my ($c, $species) = (0, $ARGV[0]);

open my $outfh, '>', $species . ".new" || die $!;

while(<>) {
    chomp;
    if(length) {
        my ($seq, $scount) = split /\s+/;
        if($scount >= 2 && length $seq >= 15 && length $seq <= 30) {
            print $outfh ">$species" . $c++ . "_count=$scount\n$seq\n";
        }
    }
    if (eof()) {
        ($species, $c) = ($ARGV[0], 0);
        close $outfh || die $!;
        open $outfh, '>', $species . ".new" || die $!;
    }
}