[Bioperl-l] Bio::Ontology fails test with current SOFA

[Scott Cain]

Hi Hilmar,

I realize Bio::Ontology is starting to show its age, and I am planning
on migrating away from its use, but I was wondering if you have any
ideas on what it would take to get Bio::OntologyIO to support the
current SOFA.  The first hangup is that it defines several relationship
types in the file, which causes it to throw this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: format error (file t/data/sofa.ontology) offending line:
    )pseudogene ; SO:0000336 % pseudogenic_region ; SO:0000462

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/Root/Root.pm:328
STACK: Bio::OntologyIO::dagflat::_parse_flat_file /usr/lib/perl5/site_perl/5.8.5/Bio/OntologyIO/dagflat.pm:623
STACK: Bio::OntologyIO::dagflat::parse /usr/lib/perl5/site_perl/5.8.5/Bio/OntologyIO/dagflat.pm:284
STACK: Bio::OntologyIO::dagflat::next_ontology /usr/lib/perl5/site_perl/5.8.5/Bio/OntologyIO/dagflat.pm:317
STACK: t/Ontology.t:44
-----------------------------------------------------------


Thanks,
Scott

-- 
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory