[Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO

Allen Day allenday at ucla.edu
Fri Oct 15 16:58:29 EDT 2004

possibly, but it's going to take some typemapping work.  Bio::FeatureIO
departs from other SeqFeature handling classes in that it doesn't allow
features to be untyped... it uses SeqFeature::Annotated instead of
SeqFeature::Generic, which is required to have a SO or SOFA type attached
in the form of a Annotation::OntologyTerm.


On Fri, 15 Oct 2004, Hilmar Lapp wrote:

> On Thursday, October 14, 2004, at 01:05  PM, Allen Day wrote:
> > I would advise against adding more features into Bio::Tools::GFF.  I 
> > can't
> > speak for all others, but my future development will not use it, and 
> > I'm
> > in the process of converting code which does use it to depend on
> > Bio::FeatureIO::gff.
> >
> Is it possible to rewrite Bio::Tools::GFF as a simple thin wrapper 
> around methods/classes from Bio::FeatureIO?
> 	-hilmar

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