[Bioperl-l] BioPerl parse interproscan xml not working

blpapery at gmail.com blpapery at gmail.com
Wed Nov 6 15:35:42 UTC 2013

Hi all,

I have been trying to use Bio::SeqIO to parse an XML interproscan result 
(XML version 1.0 is what interproscan outputs),
but I keep getting the following error:

no element found at line 24, column 0, byte 1421 at 
line 187

My code is below:

use Bio::SeqIO;

$io = Bio::SeqIO->new(-format => "interpro",-file   => "ipr.xml");

  while ($seq = $io->next_seq) {
    print $seq->accession; # trying to print out anything here

XML file is shown below:

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
        <xref id="ecoli_3"/>
            <hmmer3-match evalue="1.0E-57" score="193.0">
                <signature ac="PF05981" desc="CreA protein" name="CreA">
                    <entry ac="IPR010292" desc="Uncharacterised protein 
family CreA" name="Uncharacterised_CreA" type="FAMILY"/>
                        <model ac="PF05981" desc="CreA protein" 
                    <signature-library-release library="PFAM" 
                    <hmmer3-location env-end="157" env-start="24" 
score="192.8" evalue="1.2E-57" hmm-start="1" hmm-end="128" hmm-length="0" 
start="24" end="156"/>

Thanks in advance for your help.


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