pabla23 has asked for the wisdom of the Perl Monks concerning the following question:

Good morning! I've this code: 

use strict;
use warnings;
use Data::Dumper;
open (FILE, "/Users/Pabli/Desktop/gene_association.goa_human");
open (FILE2, "/Users/Pabli/Desktop/go3.obo");  
$main::mio;
$main::mio2;
$main::mio4;
$main::words2;
my $i=0;
my %go_accession_hash=();
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

    }
       
}

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

while($line=<FILE2>){
   @words2 = split(" ",$line);
   #print "$words2[1]\n";        
  $i=5; 
while($line2=<FILE3>){
    $i = $i - 1;
    if ($i >= 0)
    {
        @words = split(" ",$line2);
        
    }    
  
}   
    print $words[0]."\n";
   
   
   #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 program out of second "while" prints "$words[0]" not for one time (single row) but for a lot of time! I don't understand the reason! There is a solution? Can someone help me? Thanks Paola

Replies are listed 'Best First'.
Re: While problem
by marto (Cardinal) on Oct 27, 2014 at 09:38 UTC

    "Can someone help me?"

    You could fix the problems perl tells you about when you try to run the script?

    Variable "$mio" is not imported at x.pl line 18.
Variable "$mio" is not imported at x.pl line 22.
Variable "@words2" is not imported at x.pl line 31.
Global symbol "$mio" requires explicit package name at x.pl line 18.
Global symbol "$mio" requires explicit package name at x.pl line 22.
Global symbol "$line" requires explicit package name at x.pl line 30.
Global symbol "@words2" requires explicit package name at x.pl line 31
+.
Global symbol "$line" requires explicit package name at x.pl line 31.
Global symbol "$line2" requires explicit package name at x.pl line 34.
Global symbol "@words" requires explicit package name at x.pl line 38.
Global symbol "$line2" requires explicit package name at x.pl line 38.
Global symbol "@words" requires explicit package name at x.pl line 43.
Execution of x.pl aborted due to compilation errors.

    [download]

    You've been told this before. Also, use the three argument open, and report on errors (for exmaple ... or die "cannot open < input.txt: $!";).

[reply]
[d/l]
[select]
      There isn't any errors!!! This is the outpur of the compiler: 

      GO:0000060GO:0000122GO:0000979GO:0001077GO:0001701GO:0001756
</p>
<p>
GO:0000060GO:0000122GO:0000979GO:0001077GO:0001701GO:0001756
</p>

      [download]
      I want for example only the first row!! Thanks!!
[reply]
[d/l]

        "There isn't any errors!!!"

        Then you are not running the code you posted here. Don't bother posting code here which you aren't actually running, it's a waste of our time. As roboticus pointed out previously:

        "Try posting the code you actually run or don't gratuitously paste in a "use strict; use warnings;" at the beginning if you're not actually using them."

[reply]

        Then you are not running the script that you posted. Please make sure that the code you post and the code you run are the same.

[reply]

        For what it's worth, I get all the same errors marto saw. If you're not seeing any errors, what motivated these lines at the top of your script? :

        $main::mio;
$main::mio2;
$main::mio4;
$main::words2;

        [download]

        In your script there are a number of variables that haven't been prefixed with "my" when initially declared. Fixing those would be a good first step.

[reply]
[d/l]

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