[Biopython-dev] Namespace for online resources?

[Kevin Murray]

Hi All,

How about this:
In the vein of Lenna's last email, we create a module WebSeq (or Seq.Web,
or whatever), containing modules whose sole purpose is to get sequences
(Seq/SeqRecord objects) from an internet database. This would i think
provide a good balance between a messy top-level domain full of modules
like Bio.tair, and the absolutisim of having anything vaugly web related in
a single WWW module. It should also provide the unified theme per module
which Michiel talks of, and unit/doctests should be fine, as no modules
will be split (simply moved in their entirety from Bio.x to Bio.WebSeq.x).

>From a quick look, the only candiate (apart from TAIR) for a shift is
TogoWS, and even then I'm not sure, as TogoWS isn't used just for Seq's
(and does not return them).

Regards
Kevin Murray


On 2 February 2013 08:00, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Fri, Feb 1, 2013 at 7:05 PM, Lenna Peterson <arklenna at gmail.com> wrote:
> > 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?
>
> Yes that sounds about right :)
>
> Of course, the historical muddle of Bio.Seq* is something we've talked
> about addressing recently - see this thread from October,
> http://lists.open-bio.org/pipermail/biopython-dev/2012-October/009999.html
>
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>