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my ($c, $species) = (0, shift());

...
    next if $scount < 2 || length $seq < 15 || length $seq > 30;
    print ">$species" . $c++ . "_count=$scount\n$seq\n";
}

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

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