#!/usr/bin/perl
 use strict;
 use warnings;

my %windowSeqScore = ();                

my $input_file = '/scratch/Drosophila/dmel-all-chromosome-r6.02.fasta';

my $sequenceRef = loadSequence($input_file);

my $output_file = 'unique12KmersEndingGG.fasta';
open (KMERS,">", $output_file) or die $!;

my $windowSize = 21;                    
my $stepSize = 1;                       

for ( my $windowStart = 0 ; $windowStart <= ( length ( $$sequenceRef ) - $windowSize );
                $windowStart += $stepSize ) {
        my $windowSeq = substr ( $$sequenceRef, $windowStart, $windowSize);

       if ($windowSeq =~ /([ATCG]{10}GG$)/) {
                $windowSeqScore{$windowSeq}++;
        }
}

my $count = 0;                          

for (keys %windowSeqScore){             
        $count ++;                    
        if ($windowSeqScore{$_} == 1 ) {
        print KMERS ">crispr_$count", "\n", $_, "\n";
       }
}
sub loadSequence {
        my ($sequenceFile) = @_;        
        my $sequence = "";              
        unless ( open( FASTA, "<", $sequenceFile ) ) {
                die $!;
        }
        while (<FASTA>){                
                my $line = $_;          
                chomp ($line);          
                if ($line !~ /^>/ ) {   
                $sequence .= $line;     
                }
        }
        return \$sequence;
}