hi all , I have written a script to count the number of RNAs that have exact matches to the genome. the code works just fine. but the problem is I would like to improve the code make that work faster. the genome has 5 chromosomes. and they are all >= 3045655 (in length) 
#!/usr/bin/perl -w
use DBI;
use strict;
use Bio::SeqIO;
use Bio::Perl;
use GD::Graph::bars; 

$|=1;

my $window_size = 500;
my $step_size = 500;

my $connect;
my $database = 'Cloned_RNA_2_dev';
my $user ='root';
my $pass = '';
my $host = 'localhost';
my %sequences;
my $total_length;
my $length;
open (RESULT, ">result.csv");
my $dsn = qq(DBI:mysql:database=$database; host=$host);

$connect = DBI-> connect($dsn, $user, $pass,{printError =>1}) or die $
+DBI::errstr;

#querying the database
my $query = qq/select count(c.Rna_sequence_sequence) 
    from Cloned_rna c, Hsp h  
    where c.Rna_sequence_sequence=h.Rna_sequence_sequence
    and c.Project_idproject =72
    and h.Sequence_db_idSequence_db =1133
    and h.accession =?
    and h.hit_start >= ? 
    and h.hit_end<=?
    group by h.accession/;


    
my $sql = $connect->prepare($query);
my %window_counts ;

print RESULT "\"Chromosome\"\t\"start\"\t\"end\"\t\"counts\"\n" ;
my $genome = Bio::SeqIO->new(-file=>'/home/shared-projects/sequence-db
+s/TAIR7/TAIR7_nuclear_genome.fna', -format=>'fasta');

while (my $seq = $genome->next_seq()){
    $length = $seq->length();
    my $id =$seq->id();
    warn "Processing on Chromosome $id\n";
#walking along the genome 
    for(my $i=1;$i<=($length-$window_size); $i+=$step_size){
    my $window_start = $i;
    my $window_end = $i+$window_size-1;

    my $sucess=($sql->execute($id, $window_start, $window_end));
    die "query failed!\n $query \n" unless $sucess;
    my $window_id = "$id,$window_start" ;
    if (my @result = $sql->fetchrow_array() ) {        
       ( $window_counts{$window_id})= @result; # has the counts as the
+ value of the hash
        
        warn "\$window_counts{$window_id}='$window_counts{$window_id}'
+\n";
       
        print RESULT "$id\t$window_start\t$window_end\t$window_counts{
+$window_id}\n" ;

    }
        #    exit if $i > 50000;

      
    }
}

[download]
is there any other way to do this??? thanks in advance.

In reply to how to improve this? by sirna

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