Hi perl monks, I am trying to compare 2 files with similar data. I want to check if any of the lines in file 1 are contained in File2 and if they aren't to print that line in File 1 (with an additional column 0) and if they are present to print the line from File 2

eg

File 1:

133-1452_chromosomal_replication_initiation_protein_

1457-2557_DNA_polymerase_III_subunit_beta_

2579-3670_recombination_protein_F_

3687-6104_DNA_gyrase_subunit_B_

c8268-7159_aspartate-semialdehyde_dehydrogenase_

c8692-8471_prophage_p2_ogr_protein_

File 2:

c8268-7159_aspartate-semialdehyde_dehydrogenase_ 33

c8692-8471_prophage_p2_ogr_protein_ 574

1457-2557_DNA_polymerase_III_subunit_beta_ 123

Output file:

133-1452_chromosomal_replication_initiation_protein_ 0

1457-2557_DNA_polymerase_III_subunit_beta_ 123

2579-3670_recombination_protein_F_ 0

3687-6104_DNA_gyrase_subunit_B_ 0

c8268-7159_aspartate-semialdehyde_dehydrogenase_ 33

c8692-8471_prophage_p2_ogr_protein_ 574

The files are not sorted in any way, so the lines are not consecutive in either file. I have tried adapting a number of bits of code that I have found on the web, but none of these are working properly. So far I have this:

#!/usr/bin/perl

use strict;
use warnings;

open (OUT,">outputfile.txt");
open my $fh1, '<', 'file1.txt';
open my $fh2, '<', 'file2.txt';

while(
  defined( my $line1 = <$fh1> )
  and
  defined( my $line2 = <$fh2> )
){
  chomp $line1;
  chomp $line2;
  
  my $string = $line2;
  $string =~ m{^*\t};
 print $string."\n";
  if( $line1 eq $string ){
    print OUT $line2."\n";
  }else{
    print OUT $line1."\n";
  }
}

close $fh1;
close $fh2;
close OUT;

[download]

But this just print out a list of lines from the second file. Any help would be appreciated!

In reply to comparing 2 files by garyboyd

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