Thank you for the consideration, I truly appreciate it! My data spans 155,000,000 nucleotides. In my original code I opened the file: INTERVALS which stores the windows of varying sizes I'd like to use for sorting,

chrX    1    1000000
chrX    1000001    2000001
chrX    2000001    3000001

...etc.
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the largest being 1Mb (1,000,000) and assigned it to a scalar variable $interval. I chomp this scalar, assign an array to the split function of that $interval scalar and establish $start and $end variables by assigning them to the 1 and 2 array slices respectively. I don't wish to hard code my range because I have multiple windows to work with

open (INTERVAL, "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/g
+alaxy_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];
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from here i used an arbitrary switch variable to control when printing to a given output file should stop and a new file should begin to be printed to.

My condition, while $switch == 1 I open my data input file, specify and open my output file

    
        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 "ca
+n't open CG     file\n";
        
        my $output_file = "/Users/logancurtis-whitchurch/Desktop/temp_
+$count.txt";
            open(OUT, ">$output_file");
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Then with these 3 lines I create an array for the whole input file (@SNPs), make an array from each line or string in the input file (@get_SNP) and create a variable accounting for position ($position) that increments as the data is read via my placeholder variable ($placeholder)

   my @SNPs = <CG>; 
        my @get_SNP = split(/\t/, $SNPs[$placeholder]); 
        my $position = $get_SNP[3];
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I then use an if statement to say if my position in lt or eq to the end and greater than the start, print the $SNP[$placeholder] string corresponding to one data line, then increment $placeholder value, repeating the loop until the if statement is false. Then state else set $switch = 0 ending the while loop. Once this is done I increment a global variable $count that tells the open function to create a new output file since i interpolated the variable $count into the output file name earlier

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

        }
        }
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