[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 9:35 AM, Kai Blin
<kai.blin at biotech.uni-tuebingen.de> wrote:
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> Hi folks,
>
> In the summer, I've written a HMMer2 parser based on Bow's SearchIO
> code. I'm finally getting around to continue work on the project I
> needed this parser for, and I'm trying to get my code up-to-date.
>
> I notice that Bow's code hasn't hit the biopython master tree yet, and
> also doesn't rebase cleanly on top of it. A merge gives a couple of
> merge conflicts, but seems manageable. However, I'd prefer to stick to
> the upstream sources instead of maintaining my own branch containing
> Bow's SearchIO code merged to master.
>
> What's the chance of this happening any time soon, and can I help?
>
> Cheers,
> Kai

I'm not sure where the merge conflict is - Bow can probably help
and confirm you're looking at the appropriate branch.

What would help is comments on the name space ideas in this
thread, since one major point we need to settle ASAP is where
in the namespace SearchIO would go (since it probably won't
just stay as Bio.SearchIO as it is on the branch):

http://lists.open-bio.org/pipermail/biopython-dev/2012-September/009910.html
...
http://lists.open-bio.org/pipermail/biopython-dev/2012-October/009999.html
...

Peter