How to compare lines from two files and print the number of matches and mismatches

jv61 · 08-26-2013, 06:42 AM

Hello everyone,

I want to compare lines from two files and print the number of matches and mismatches for each position in the line.

Code:

My first file has 800 lines like this 

BIN1: ABHHHABBHAB
BIN2: ABBHBBBBBBA

My second file has 10000 lines like this. 

m1: AB--HHABBHA
m2: ABBHBB----A
m3: ABBHBBBBBBA

I want to compare the lines of my second file to the first one and print the results by percentage identity. My results should look like

Code:

m1 matches to BIN1 with 8 matches and 3 mismatches-perenctage identity is 72.7 
m2 matches to BIN2 with 7 matches and 4 mismatches-perenctage identity is 63.6
m3 matches to BIN2 with 11 matches and no mismatches-perenctage identity is 100

Could anyone give me some suggesstions of how to do this?

Thank you,

jpollard · 08-26-2013, 05:06 PM

Have you looked into the diff utility?

Usually something like a percentage of difference is useless.

jv61 · 08-26-2013, 07:11 PM

Just an update, I had a go with String::Approx module in perl and it seems to be getting there. Here is the code

Code:

#!/usr/bin/perl -w

use String::Approx 'amatch';

open (DICT,"first.txt") or die "Can't open dict: $!";
open (PAT,"second.txt") or die "Can't open pattern: $!";
my @in=<DICT>;
my @pat=<PAT>;
my $lines;
my @MATCHED;
my $pat;
my $patl;
foreach $pat(@pat){
my @patl=split('\t',$pat);
 
foreach $lines(@in){
 
if(my @MATCHED=amatch($patl[1],["20%"],$lines))
{
print $patl[0],":",@MATCHED;
} }
}

I am learning to program in perl, any suggestions to improve are welcome

Thanks for the reply jpollard. I haven't tried using diff yet. I will see how it works.

Thanks again