Consider using XML::Twig, which can parse large files without consuming a lot of memory: 
#!/usr/bin/perl
use warnings;
use strict;
use XML::Twig;
use feature 'say';

my $parser = XML::Twig::->new(
    twig_handlers => {
        '/pathway/reaction[@name=~/^rn:/]' => \&handle,
                # use XPath to describe what you want to handle
    }
);

$parser->parsefile("myfile");

sub handle {
    my($twig, $elt) = @_;
        # handlers are given an XML::Twig object and an XML::Twig::Elt
+ object
    say $elt->att("name");
    say " substrate[s]: ", map { $_->att("id")." " } $elt->children("s
+ubstrate");
    say " product[s]: ", map { $_->att("id")." " } $elt->children("pro
+duct");
}

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Sorry if my advice was wrong.

In reply to Re: Parsing an XML file by aitap
in thread Parsing an XML file by zing

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