[Bioperl-l] tigrxml parsing

[Chris Fields]

Robert,

This popped up recently (may be related):

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/19782
http://bugzilla.open-bio.org/show_bug.cgi?id=2868

It might be possible to map this into bioperl, but someone needs to  
take it up.

chris

On Aug 6, 2009, at 12:14 PM, Robert Buels wrote:

> Hi all,
>
> Recently in #bioperl somebody came by trying to use  
> Bio::SeqIO::tigrxml.pm to parse the medicago genome annotations at http://www.medicago.org/genome/downloads/Mt2/MT2.0_medicago_chrX_20080103_NoOverlap.xml.tar.gz
>
> svn HEAD tigrxml.pm was not at all happy with these files,  
> eventually dieing with
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: start is undefined
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
> STACK: Bio::RangeI::contains Bio/RangeI.pm:255
> STACK: Bio::SeqFeature::Generic::add_SeqFeature Bio/SeqFeature/ 
> Generic.pm:783
> STACK: Bio::SeqIO::tigrxml::start_element Bio/SeqIO/tigrxml.pm:206
> STACK: try{} block /usr/share/perl5/XML/SAX/Base.pm:292
> STACK: XML::SAX::Base::start_element /usr/share/perl5/XML/SAX/ 
> Base.pm:266
> STACK: XML::SAX::Expat::_handle_start /usr/share/perl5/XML/SAX/ 
> Expat.pm:225
> STACK: XML::Parser::Expat::parse /usr/lib/perl5/XML/Parser/Expat.pm: 
> 469
> STACK: XML::Parser::parse /usr/lib/perl5/XML/Parser.pm:187
> STACK: XML::SAX::Expat::_parse_bytestream /usr/share/perl5/XML/SAX/ 
> Expat.pm:45
> STACK: XML::SAX::Base::parse /usr/share/perl5/XML/SAX/Base.pm:2602
> STACK: XML::SAX::Base::parse_file /usr/share/perl5/XML/SAX/Base.pm: 
> 2631
> STACK: Bio::SeqIO::tigrxml::next_seq Bio/SeqIO/tigrxml.pm:116
> STACK: /crypt/rob/test2.pl:10
> -----------------------------------------------------------
>
> Looking at the medicago XML and comparing it to the bioperl-live/t/ 
> data/test.tigrxml, the two look VERY different in structure.  Lots  
> of things that are attrs in test.tigrxml seem to be elements in the  
> medicago XML, for example.
>
> So I guess the question is:  is the medicago TIGR XML malformed?   
> Can tigrxml.pm be expected to parse it?  What, if anything, should  
> be done about this?
>
> Rob
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
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