#! /usr/bin/perl -w
# i worked with homayun mehrabani
open (FILE, $ARGV[0]) || die "Could not open file!\n";

$dna = "";
$revdna = "";
$firstline = "";
$length = 0;

while ($line = <FILE>) {
	chomp $line;

	if  ($line =~ /^>/) {
		if ($firstline ne ""){
			$length = length ($dna);
			print "$firstline, $length bp\n";
			$firstline = $line;
		}

		else {
			$firstline = $line;
		}
		
		if ($dna ne "") {
			$revdna = reverse ($dna);

			if (defined ($ARGV[1])) {
				if ($ARGV[1] eq "rna") {
					$revdna =~ tr/AGTC/UCAG/;
					$start = 0;
				while ($start <= $length) {
					$printstring = substr($revdna, $start, 80);
					print "$printstring\n";
					$start = $start +80
				}
				$dna = "";
				}
			}
			else {
				$revdna =~ tr/AGTC/TCAG/;
				$start = 0;
				while ($start <= $length) {
					$printstring = substr ($revdna, $start, 80);
					print "$printstring\n";
					$start = $start +80;
				}
				$dna = "";
			}
		}
	}
	else {
		$dna.=$line;
	}
	}


	$revdna = reverse ($dna);
	if (defined ($ARGV[1])) {
		if ($ARGV[1] eq "rna") {
			$revdna =~tr/AGTC/UCAG/;
		}
	}
	else {
		$revdna =~ tr/AGTC/TCAG/;
	}
	$length = length ($dna);
	print "$firstline, $length bp\n";
	$start = 0;
	while ($start <= $length) {
		$printstring = substr ($revdna, $start, 80);
		print "$printstring\n";
		$start +=80;
	}