[Biopython-dev] Plans for Biopython 1.53

Peter biopython at maubp.freeserve.co.uk
Wed Dec 9 13:21:50 UTC 2009

On Tue, Dec 8, 2009 at 10:18 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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.

I'm stuck again with Bio.Restriction under Jython. I've got the
Bio/Restriction/Restriction_Dictionary.py to load under Jython
(just = the Nov 2009 update isn't helping to keep the code
size down), but doing test_Restriction.py hits the JVM limit.

Furthermore, there is a little bit of C code in Bio.Restriction
(which I think we can replace with plain python).


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