[Biopython-dev] Namespace for online resources?

Lenna Peterson arklenna at gmail.com
Tue Jan 29 20:05:15 UTC 2013

I agree with Bow that centralizing all online database access makes sense.
It would also simplify the testing process (i.e. anything that requires a
network connection goes into the web namespace and can be skipped when
testing offline).

In situations like Entrez, the network access portion could be separated
out and put into the web namespace under the same name:

    import Bio.www.Entrez  # for downloading the data
    import Bio.Entrez  # for parsing/using the downloaded data



On Tue, Jan 29, 2013 at 2:52 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> Hi everyone,
> > We used to have Bio.WWW for assorted online tools, but that
> > was deprecated some time back. Is there a case for bringing it
> > back, or something similar like Bio.WebTools as suggested by
> > Kevin Murray on this pull request?:
> >
> > https://github.com/biopython/biopython/pull/132
> >
> > In this case, since this is to fetch Arabidopsis sequence via
> > an accession number, perhaps Bio.SeqUtils might be better?
> > (As an aside, recall we've talked about merging Bio.Seq* at
> > some point).
> Why was Bio.WWW deprecated in the first place?
> Personally, I would prefer to have all online database access
> centralized in one place, if possible. It makes for a less-cluttered
> root namespace and may be more intuitive in most cases. I do notice
> that for cases like Bio.Entrez, sometimes we need to only parse the
> data locally since it has been downloaded previously (hence no online
> access). To do this task, Bio.www (basically the centralized online
> module) may not be the most intuitive place to look in, for most
> people, although an argument can be made that we are still parsing
> data whose format is specific for an online resource.
> However, looking at the way we are doing this now (with the current
> codebase placing Entrez access and parsing in Bio.Entrez; similarly
> for Bio.ExPASy) locating the module in Bio.TAIR (or Bio.tair? PEP-8
> compliance?) looks more consistent. If we are to create a new module
> for online access (e.g. Bio.webtools. Bio.www) for Bio.TAIR, for
> consistency we may have to juggle Entrez and ExPASy around as well,
> right?
> Putting Bio.TAIR in Bio.SeqUtils doesn't seem..right to me. My
> impression is that SeqUtils is supposed to be for functions acting on
> sequence strings (or Seq objects) and nothing else. After all, we can
> also retrieve GenBank sequences from Biopython but that functionality
> is separated on its own Bio.Entrez not Bio.SeqUtils.
> .
> Just my two cents :),
> Bow
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