use warnings;

$average_length = 0;
srand(time|$$);

open (DOG, ">>/RandGenNew/filelist.txt") || die "Couldn't open DOG.\n";

for ($p=1; $p<2001; $p++)
{
	$filename = ">>/RandGenNew/Genes/RandGen-";
	$filename .= $p;
	$filename .= ".txt";
	$sequence = "ORIGIN";
	$sequence .= "\n";
	$sequence .= "atg";
	print DOG $filename;
	print DOG "\n";
        open (CAT, $filename ) || die "Couldn't open CAT.\n";

	$number_exons = int(rand(20));
	$number_exons = $number_exons + 1;
	print "Number of middle exons: $number_exons \n";


		#First exon
		$length_first_exon = int(rand(200));
		$length_first_exon = $length_first_exon + 50;

		for ($k=1; $k<$length_first_exon; $k++)
			{
			$number = int(rand(1000));
			if($number <= 300)
				{
				$sequence .= "c";
				}
			elsif($number > 300 && $number <= 630)
				{
				$sequence .= "g";
				}
			elsif($number > 630 && $number <= 820)
				{
				$sequence .= "t";
				}
			elsif($number > 820 && $number <= 1000)
				{
				$sequence .= "a";
				}
			}

		#Middle exons
		for ($i=1; $i<$number_exons; $i++)
			{
			$size = 0;
			$size = int(rand(500));
			$size = $size + 50;
			
		for ($t=1; $t<$size; $t++)
			{
			$number = int(rand(1000));
			if($number <= 250)
				{
				$sequence .= "c";
				}
			elsif($number > 250 && $number <= 500)
				{
				$sequence .= "g";
				}
			elsif($number > 500 && $number <= 725)
				{
				$sequence .= "t";
				}
			elsif($number > 725 && $number <= 1000)
				{
				$sequence .= "a";
				}
			}
		}

		#Last exon
		$length_last_exon = int(rand(200));
		$length_last_exon = $length_last_exon + 50;
		
			for ($o=1; $o<$length_last_exon; $o++)
			{
			$number = int(rand(1000));
			if($number <= 230)
				{
				$sequence .= "c";
				}
			elsif($number > 230 && $number <= 460)
				{
				$sequence .= "g";
				}
			elsif($number > 460 && $number <= 740)
				{
				$sequence .= "t";
				}
			elsif($number > 740 && $number <= 1000)
				{
				$sequence .= "a";
				}
			}

	print CAT $sequence;
	$average_length = $average_length + length $sequence;
	close (CAT);
}
$average_length = $average_length / $p;
$average_length = int($average_length);
print "Average length is $average_length bases.";
print DOG "\n";
print DOG "Average length is $average_length bases.";
close (DOG);
exit;