Hi,
I am in the process of extracting human annotation done with Apollo from
a Chado database to feed another Chado database. Using a perl-script
(mixing a Class::DBI interface to Chado and BioPerl), I am able to
generate a GFF file containing properties, synonyms and comments
generated in the Annotation Info editor of Apollo. But I am facing
trouble while loading, the gmod_bulk_loader_gff3.pl does not like the
tag "comment". I get the following error message :
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object Acyrthosiphon pisum ribosomal prtein L12 was not valid with
key comment. If you were adding new keys in, perhaps you want to make
use of the archetype method to allow registration to a more basic type
STACK: Error::throw
STACK: Bio::Root::Root::throw
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Annotation::Collection::add_Annotation
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/Annotation/Collection.pm:274
STACK: Bio::SeqFeature::Annotated::add_Annotation
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/SeqFeature/Annotated.pm:521
STACK: Bio::FeatureIO::gff::_handle_non_reserved_tag
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/FeatureIO/gff.pm:775
STACK: Bio::FeatureIO::gff::_handle_feature
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/FeatureIO/gff.pm:736
STACK: Bio::FeatureIO::gff::next_feature
/local/perl/5.8.8/lib/site_perl/5.8.8/Bio/FeatureIO/gff.pm:165
STACK: /usr/bin/gmod_bulk_load_gff3.pl:693
-----------------------------------------------------------
Issuing rollback() for database handle being DESTROY'd without explicit
disconnect().
"Acyrthosiphon pisum ribosomal prtein L12" is the value of the comment
tag. I investigated a bit and found that Bio::Annotation::Collection
was waiting for a Bio::Annotation::Comment as described in the
Bio::Annotation::TypeManager but get a string ("Acyrthosiphon pisum
ribosomal prtein L12") instead.
At the moment I've fixed it here by modifying
Bio::Annotation::TypeManager (I simply remove the type
Bio::Annotation::Comment) but I am not very happy with that. Looks like
a BioPerl problem, but I post here because maybe some of you had the
same problem, and a better solution.
Cheers,
Fabrice Legeai (AphidBase)
--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
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