print $xml->{gene_seq}{$id}{'startpos'}, "\n";
    

##</code><code>##


#!/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 => 1);# this is what you want
my $xml  = XMLin($data);

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

for my $id (1,2) {
  
    print $xml->{gene_seq}{$id}{'startpos'}, "\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>