[Biopython-dev] DAS client in biopython

[Andrea Pierleoni]

> 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.
>

BioSQL2py is just an empty directory on that branch,
It will be filled in an other specific branch (actually it shouldn't be
there :) )

>> 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?
>

I'm not planning on having other file. but since this was a proposal,
I build the Bio/DAS structure to host any additional client available,
if there are any.
howver if it will be the only way to parse DAS file we can simplify
to a Bio/DAS.py file. much better to me.

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

DASpy is the way I'm used to call this client, and that is the main class
but can be renamed to something more meaningful

> 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.
>

well, I think a DASSeq can fit comfortably in a SeqRecord.
this would also simplify the build of a SeqRecord object in
DASpy.fetch_to_seqrec.

Thanks for the advices Peter

Andrea