my @file1 = ();
open(FILE, @ARGV[0]) || 
	die ("could not open file @ARGV[0]\n");

    while (my $line = <FILE>) {
	chomp $line;
	my ($chr, $start, $stop) = split(/\t/, $line);
        push @file1, [$chr, $start, $stop];
	}
close FILE;

open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n");
	
	while(<FILE>){
		($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= split;		
#		foreach (line in genes.db){   # I don't know what to put here.
		foreach my $line (@file1){
			my ($chr, $start, $stop) = @$line;
			if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModEnd){
			$Count++;
			print ;($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB,$Count)
			}	
	}