[Bioperl-l] Re: More unresolved issues with Bio::AnnotatableI

Allen Day allenday at ucla.edu
Wed Jun 22 20:43:44 EDT 2005


Where is the dependency on Graph::Directed introduced?  A grep through
Bio/* in bioperl-live on HEAD reveals several references in the POD to
Graph.pm, but I don't see it anywhere in the code.

I don't know if Chris Mungall's GO-Perl API removes the dependency on
Graph::Directed, but it is certainly easier to use than Bio::OntologyIO as
a means to access the OBO ontologies.  I'm willing to look into converting
Bio::Annotation::OntologyTerm to use GO::Model::* instead of
Bio::Ontology::Term, but it may interfere with other projects using the
class (e.g. bioperl-db).

Hilmar, I know you were looking at the GO-Perl codebase recently, can you
comment on any of the above?


On Wed, 22 Jun 2005, Aaron J. Mackey wrote:

> Because AnnotatableI has implementations for add_tag and get_tag that  
> invoke Bio::Annotation::OntologyTerm, and therefore Graph::Directed,  
> which relies on Scalar::Util::weaken(), therefore I cannot even use  
> basic Bio::Seq functionality on any perl that doesn't have weak  
> references (oddly, this cropped up in a 5.8.0 install via an RPM that  
> was evidently compiled without support for weak references, so this  
> isn't just an "ancient perl" problem).
> This is something of a showstopper for any 1.6; in effect, we'd need  
> to disable Annotation::OntologyTerm use for any Perl without weak  
> reference support.
> We've said it before, and we need to say it again: the changes made  
> to the feature/annotation object model are seriously impeding our  
> ability to move forward to a release (and frighteningly, the GBrowse  
> distribution now includes those parts of 1.5 that it relies on, so a  
> user's BioPerl install could be a hodge-podge of 1.4/1.5 code).  This  
> seems important to all GMOD projects, so why hasn't there been any  
> work on it?
> Thanks,
> -Aaron

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