perl XML::Simple for repeated elements - perl

Question

I have the following xml code
<?xml version="1.0"?>
<!DOCTYPE pathway SYSTEM "http://www.kegg.jp/kegg/xml/KGML_v0.7.1_.dtd">
<!-- Creation date: Aug 26, 2013 10:02:03 +0900 (GMT+09:00) -->
<pathway name="path:ko01200" >
<reaction id="14" name="rn:R01845" type="irreversible">
<substrate id="108" name="cpd:C00447"/>
<product id="109" name="cpd:C05382"/>
</reaction>
<reaction id="15" name="rn:R01641" type="reversible">
<substrate id="109" name="cpd:C05382"/>
<substrate id="104" name="cpd:C00118"/>
<product id="110" name="cpd:C00117"/>
<product id="112" name="cpd:C00231"/>
</reaction>
</pathway>
I am trying to print the substrate id and product id with following code which I am stuck for the one that have more than one ID. Tried to use dumper to see the data structure but I don't know how to proceed. I have already used XML simple for the rest of my parsing script (this part is a small part of my whole script ) and I can not change that now
use strict;
use warnings;
use XML::Simple;
use Data::Dumper;
my $xml=new XML::Simple;
my $data=$xml->XMLin("test.xml",KeyAttr => ['id']);
print Dumper($data);
foreach my $reaction ( sort keys %{$data->{reaction}} ) {
print $data->{reaction}->{$reaction}->{substrate}->{id}."\n";
print $data->{reaction}->{$reaction}->{product}->{id}."\n";
}
Here is the output
$VAR1 = {
'name' => 'path:ko01200',
'reaction' => {
'15' => {
'substrate' => {
'104' => {
'name' => 'cpd:C00118'
},
'109' => {
'name' => 'cpd:C05382'
}
},
'name' => 'rn:R01641',
'type' => 'reversible',
'product' => {
'112' => {
'name' => 'cpd:C00231'
},
'110' => {
'name' => 'cpd:C00117'
}
}
},
'14' => {
'substrate' => {
'name' => 'cpd:C00447',
'id' => '108'
},
'name' => 'rn:R01845',
'type' => 'irreversible',
'product' => {
'name' => 'cpd:C05382',
'id' => '109'
}
}
}
};
108
109
Use of uninitialized value in concatenation (.) or string at line 12.
Use of uninitialized value in concatenation (.) or string at line 13.

Answer 1

First of all, don't use XML::Simple. it is hard to predict what exact data structure it will produce from a bit of XML, and it's own documentation mentions it is deprecated.
Anyway, your problem is that you want to access an id field in the product and substrate subhashes – but they don't exist in one of the reaction subhashes
'15' => {
'substrate' => {
'104' => {
'name' => 'cpd:C00118'
},
'109' => {
'name' => 'cpd:C05382'
}
},
'name' => 'rn:R01641',
'type' => 'reversible',
'product' => {
'112' => {
'name' => 'cpd:C00231'
},
'110' => {
'name' => 'cpd:C00117'
}
}
},
Instead, the keys are numbers, and each value is a hash containing a name. The other reaction has a totally different structure, so special-case code would have been written for both. This is why XML::Simple shouldn't be used – the output is just to unpredictable.
Enter XML::LibXML. It is not extraordinary, but it implememts standard APIs like the DOM and XPath to traverse your XML document.
use XML::LibXML;
use feature 'say'; # assuming perl 5.010
my $doc = XML::LibXML->load_xml(file => "test.xml") or die;
for my $reaction_item ($doc->findnodes('//reaction/product | //reaction/substrate')) {
say $reaction_item->getAttribute('id');
}
Output:
108
109
109
104
110
112