[Biopython-dev] Plans for Biopython 1.53

[Peter]

On Tue, Dec 8, 2009 at 10:00 PM, Kyle Ellrott <kellrott at gmail.com> wrote:
>
> Speaking of stuff that may not be ready for 1.53, but should start speeding
> up for 1.54, I've translated a bunch of HMMER3 / PfamScan code in the
> Bio.HMMER and Bio.Pfam modules in my github branch (right now it's sitting
> in the jython branch, but I can spin it into a separate branch).
> Right now it's missing the code to parse HMMER2, there needs to be more
> extensive unit testing, and the API needs to be nailed down with some
> documentation.
> Is there anybody else that needs HMMER and Pfam support?
>
> Kyle

That had caught my eye, and it is potentially of direct interest to
me personally. I will probably skip HMMER2 and go straight to
HMMER3 though ;)

On a related point, I am reasonably confident we can get most
of Biopython running on Jython 2.5.1 in time for the release.
Other than things that Jython doesn't support at all, i.e. the C
code, DTD parsing (needed for Bio.Entrez), and the lack of a
buffer function (not important, only used in deprecated code
now), the only remaining hurdle is Bio.Restriction, and I think
I have solved that. I will be testing this tomorrow (time
permitting). Your groundwork has been very useful here Kyle.

Thanks,

Peter