[Biopython-dev] DAS implementation

[Brent Pedersen]

On Mon, Apr 4, 2011 at 10:44 AM, Bernardo Clavijo <bjclavijo at gmail.com> wrote:
> On Mon, Apr 4, 2011 at 1:35 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo <bjclavijo at gmail.com> wrote:
>>> Hello everyone, new subscriber here, hopefully lending a hand around
>>> from now on (Python fan working on bioinformatics, so this is the
>>> place).
>>> I've been searching for a DAS server/client but found none written in
>>> python. Since I'm writting some Chado+Gbrowse+tools web glue in
>>> python, don't want to attach a perl implementation or such.
>>> Have anyone some code for this? Maybe it's just that my googling
>>> skills aren't so good. If not, wouldn't it be nice to have such a
>>> module in biopython?
>>> I'm not the best developer in the world, but maybe I could code
>>> something that serves us all and then it could be included in
>>> biopython.
>>> Well, that all for now... hope to hear some answers, and if you think
>>> that impelmenting DAS would be a nice idea, I'm sure you could provide
>>> me with a hint in how I could design it (a module interacting with
>>> Seq? Is there some webserver capabilities, or just write functions and
>>> let the code ready to glue into a webserver?, etc).
>>>
>>> Greets
>>>
>>> bj
>>
>> Hi Bernardo,
>>
>> Andrea Pierleoni started looking at a DAS client last year:
>> http://github.com/apierleoni/biopython/tree/das-client
>> http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html
>>
>> More eyes on this code would be good :)
>>
>> Peter
>>
>
> Great! a starting point for the client part... i'll check it out that
> for a starting point, I see there are some "TODO" parts... i'll try to
> handle those.
> Anyone having something similar as for the server part?
>
> Greets
>
> bj
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>

if you fork this on github (and especially if you start the server
stuff) and link back here, perhaps you'll
get some help. i'd be very interested in server and client for biodas
in biopython.
-brentp