#!/usr/bin/perl

use Data::Dumper;

open $f,$ARGV[0];

while(<$f>)
{
        chomp;
        $id = $_; #eat up the header line
        chomp($s = <$f>);
        if($s !~ /^>/)
        {
        	push @seq,$s;    
        }
}

open $fa, "top_10_hexamers.txt";

while(<$fa>)
{
        chomp;
        $hx{$_}++; #hash of 10 hexamer
}

@words = sort keys %hx;

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

foreach $x(@seq)
{
                for($j = 0; $j < (length($x) - 6);$j++)
                {
                        $wrd = substr $x,$j,6;  #getting the hexamer combinations
                        foreach $w(@words)
                        {
                                if($w eq $wrd)  # comparing with the word
                                {
                                        $result->{$j}->{$wrd}++; # trying to get position, word and frequency
                                }
                        }
                }
                $wrd = "";
}
print  Dumper $result;