[Bioperl-l] Unigene proposal and basic implementation

[Jason Stajich]

On Tue, 16 Apr 2002, Kris Boulez wrote:


> We have
>
> Bio::AlignIO
>      AnnSeqIO
>      MapIO
>      SearchIO
>      SeqIO
>      TreeIO
>
> but also
>
> Bio::LiveSeq::IO
>      Variation::IO
>      Structure::IO
>      Biblio::IO
>
>
> What do people think about Bio::IO ?

No - this AlignIO -> LiveSeq::IO transition was designed so we
don't create 2 top level directories for each new for data system.  But
it is not part of the unwritten bioperl best practices document.  I'm
pretty much okay with mixing the two for now but I definitely agree that
it would be better to use a single paradigm when naming.

I don't think Bio::IO would be a good way to group though, I really prefer
that the parser stay closer to the data objects wrt to namespace.

Just my opinion though...  Counter arguments welcomed.

-j
>
> Kris,
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>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu