[Biopython-dev] Namespace for online resources?

[Kevin Murray]

Hi all,

Essentially, I agree with everything Bow and Lenna have said. If all
web-based tools are in a single root-level package, then with appropriate
documentation I think users should know where to find any function. People
are at least going to know if their required module interfaces with some
website.

I guess the problem is that moving all the web stuff into one package will
break alot of code, which leads me back to my original idea of just copying
where stuff like TOGOws and ExPASy is located, i.e. sticking TAIR in the
root level directory.

Peter and Michiel, do you think that Lenna's suggestion is workable? Would
it make sense to go all in and simultaneously refactor parsers into
Bio.parse,  Bio.*IO into Bio.io.*, etc etc. Perhaps this could be delayed
until the next major release (or form the beginings of a biopython2
branch?).

Cheers,
Kevin Murray


On 30 January 2013 13:00, 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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