I am try to search for the number of occurrence of 10 hexamer word in a big file of fasta sequence.
Did you try using BioPerl (http://bioperl.org)?

for($i = 1;$i < 5000;$i++)
{
        for($j = 0;$j <= $#words;$j++)
        {
                $result[$i][$j] = 0; # array of 5000 columns of positi
+on and words as columns 
        }
}

[download]
If you want to initialise your array for better handling of large data, look there: Re^3: how apply large memory with perl?. By the way, this initialisation is lost because you initialize an array and work later with a hash reference. strict would never allow it.

Sorry if my advice was wrong.

In reply to Re: Dumb problem with dumper. by aitap
in thread Dumb problem with dumper. by oxydeepu

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