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Gmane
From: <blpapery <at> gmail.com>
Subject: BioPerl parse interproscan xml not working
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 6th November 2013 15:35:42 UTC (over 2 years ago)
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 
/System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level/XML/Parser.pm

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:


http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
    
        MKYKHLILSLSLIMLGPLAHAEEIGSVDTVFKMIGPDHKIVVEAFDDPDVKNVTCYVSRAKTGGIKGGLGLAEDTSDAAISCQQVGPIELSDRIKNGKAQGEVVFKKRTSLVFKSLQVVRFY
DAKRNALAYLAYSDKVVEGSPKNAISAVPVMPWRQ
        
        
            
                
                    
                    
                        
                    
                    
                
                
                    
                
            
        
    





Thanks in advance for your help.

Ben
 
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