[Biopython-dev] DAS client in biopython

[Peter]

On Tue, Jul 20, 2010 at 3:51 PM, Andrea Pierleoni wrote:
> Hi all,
> I've been working a little do develop a DAS client in python, and I
> thought it could be a nice addition to biopython.

Hi Andrea,

This does look interesting - I've never needed to work with
DAS but maybe one day...

> So I build up a branch on github that can be found here:
>
> http://github.com/apierleoni/biopython/tree/das-client

It looks like you have lots of other code on that branch too,
like BioSQL2py (your BioSQL via web2py DAL) - this isn't
a problem for now but would complicate merging later.

> The DAS module is under Bio and can be imported using
>
>>>> from Bio.DAS.DASpy import DASpy

The heirachy seems unnecessarily nested, why not move the
code in Bio/DAS/DASpy.py into Bio/DAS/__init__.py? Or
even into Bio/DAS.py instead? Then that import becomes:
from Bio.DAS import DASpy, which also avoids the ambiguity
of DASpy for a module and a class. Are you expecting to have
other files under Bio/DAS?

Also the name DASpy confuses me, maybe the class
should be something about DAS Servers?

Would it be right to regard the class DASSeq as a subclass
of SeqRecord? It looks like a minimally annotated sequence.
See also the DBSeqRecord in BioSQL.

Regards,

Peter