[Bioperl-l] TIGR parser for SeqIO

[Ed Robinson]

I am trying to get the tigr parser to work on our files.  My
script is otherwise ok, because when I call a genbank file
with the genbank parser, I am able to load data.  I have
downloaded the most recent tigr.pm from the CVS.  When I run
it, I get this:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: [46]Required <EXON> missing
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.6.1//Bio/Root/Root.pm:328
STACK: Bio::SeqIO::tigr::throw
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:1343
STACK: Bio::SeqIO::tigr::_process_model
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:1006
STACK: Bio::SeqIO::tigr::_process_tu
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:730
STACK: Bio::SeqIO::tigr::_process_protein_coding
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:541
STACK: Bio::SeqIO::tigr::_process_gene_list
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:507
STACK: Bio::SeqIO::tigr::_process_assembly
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:315
STACK: Bio::SeqIO::tigr::_process_tigr
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:220
STACK: Bio::SeqIO::tigr::_process
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:188
STACK: Bio::SeqIO::tigr::_initialize
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigr.pm:88
STACK: Bio::SeqIO::new
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO.pm:358
STACK: Bio::SeqIO::new
/usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO.pm:378


When I use the tigr.pm that comes with the bioperl release we
have installed, I get the following:

A whole bunch of warnings such as:

-------------------- WARNING ---------------------
MSG: Unknown element GENE_LIST, ignored
 
---------------------------------------------------
 
-------------------- WARNING ---------------------
MSG: Unknown element PROTEIN_CODING, ignored
 
---------------------------------------------------


followed by this:

Died at /usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigrxml.pm
line 150.
 at
/usr/lib/perl5/site_perl/5.6.1/i386-linux//XML/LibXML/SAX.pm
line 63

Indicating it died for some reason once it got to the
feature_type.


The XML I have is valid XML, although it is from August of
this year.  It is also a full XML file, it is not a coordset file.

Any suggestions would be appreciated.  I've even updated a
number of our Perl modules to rule those problems out.

-Ed R

-----------------
Ed Robinson
Program Specialist
Center for Tropical and Emerging Global Diseases
and Dept. of Genetics
University of Georgia, Athens, GA 30602
erobinso at uga.edu/(706) 542.1447