Thanks a lot BrowserUk!!!

As you suggested I read the csv file line by line and did a search directly in the hash and completed the task in 6 seconds!

sub dataextractor($)
{
    my $input = shift;
    my $output = shift;
    my $order = shift;
    my (@data);
    open(OUT,">".$output) or die "Can't open the file $output\n";
    open(IN,"<".$input) or die "Can't open the file $input\n";
    while (<IN>)
    {
        if ($. eq 1)
    {
        print OUT $_;
        next;
    }
    s/\r?\n$//;
    @data = split (',',$_);
    if ($data[1] eq $site_peakhr{$data[$order]})
    {
        print OUT $_."\n";
    }

    }#while
    close(IN);
    close(OUT);
    return($output);    
}
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