[Biopython-dev] Status of SearchIO

[Wibowo Arindrarto]

Hi Kai, Peter,

For the merge conflict, which branch are you using? Can you point to
specific commits that cause the conflicts? I haven't tried merging /
rebasing my own branch to the current master myself ~ so knowing this
should help the process as well.

And suggestions are still welcomed for the namespace :). Bio.SearchIO is
the current one, but we have other alternatives (the most recent one being
Bio.seq.search; following the change in Bio.Seq -> Bio.seq namespace
change).

Also, I think there are still some issues that need to be dealt with before
we put SearchIO into master, notably with Bio.BLAST module. If not the
official deprecation notice, at least the the tutorial has to be updated
(let Bio.BLAST readers know about the plan with SearchIO). I've written a
short tutorial here: http://bow.web.id/biopython/Tutorial.html. This is
still a draft, but you can already see that there are some obvious overlaps
between Bio.BLAST and Bio.SearchIO, which is confusing to new readers.

regards,
Bow

On Fri, Oct 26, 2012 at 11:21 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Oct 26, 2012 at 9:35 AM, Kai Blin
> <kai.blin at biotech.uni-tuebingen.de> wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > 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
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