chr1 3204562 3661779 chr1 4334223 4350673 chr1 4481008 4486694 chr1 4764014 4775968 chr1 4797773 4836816 chr1 4847574 4887987 chr1 4847574 4887987 chr1 4848208 4887987 chr1 4900049 5009660 chr1 5073053 5152630 #### Xkr4 chr1 3204562 3661779 - 3 457.217 Rp1 chr1 4334223 4350673 - 4 16.45 Sox17 chr1 4481008 4486694 - 5 5.686 Mrpl15 chr1 4764014 4775968 - 5 11.954 Lypla1 chr1 4797773 4836816 + 9 39.043 Tcea1 chr1 4847574 4887987 + 10 40.413 Tcea1 chr1 4848208 4887987 + 10 39.779 Rgs20 chr1 4900049 5009660 - 5 109.611 #### open(FILE, @ARGV[0]) || die ("could not open file @ARGV[0]\n"); while (my $line = ) { chomp $line; my ($chr, $start, $stop) = split(/\t/, $line); } close FILE; open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n"); while(){ ($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= split; foreach (line in genes.db){ # I don't know what to put here. if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModEnd){ $Count++; print ;($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB,$Count) } }