Re: Problem of context?

[hippo]

You have declared @test2 inside an if block inside the first while loop. As soon as execution leaves the if block the array goes out of scope. See Coping with Scoping for more details.

Update: Example - compare these two:

use strict;
my $foo = 0;
for (1..5) { $foo += $_; }
print $foo;

and

use strict;
for (1..5) {
    my $foo = 0;
    $foo += $_;
}
print $foo;

In each case the scope of $foo ends at the end of the block enclosing its declaration. Since the first example has the declaration outside the loop the scope persists to the end of the script. In contrast, the second example gives $foo scope only until the end of the for loop thus making the $foo in the print statement undeclared which will be trapped at compile time.

[pabla23]

Thanks! But for example:

use strict;
use warnings;
use Data::Dumper;
open (FILE, "/Users/Pabli/Desktop/gene_association.goa_human");
open (FILE2, "/Users/Pabli/Desktop/go3.obo");  

my %go_accession_hash=();
while(<FILE>) { 
                   
    my @array_with_all_fields=split(/\t/);
  
    if ($array_with_all_fields[2] eq "TP53"){
    
       my $mio=$array_with_all_fields[4];
       %go_accession_hash=($mio,'');
  
    }
    print "".Dumper(%go_accession_hash)."\n";
    my @test2= keys %go_accession_hash;
  
    }
         
while(<FILE2>){
    
    print "".$test2[0]."\n";

}
close FILE;
close FILE2;

When i print the entire hash table outside from the "if", it prints only the last element (key) of the hash table for "n" times and i don't understand the reason!

Thanks for help

Paola

[choroba]

You are overwriting the hash in each step:

%go_accession_hash=($mio,'');

To set a single key-value pair, use the following syntax:

$go_accession_hash{$mio} = '';

[biohisham]

Are all the entries in the fifth column of my $mio=$array_with_all_fields[4] unique ?

If the answer is "yes" then your hash can be re-written as has been suggested to you (i.e.  %go_accession_hash{$mio}=' ';). If the answer is "no" then you might want to consider using an advanced data structure that is more appropriate to capture each variation associated with $mio.

In order to help you understand the problem and solution better It will be more useful to actually show a representative example of how your data look like and what you want to achieve from reading it in.

[pabla23]

Thanks so so so much for your help! The situation is complicated and i'm new in "Perl"! Then: if i print "array_with_all_fields4" this is my output:

GO:0000060 GO:0000122 GO:0000979 GO:0001077 GO:0001701 GO:0001756 GO:0001836 GO:0002309 .....

After i store this output into "mio" for a particular need. After i store "mio" into an hash table as the keys of the hash table. If i print the hash table this is the output:

$VAR1 = 'GO:0000060'; $VAR2 = ''; $VAR1 = 'GO:0000122'; $VAR2 = ''; $VAR1 = 'GO:0000979'; $VAR2 = ''; $VAR1 = 'GO:0001077'; $VAR2 = ''; $VAR1 = 'GO:0001701'; $VAR2 = ''; .....

the final step for me is to store keys into an array "test2" and after use this array in another "while" and in another "FILE2".

I know that is so difficult to explain but if you want i can write to you from my personal mail!

Thaks a lot Paola

[Anonymous Monk]

you're not checking for errors :) autodie