[Bioperl-l] tigrxml parsing

[Robert Buels]

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