#!/usr/bin/perl -w

use strict;
use warnings;
use XML::Simple;
use Data::Dumper;

my $data = do {local $/;<DATA>};
my $xml  = new XML::Simple(keeproot => 2);# this is what you want
$xml  = XMLin($data);

print Dumper($xml), "\n\n";

for my $id (keys %{ $xml->{gene} }) {
  # print $xml->{gene}{$id}{'label'}, "\n";
   # print $xml->{gene_seq}{$id}{'label'}, "\n";
    print $xml->{gene}{$id}{gene_seq}{'startpos'}, "\n";
#print "$xml->{'gene'}{'id'}, $xml->{'gene'}{'label'}\n";
}

__DATA__
<?xml version="1.0" ?>
<many_genes>
 <gene id = "1" label = "gene_of_interest">
  <gene_seq id = "1" startpos = "5999"/>
 </gene>
 <gene id = "2" label = "Another_gene_of_interest">
  <gene_seq id = "2" startpos = "96819"/>
 </gene>
</many_genes>
[download]

yields

$VAR1 = {
          'gene' => {
                      '1' => {
                               'gene_seq' => {
                                               'startpos' => '5999',
                                               'id' => '1'
                                             },
                               'label' => 'gene_of_interest'
                             },
                      '2' => {
                               'gene_seq' => {
                                               'startpos' => '96819',
                                               'id' => '2'
                                             },
                               'label' => 'Another_gene_of_interest'
                             }
                    }
        };


5999
96819

It's like a tree ;)

# you start with
$xml->{gene}->{1}->{gene_seq}->{startpos};
# and you make it variable
$xml->{gene}->{$id}->{gene_seq}->{startpos};
# and its same as
$xml->{gene}{$id}{gene_seq}{startpos};
$$xml{gene}{$id}{gene_seq}{startpos};
$$xml{gene}->{$id}{gene_seq}->{startpos};

MJD says you can't just make shit up and expect the computer to know what you mean, retardo! ** The Third rule of perl club is a statement of fact: pod is sexy.