[Biopython-dev] TAIR/AGI support

[Kevin Murray]

Brad,

I shall work on this as time permits, and get back to you all when complete.
Cheers,

Regards
Kevin Murray


On 5 October 2012 11:02, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> 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
> >>
> >>
>