Hello Wonderful Perl Monks! I have a tab delimited text file made up of many lines of numerical entries, for example: 


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

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...etc. The fifth element of each line corresponds to the locus along a chromosome.

What I would like to do is:

-identify each line by its locus

-sort the lines in the same format to smaller files, grouping them by location along the chromosome.

So, all lines with loci between 1 and 1,000,000 go to one file, lines with a loci between 1,000,001 and 2,000,000 go to the next file ...etc.

and so here is my code 


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

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

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


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

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I print out the correct first temp_2.txt file but no lines are printed to it

I then receive a continuous 

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

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and there are no spaces at the end of my input file, I checked. Any wisdom is much appreciated!

In reply to Use of Uninitialized in Concatenation or String Error? by ccelt09

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