[Biopython-dev] Namespace for online resources?

[Lenna Peterson]

On Fri, Feb 1, 2013 at 9:14 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
> People leaning for a Bio.WWW grouping: Bow, Lenna, Kevin
> (which could be a big disruption with lots of code relocation)
>
> People leaning against a Bio.WWW grouping: Michiel, Peter (me)
> (which would also be the status quo, so no disruption).
>
>
I concede that the potential benefit of refactoring to separate WWW is
outweighed both by potential downsides and the disruption and effort
involved.

In the specific case of Kevin's TAIR code for fetch Arabidopsis sequences,
> Bio.TAIR (lower case?) is consistent with current usage. Somewhere under
> Bio.Seq* also seems sensible to me, as I wrote at the start of this thread.
>
>
Populating the top level namespace with a submodule for each web-only
service has the risk of creating too many submodules. Bio.Seq* makes sense,
because the TAIR code pulls data into a Seq. Web services that connect to a
single biopython representation can be organized under that submodule. Web
services that return multiple types of information (e.g. Entrez) are big
enough to logically comprise their own submodule.

Is my interpretation of the biopython classification scheme more or less
correct?

Cheers,

Lenna