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

Aaron J. Mackey amackey at pcbi.upenn.edu
Thu Oct 14 13:29:54 EDT 2004

On Oct 14, 2004, at 1:05 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.

I would concur with Allen that "features" have gained enough status in 
the bioperl world to warrant their own namespace; thus, Bio::Tools::GFF 
should be refactored into Bio::FeatureIO::gff, and we might 
(eventually) deprecate Bio::Tools::GFF I expect.

Having made many trips through Bio::Tools::GFF, I know what an ugly 
hack it has become to be; in reality, it'll probably remain, if only to 
support older GFF variants.  Vive la GFF3! (and FeatureIO!)  But if you 
have desperate patches to put into Bio::Tools::GFF while FeatureIO 
stabilizes, feel free.

We had a similar situation with Bio::Tools::Blast and Bio::SearchIO; 
the transition may be rocky, but it's worth it in the end.


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