[Biopython-dev] Jython and sqlite

Peter biopython-dev at maubp.freeserve.co.uk
Thu Aug 30 14:51:17 UTC 2007

Tiago Antão wrote:
> Hi!
> Just a mail to ask about Jython and sqlite.
> About Jython: Is there any policy on Jython support? I am myself a
> Jython user, and in the code that I submitted to Bio.PopGen I tend to
> try to support Jython at least partially.

I'm not aware of anyone trying Biopython on Jython (or even other 
variants like Iron Python).  Trying Bio.PopGen on Jython sounds sensible 
- have you tried the Biopython unit tests to see what happens?

> I sometimes use older Python
> dialects (because Jython is still on 2.2) ...

Biopython has a stated dependence on Python 2.3 or later, so writing to 
Python 2.2 should be fine.  I myself use both Python 2.3 and 2.4, but 
some of the new stuff in 2.5 like generator expressions may tempt me to 
update my machines.

 > ... and avoid changing
> directories when calling external applications (the JVM doesn't
> support the concept of changing directories). The code that I have
> submitted (not the test code) supports Jython even when calling
> external applications.

Good - I would agree with you avoiding changing the current directory is 
wise (especially as we support multiple OS). Leave that up to the user.

> sqllite: On code that I intend to submit in the near future (HapMap
> related), I currently use the sqlite module. The major problem is,
> that module is Python 2.5 only. Therefore it requires a new version of
> Python (and probably won't be supported in Jython in the near future
> or ever). OTOH it is quite convenient: An embedded relational database
> (without the hassle of asking users to install a database server). Any
> ideas on this?

I haven't used sqllite before, but my initial reaction is wanting to use 
a Python 2.5 only module would be bad.  Have you looked at the existing 
BioSQL code in Biopython...


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