[Biopython-dev] GSoC SearchIO project

[Peter Cock]

On Mon, Sep 3, 2012 at 11:14 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hello everyone,
>
> I'd like to update everyone on my latest SearchIO(?) developments. There
> has been some progress and bug fixes since GSoC officially ended two weeks
> ago. Some of them I'd like to share here:
>
> 1. I've written a draft tutorial chapter for the submodule. It' been pushed
> to my development repo (https://github.com/bow/biopython/tree/searchio) and
> I'm hosting the HTML temporarily on my site (
> http://bow.web.id/biopython/Tutorial.html). Comments and critiques are
> welcomed :).

Oh - excellent - I'll read that in the next few days :)

> 2. Back on the naming issue, I'm still using SearchIO for now. I've
> experimented with other names (Bio.Search and Bio.SeqSearch), and my
> impression is I like Bio.SeqSearch the most, followed by Bio.Search, and
> Bio.SearchIO. It does feel confusing initially (we have SeqUtils,
> SeqFeature, etc.), but after a while it's the one that feels most natural.


Initially Bio.SeqSearch sounds a bit long... but maybe it will
grow on me...

> 3. And finally, Peter and I discussed this briefly previously: what about
> if we merge the existing BLAST wrappers and NCBI qblast into Bio.(SeqSearch
> / Search / SearchIO)? I felt there were a lot of overlap between this
> submodule and Bio.BLAST when writing the tutorial, so merging surfaced in
> my thoughts again. We could put the BLAST wrappers under
> Bio.SeqSearch.Applications (for example), along with other wrappers (I have
> a yet-untested Bio.HMMER3 wrapper and possibly Bio.BLAT wrapper that put
> here as well). As for qblast (and other remote searches, like the one
> provided by HMMER at the moment), we could put them in
> Bio.SeqSearch.Remote, perhaps. I think this would make it easier for anyone
> who works with BLAST / other sequence search tools as all Biopython-related
> functionalities are grouped in one place.

As per my discussion with Bow, I'm OK with aiming to deprecate the
Bio.BLAST namespace as part of introducing Bio.SeqSearch/Search/..,
although I hadn't a strong preference on a naming convention for any
online functionality. Possibly www is shorter than remote and also
clear?

> This is just a thought for now, but I'd love to hear your thoughts on the
> merge (and the naming ;) ).
>
> cheers,
> Bow

Thanks Bow :)

Peter