[Biopython-dev] Namespace for online resources?

[Lenna Peterson]

Michiel,

You raise an excellent point that separating the modules in this way will
complicate doctests.

Regarding point (2), is your primary concern namespace clutter or importing
efficiency?

I still maintain that the category of internet access is more fundamental
than the category of parsers. For point (1), if every database is accessed
using a WWW submodule, a user will know to look there.

Obviously moving everything would be a lot of work...

Cheers,

Lenna



On Tue, Jan 29, 2013 at 9:00 PM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:

> Bio.WWW was one of those modules that seem a good idea at first, but then
> failed to gain general acceptance. There are three problems with Bio.WWW:
>
> 1) From the module name, it's not clear what you would find in it. For
> example, if you want to access the Entrez database, would you first look in
> Bio.Entrez or in Bio.WWW? Similarly for TAIR: Would you look for it in
> Bio.TAIR, or in Bio.WWW?
>
> 2) The modules in Bio.WWW don't have much to do with each other, except
> that they access the internet. But any given user probably is mainly
> interested in Entrez, or ExPASy, or some other database, not in all of them
> at the same time.
>
> 3) The flip side of this is that a user accessing e.g. ExPASy would have
> to import both Bio.WWW and Bio.ExPASy to be able to use ExPASy. Doctests
> get more complicated also, as they would span more than one module. Here is
> an example from Bio.Entrez that accesses the database, and then parses the
> results:
> >>> from Bio import Entrez
> >>> Entrez.email = "Your.Name.Here at example.org"
> >>> handle = Entrez.einfo() # or esearch, efetch, ...
> >>> record = Entrez.read(handle)
> >>> handle.close()
>
> The ultimate question is whether we organize the code in Biopython by
> their functionality from a user perspective, or by the kind of things they
> do? Almost all of Biopython is organized according to the former. For
> example, we don't have a Bio.Parsers module for all the parsers; similarly,
> we don't have Bio.WWW for internet access.
>
> Best,
> -Michiel.
>
>
> --- On Tue, 1/29/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> > From: Peter Cock <p.j.a.cock at googlemail.com>
> > Subject: Re: [Biopython-dev] Namespace for online resources?
> > To: "Wibowo Arindrarto" <w.arindrarto at gmail.com>
> > Cc: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
> > Date: Tuesday, January 29, 2013, 4:11 PM
> > On Tue, Jan 29, 2013 at 9:03 PM,
> > Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> > > On Tue, Jan 29, 2013 at 7:52 PM, Wibowo Arindrarto
> > > <w.arindrarto at gmail.com>
> > wrote:
> > >> Hi everyone,
> > >>
> > >> Why was Bio.WWW deprecated in the first place?
> > >>
> > >
> > > The flippant answer is everything under Bio.WWW was
> > moved
> > > or deprecated:
> > >
> http://lists.open-bio.org/pipermail/biopython-dev/2008-July/004059.html
> > >
> > > I'm trying to identify the discussions prior to that
> > covering the moves:
> > >
> > > Bio.WWW.ExPASy -> Bio.ExPASy
> > > Bio.WWW.InterPro -> Bio.InterPro
> > > Bio.WWW.NCBI -> Bio.Entrez
> > > Bio.WWW.SCOP -> Bio.SCOP
> >
> > Probably this thread,
> >
> http://lists.open-bio.org/pipermail/biopython-dev/2007-November/003241.html
> >
> > Also a bit more background on the NCBI Entrez side:
> >
> http://lists.open-bio.org/pipermail/biopython-dev/2008-February/003423.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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