This seems to be more or less what you are looking for: 
use strict;
use warnings;

my ($mio, $mio2);     

my $filename = '/Users/Pabli/Desktop/do_human_mapping.gmt';
my $match = 'DOID:2055';
unlink ("myoutputfilename3.txt");
unlink ("myoutputfilename4.txt");
open(my $file, '<', $filename) or die "open: $!";

open my $out_file3, '>', 'myoutputfilename3.txt' or die "$!"; 
open my $out_file4, '>', 'myoutputfilename4.txt' or die "$!"; 

while (<$file>){
  my ($name,$id,@genes) = split /\t/;
  if ($id eq $match) {
     $mio= join("\n",@genes);
     print $mio."\n";

     print $out_file3 $mio."\n"; # print sul file
  }
  if (grep/^$match$/, @genes){
       $mio2=$id;
       print $mio2."\n";

       print $out_file4 $mio2."\n"; # print sul file
   }
}

[download]
I have taken the liberty to move the opening of the files out of the while loop, because it seems inefficient to open the file each time you get a match, but it really depends on you data (how often it matches).

In reply to Re: Unify two files by Laurent_R
in thread Unify two files by pabla23

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