This is really frustrating me. The script I'm writing is indexing coordinates in a hash and then using those index numbers to pull out values from an array.

The weird thing is that if the value begins with 2 or 22 it will not print. Any other number works. I'll show you two variations and output of the script.

First variation. This is what I want the script to do. Print chromosome, position, value.

                                                    
#!/usr/bin/perl

use strict;
use warnings;
use File::Find;
use Scalar::Util qw(looks_like_number);

open IN, "/home/big/scratch/affy_map.txt" or die "Cannot open referenc
+e\n";
my %ref;
my $head = <IN>;
my $index = 0;
while(<IN>){
    chomp $_;
    my @row = split /\t/, $_;
    my $value = join "\t", $row[1],$row[2];
        if($row[1] == 2 && $row[2] <= 50000 && $row[2] <= 51113178) { 
+$ref{$index}=$value; print $index."\t".$value."\n";}
        if($row[1] == 22 && $row[2] <= 16300001 && $row[2] <= 20500000
+) { $ref{$index}=$value; print $index."\t".$value."\n"; }
        $index++;
}
close(IN);

my @files;
my $masterDirect = "/nfs/archive02/big/Norm/norm_gcc/";

find(\&file_names, $masterDirect);

sub file_names {

  if( -f && $File::Find::name=~/\.nzd$/)
   {
       push @files, $File::Find::name;

     }
 }

my $count=0;
foreach(@files){
    $count++;
    if($count % 100 == 0 ){ print "\n","-" x 10, " $count ", "-" x 10,
+"\n";}
    undef my @probes;
    open IN, $_;

    #file name handling
    my @inDir = split "\/", $_;
    my $id = pop(@inDir);
    $id =~ s/\.gcc.nzd$//;

    #header test
    $head =<IN>;
    if(looks_like_number($head)) { push @probes, $head; }

    #open output
    open OUT, ">/home/big/scratch/phase1_affy/".$id."_select_probeset.
+txt";

    #load probe array
    @probes = <IN>;
    close(IN);
    foreach my $key (sort keys %ref){
       #intended function
        print OUT $ref{$key}."\t".$probes[$key];
       #testing   
       my @temp = split "\t", $ref{$key};
        foreach(@temp){if($temp[0] == 2){print $key."\t".$ref{$key}."\
+t".$probes[$key];}}
    }
    close(OUT);
}
[download]

Here's the output for the test. The printing from the reference file is flawless. The first number is the $key or index number. The second is frome $probes$key why is the $ref{$key} missing?

146529  0.777314368326637
146529  0.777314368326637
146530  0.116241153901913
146530  0.116241153901913
146531  0.940593233609167
146531  0.940593233609167
146532  -0.150051720847835
146532  -0.150051720847835
146533  0.037500790454267
146533  0.03750079045426
[download]

Variation 2.

...
 foreach my $key (sort keys %ref){
        print OUT $ref{$key}."\t".$probes[$key];
        my @temp = split "\t", $ref{$key};
        foreach(@temp){if($temp[0] == 2){print $key."\t".$ref{$key}."\
+n";}}
    }
[download]

And its output. See now it's printing correctly. $key and $ref{$key}

146542  2       31852
146542  2       31852
146543  2       37693
146543  2       37693
146544  2       40415
146544  2       40415
146545  2       40814
146545  2       40814
146546  2       41256
146546  2       41256
146547  2       43652
146547  2       43652
[download]

I'm not as experienced as a lot of you monks out there but I've never experienced this error. I thought it might be a DOS->UNIX file problem but I performed perl -pi -e 's/\R/\n/g' input_files.txt for all the input the script sees. It prints the same value twice because there are two elements in the @temp array. I'm really at a loss right now.