[Biopython-dev] Namespace for online resources?

[Wibowo Arindrarto]

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