Ok sorry for my habit i include strict and warning when i wrote here! This is my code and now isn't running! 

use strict;
use warnings;
use Data::Dumper;
my $mio2;
my $mio;
my $line;
my $line2;
my $words;
my $words2;
my $i=0;
my %go_accession_hash=();
open (FILE, "/Users/Pabli/Desktop/gene_association.goa_human");
open (FILE2, "/Users/Pabli/Desktop/go3.obo");  

while(<FILE>) { 
                   
    my @array_with_all_fields=split(/\t/);
    
    if ($array_with_all_fields[2] eq "TP53"){
    
       $mio=$array_with_all_fields[4];
       open my $out_file, '>>', 'myoutputfilename.txt' or die "$!"; 
       
       #print "".$mio."\n"; 
       print $out_file $mio; # print to file

    }
    
    
    #print "".$mio."\n"; 
    
       #}
       #%go_accession_hash=($mio,'');
       
    #my @test2= keys %go_accession_hash;
    
    #print "".$test2[0]."\n";
   
    #print "".$mio."\n"; 
}

open (FILE3, "/Users/Pabli/Documents/workspace/PerlProva/myoutputfilen
+ame.txt");

while($line=<FILE2>){
   $words2 = split(" ",$line);
   print "$words2[1]\n";        
  $i=2; 
while($line2=<FILE3>){
    $i = $i - 1;
    if ($i >= 0)
    {
        $words = split(" ",$line2);
         
        #print $words[0]."\n";
    }    
   $mio2=$words[0];
   
   #print "$words2[1]\n";
   #print $words[0]."\n";
}   
    #print "$words2[1]\n"; 
    #print $words[0]."\n";
    #$line= split(/\s+/);
   
   #if ($words2[0] eq "id:") {
        
        #$mio4=$words2[1];
        #print $mio4."\n";
   # }
    
    #elsif ($words2[0] eq "name:"){
    
    #if ($mio4 == $mio2){
    #print "name: ".$words2[1]."\n"; 
            #}
        #}    
    #}     

}  

close FILE;
close FILE2;
close FILE3;

[download]

The error is about "words" and "words2". The program needs global declaration i think so (i did it at first row) but i don't know the way to do it. Thanks

In reply to Re^4: While problem by pabla23
in thread While problem by pabla23

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