the run time becomes incremental and useless. How am I supposed to get the two for loops going?

Cheers, Chavanak