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Gmane
From: <blpapery <at> gmail.com>
Subject: Re: BioPerl parse interproscan xml not working
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Friday 8th November 2013 07:08:58 UTC (over 3 years ago)
Thanks Chris, I just filed the bug.

Ben

On Thursday, November 7, 2013 9:25:43 PM UTC-5, Christopher Fields wrote:
>
> This looks like an XML parser issue, not BioPerl.  However, it seems 
> well-formed, and I can reproduce this.  Can you file this as a bug?  We
may 
> need to switch out the backend parser, I don’t believe XML::Parser is 
> well=supported anymore. 
>
> chris 
>
> On Nov 6, 2013, at 9:35 AM, blpa...@gmail.com  wrote: 
>
> > 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: 
> > 
> >  
> >  > xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">

> >     
> >         > 
>
md5="d95d12290aaa87a91f47d25299cfb6ce">MKYKHLILSLSLIMLGPLAHAEEIGSVDTVFKMIGPDHKIVVEAFDDPDVKNVTCYVSRAKTGGIKGGLGLAEDTSDAAISCQQVGPIELSDRIKNGKAQGEVVFKKRTSLVFKSLQVVRFY

>
> > DAKRNALAYLAYSDKVVEGSPKNAISAVPVMPWRQ 
> >         
> >         
> >             
> >                

> >                     
> >                     
> >                         > name="CreA"/> 
> >                     
> >                     > version="27.0"/> 
> >                 
> >                 
> >                     > 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. 
> > 
> > Ben 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop...@lists.open-bio.org  
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

>
>
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