[Bioperl-l] TIGR parser for SeqIO

Ed Robinson erobinso at uga.edu
Fri Nov 12 16:05:02 EST 2004

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
STACK: Bio::SeqIO::tigr::throw
STACK: Bio::SeqIO::tigr::_process_model
STACK: Bio::SeqIO::tigr::_process_tu
STACK: Bio::SeqIO::tigr::_process_protein_coding
STACK: Bio::SeqIO::tigr::_process_gene_list
STACK: Bio::SeqIO::tigr::_process_assembly
STACK: Bio::SeqIO::tigr::_process_tigr
STACK: Bio::SeqIO::tigr::_process
STACK: Bio::SeqIO::tigr::_initialize
STACK: Bio::SeqIO::new
STACK: Bio::SeqIO::new

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.
line 63

Indicating it died for some reason once it got to the

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

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