99269
550
100
126477 
1700
##</code><code>##

517 1878 forward
700 2500 forward
2156 3289 forward
99000 100000 forward
22000 23000 backward 
##</code><code>##

99269 99000 100000 forward
550 517 1878 forward
1700 517 1878 forward 
##</code><code>##

 

#!/usr/bin/perl 

use strict;
use warnings;

my $outputfile = "/Users/edwardtickle/Documents/CC22CDS.txt"; 

open FILE1, "/Users/edwardtickle/Documents/CC22positions.txt" 
	or die "cannot open > CC22: $!";
	
open FILE2, "/Users/edwardtickle/Documents/CDSpositions.txt" 
	or die "cannot open > CDS: $!";	

open (OUTPUTFILE, ">$outputfile") or die "Could not open output file: $! \n";

while (<FILE1>) {
	if (/^(\d+)/) {
	my $CC22 = $1;	
		
		while (<FILE2>) {
		if (/^(\d+)\s+(\d+)\s+(\S+)/) {
		my $CDS1 = $1;
		my $CDS2 = $2;
		my $CDS3 = $3;
	
			if ($CC22 > $CDS1 && $CC22 < $CDS2) {
				print OUTPUTFILE "$CC22 $CDS1 $CDS2 $CDS3\n";
					}
				}
			}
		}
	}
	
close(FILE1);
close(FILE2);