Dear Monks,

I came across an unexpected behavior in perl and I would very much like your input on what is happening in my code.

I have an array of which I want to check every element against the keys of a hash containing reference data. Because I want to be able to exclude options (genomes in this example) I want to put a '-' in front of genomes I want to exclude later on. The code below is meant to check if I have provided correct genome names and did not misspell them.

In the first peace of code I am manipulating $_ in a foreach loop. But somehow this ends up manipulating my array @species. The last element which initially contained '-CIOINT' now contains 'CIOINT', the - is removed.

In the code below that I'm doing the same but now I am not manipulating $_. The array is not changed.

I am not working with references so I am very curious as to why the array has changed in the first instance. I'm running perl 5.8.8 on a linux machine. Could someone clarify what happens in the first peace of code? I would be very grateful because it's racking my brain!

John

Below is the isolated code with the faulty and working code in it.

#!/usr/bin/perl

use warnings;
use strict;

my %refspecies = (
    HOMSAP => 'Homo sapiens',
    MUSMUS => 'Mus musculus',
    CIOINT => 'Ciona intestinalis'
    );

my @species =('HOMSAP','MUSMUS','-CIOINT');
my @duplicate = @species;

# Incorrect working code
print "Before processing: @species\n";

foreach (@species) {
    /^-?(.+)$/;
    $_ = $1;
    unless (exists $refspecies{$_}) { # Species not in list
        die "$_ is not in the species table\n";
    }
}

print "After processing: @species\n";

#Correct working code
#Duplicate run with minor code adjustment
print "Before processing: @duplicate\n";

foreach (@duplicate) {
    /^-?(.+)$/;
    #$_ = $1; Removed this line and changed $_ below in $1. This shoul
+dn't matter because I am manipulating $_ in the code above and NOT @s
+pecies, but somehow it does!
    unless (exists $refspecies{$1}) { # Species not in list
        die "$1 is not in the species table\n";
    }
}

print "After processing: @duplicate\n";

#Output is:
#Before processing: HOMSAP MUSMUS -CIOINT
#After processing: HOMSAP MUSMUS CIOINT
#Before processing: HOMSAP MUSMUS -CIOINT
#After processing: HOMSAP MUSMUS -CIOINT

# Look at @species element 3. Why is @species changed?
[download]

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