[Biopython] BioPython wrapper for UNAFOLD and NUPACK

[Peter]

On Wed, Jun 17, 2009 at 11:27 AM, Rouilly,
Vincent<vincent.rouilly03 at imperial.ac.uk> wrote:
> Hi,
>
> First of all, I am quite new to BioPython, but I am already very
> impressed by its capabilities. Thanks to all the contributors for
> providing such an amazing tool.
>
> Also, has anyone looked at writing a BioPython wrapper for
> DNA/RNA folding/hybridization packages such as:
> UNAFOLD: http://mfold.bioinfo.rpi.edu/
> NUPACK: http://nupack.org/
>
> I couldn't find anything from the mailing list archives. Sorry, if I
> have missed it.

I don't think we do have anything in Biopython for these tools.

> If not, I would be interested to give it a go, and I would welcome any advice.
> Would it be a good start to look at the Primer3 wrapper ?

Are you thinking about writing a command line wrapper for calling the
application(s), or a parser for the output? Or both? :)

If you want to talk about implementation options, that would be better
suited to the biopython-dev mailing list. The command line wrappers in
Bio.Emboss.Applications or Bio.Align.Applications would be a good
model (in the latest code, not Biopython 1.50, this has been under
active development recently). I'm not familiar with the output for the
UNAFOLD and NUPACK tools, so wouldn't like to say which parser would
be the best style to follow.

Peter