[Biopython-dev] DAS client in biopython

[Andrea Pierleoni]

> 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?
>

hierarchy is now simplified to a single file DAS.py under Bio.

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

I renamed the DASpy class to DASregistry so the main call now
is:

from Bio.DAS import DASregistry

das = DASregistry()

simplier...


> 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.
>

I've been thinking about it and, actually, the DASSeq class
corresponds exactly to information and methods available in
the DAS sequence method, so I'd leave it this way.

Most of the time this class shouden0t be accessed. and a clean
SeqRecord object can be obtained using the "fetch_to_seqrec"
method in DASregistry.


Andrea