Hi Fabrice,
That is a BioPerl problem. The API for Bio::Annotation objects
changed some time ago, so your version of the bulk loader is out of
sync with your version of BioPerl. I believe an update of
gmod_bulk_load_gff3.pl is what you need (along with the libraries that
come in gmod-1.0).
Scott
On Fri, Oct 24, 2008 at 9:44 AM, Fabrice Legeai
<[EMAIL PROTECTED]> wrote:
> 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
>
> _______________________________________________
> apollo mailing list
> [email protected]
> http://mail.fruitfly.org/mailman/listinfo/apollo
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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