Hi monks! I am trying to count all the elements using hash but i get the error 'out of memory'. I have a fasta file as input, and i create an array with individual aminoacids as elements. Then i create an hash and count the elements of this array. But is there a more efficient way of doing this without much memory usage? The input file is 32Mb. Thanks 
#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;
open PROTEOME,'human_complete_proteome_without_isoforms.fasta';
my @proteome=<PROTEOME>;
chomp @proteome;
my @aminoacid;
my @hold;
my $peptide;
foreach my $j (@proteome)
{
    if($j!=/^>/)
    {
        
        push @hold,$j;
    }
}
print "The proteome is loaded\n";
$peptide= join ('', @hold);
undef @hold;
@aminoacid=split(//,$peptide);    
my %count;
foreach (@aminoacid)
{
    if(exists $count{$_})
    {
        $count{$_}++;
    }
    else
    {
        $count{$_}=1;
    }
}
print "hash has finished searching the document\n";
foreach (keys %count)
{
    print "$_ \t occurs $count{$_} times \n";
}

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In reply to Count the occurrence of an element in an array by rocketperl

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