[Biopython-dev] TAIR/AGI support

[Brad Chapman]

Kevin;
Thanks for making this available. This looks like a great start and
seems like it would be a nice starting place for folks dealing with
Arabidopsis data. A couple of thoughts which you've essentially already
covered:

- Could you build up a small test suite that fits into the testing
  framework:

  http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc246

  Your probably the best person to pick some disparate IDs that exercise
  different components and try to catch any edge cases.

- Additional interfaces that help folks do more than get sequence are a
  great idea. The ideas you've proposed below sound perfect.

- Provide some documentation on the Cookbook for common use cases with
  Biopython + your module. This will help motivate the addition and also
  help folks test it out on their data.

Thanks again for making this available,
Brad


> Hi Brad,
>
> My TAIR/AGI script is on github here:
> https://github.com/kdmurray91/biopython/blob/master/Bio/TAIR/__init__.py
>
> I got it to work directly from TAIR's website, however it has not been
> rigorously tested. I plan on implementing the process as i described in my
> previous email, whereby it fetches the Genbank record from TOGOws or via
> NCBI's Efetch (using biopython's interfaces of course). I will keep you all
> posted.
>
> To the list in general, I'm open to suggestions on what to work on next?
>
>
> Regards
> Kevin Murray
>
>
> On 6 September 2012 10:45, Brad Chapman <chapmanb at 50mail.com> wrote:
>
>>
>> Kevin;
>> Thanks for the e-mail and offers of code. Always happy to have other
>> folks involved with the project.
>>
>> > What's the status of TAIR AGIs in BioPython (I can see no mention of
>> them,
>> > or support for them)? I've written a brief module which allows a user to
>> > query NCBI with a TAIR AGI, returning a Seq object (via Efetch). Is there
>> > any interest in including such functionality in BioPython?
>>
>> Is the code available on GitHub to get a better sense of all the
>> functionality it supports? Do you have an idea where it would fit best?
>> As a tair submodule inside of Bio.Entrez, or somewhere else?
>>
>> > More generally, are there any particular areas of BioPython development
>> > which could use an extra pair of hands?
>>
>> Following the mailing list for discussions on current projects is the
>> best way to get a sense of what different folks are working on. The
>> issue tracker also has open issues and features that could use attention
>> if anything there strikes your fancy:
>>
>> https://redmine.open-bio.org/projects/biopython
>>
>> Hope this helps,
>> Brad
>>
>>