Hash will not print if a value begins with 2 under certain conditions

pimperator has asked for the wisdom of the Perl Monks concerning the following question:

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.

Comment on Hash will not print if a value begins with 2 under certain conditions Select or Download Code

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Re: Hash will not print if a value begins with 2 under certain conditions
by Anonymous Monk on Jul 27, 2014 at 04:00 UTC

too much code , too many file system operations

Where is the problem?

Is the problem with the data structure , or the subroutine doing the printing?

When you Data::Dump::dd()umper up the data structure and read it with your eyes, is everything there?

If you really want more help, you should whittle down your program to this

Read more... (628 Bytes)

Eliminate file system operations for files we don't have, include three lines files that replicate the problem, include them as strings

update: finally I read the whole thing you posted, just dumper up two variables and we can start debugging these two loops

    my %ref    = ... ; ## Data::Dump::dd(%ref)    output here
    my @probes = ... ; ## Data::Dump::dd(@probes) output here
##
    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];
            }
        }
    }
##
    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]

update: now that I've looked at these two loops, well, the inner foreach is completely unneeded .... and aside from the different things you print (one has probles the other doesn't), they're pretty much the same thing

Hope this help, if it doesn't, well, take a break, post short code, we'll figure it out

[reply]
[d/l]
[select]

Re: Hash will not print if a value begins with 2 under certain conditions
by frozenwithjoy (Priest) on Jul 27, 2014 at 04:44 UTC

It may not be related to your problem, but do you really mean for your if conditionals to be the following?

if($row[1] == 2 && $row[2] <= 50000 && $row[2] <= 51113178) {...}
[download]

if($row[1] == 22 && $row[2] <= 16300001 && $row[2] <= 20500000) {...}
[download]

Did you mean for the second comparison in each to actually be $row[2] >= ####?

[reply]
[d/l]
[select]

Re: Hash will not print if a value begins with 2 under certain conditions
by Athanasius (Archbishop) on Jul 27, 2014 at 04:29 UTC

Just a supplement to the advice given by Anonymous Monk:

Data::Dumper provides a Useqq configuration variable which, when set, causes Dumper to print any newline, tab, or carriage return characters as \n, \t, and \r, respectively. This makes it easier to see exactly what is present in each variable. Here is how I would deploy this feature to begin the debugging process:

...
use Data::Dumper;
$Data::Dumper::Indent = 0;
$Data::Dumper::Terse  = 1;
$Data::Dumper::Useqq  = 1;
...
foreach my $key (sort keys %ref) {
    ...
    foreach(@temp) {
        if ($temp[0] == 2) {
            printf "\$key = %s\n  \$ref{%s} = %s\n  \$probes[%s] = %s\
+n",
                    Dumper($key),
                    Dumper($key), Dumper($ref{$key}),
                    Dumper($key), Dumper($probes[$key]);
            print $key."\t".$ref{$key}."\t".$probes[$key];
        }
    }
}
[download]

Hope that helps,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,


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