chrX    1    1000000
chrX    1000001    2000001
chrX    2000001    3000001

...etc.


##</code><code>##

open (INTERVAL, "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/galaxy_chrX_data/chrX_1Mbwindow_nonoverlapping.interval") or die "can't open file\n";

while (my $interval = <INTERVAL>){ 
		
		chomp($interval);
		my @find_interval = split(/\t/, $interval);
		my $start = $find_interval[1];
		my $end = $find_interval[2];

##</code><code>##

	
		my $switch = 1; 
		
		while ($switch == 1) {
			
		open (CG, "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/CompleteGenomics/28_males_inAll/CGS.inall.28.chr.23.txt") or die "can't open CG 	file\n";
		
		my $output_file = "/Users/logancurtis-whitchurch/Desktop/temp_$count.txt";
			open(OUT, ">$output_file");

##</code><code>##

   my @SNPs = <CG>; 
		my @get_SNP = split(/\t/, $SNPs[$placeholder]); 
		my $position = $get_SNP[3]; 

##</code><code>##

 my $switch = 1; 
		
		while ($switch == 1) {
					
			if (($position < $end) && ($position >= $start)) {
			
			print OUT "$SNPs[$placeholder]\n";
				$placeholder++;
			}
			
			else {
			$switch = 0;	
			$count++;		
			}
			

		}
		}