0   50   2   48   654732   0   1   1   1   0   2   3   2   1   3 
0   50   4   46   723430   0   2   1   2   1   1   1   1   3   1 



##</code><code>##


#!usr/bin/perl -w
use strict;
use warnings;

my $count = 0; 
my $placeholder = 0; 

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];
		
		
		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 @SNPs = <CG>; 
			my @get_SNP = split(/\t/, $SNPs[$placeholder]); 
		
		
		my $position = $get_SNP[3]; 
		
		
		while ($switch == 1) {
			if (($position < $end) && ($position >= $start)) {
			
				
			my $output_file = "/Users/logancurtis-whitchurch/Desktop/temp_$count.txt";
			open(OUT, ">$output_file");
			print OUT "$SNPs[$placeholder]\n";
			close (OUT);


					
				$placeholder++;
			}
			else {
				$switch = 0; 
			}
		}
		$count++
		}
}



##</code><code>##

 Use of uninitialized value within @SNPs in concatenation (.) or string at temp_file_test.pl line 36, <CG> line 1112424.