[Biopython-dev] Namespace for online resources?

[Michiel de Hoon]

In principle I am OK with this, but is TAIR only used for sequences? Or is it possible / likely that in the future we may want to add other functionality to TAIR? Anyway, if TAIR is predominantly used for sequences, then Bio.Seq.Web is a good option I think.

Best,
-Michiel.

--- On Fri, 2/1/13, Kevin Murray <k.d.murray.91 at gmail.com> wrote:

> From: Kevin Murray <k.d.murray.91 at gmail.com>
> Subject: Re: [Biopython-dev] Namespace for online resources?
> To: "Peter Cock" <p.j.a.cock at googlemail.com>
> Cc: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
> Date: Friday, February 1, 2013, 6:59 PM
> 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
> >
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