[Biopython-dev] Plans for Biopython 1.53

[Kyle Ellrott]

>
> 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).



The last bit for 'full' jython support is getting BioSQL working.
Unfortunately MySQLdb links directly to the C mysql API, and doesn't work in
Jython.  My jython port also has work that moves the BioSQL interface from
the internal ORM to a SqlAlchemy interface.  Of course that is a little
controversial because it introduces a dependency on another python package.
Of course it takes care of sqlite and Java MySql connector support at the
same time, so it does have some pluses.

Kyle