[Biopython] BioPython wrapper for UNAFOLD and NUPACK

[Michiel de Hoon]

I'm a bit biased here, since I use UNAFold a lot for my own research.

One thing to keep in mind is that UNAFold relies a lot on Perl scripts that glue the actual executables together. A Biopython interface can either run the Perl scripts (which would introduce a Perl dependency), or replicate the Perl scripts in Python (which is more difficult to maintain, but may give us a more Pythonic way to run UNAFold). You could also consider to contact the UNAFold developers directly; they may be interested in a Python wrapper in addition to the Perl wrapper to their software (so, the Python wrapper would be part of UNAFold rather than of Biopython).

--Michiel.

--- On Wed, 6/17/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] BioPython wrapper for UNAFOLD and NUPACK
> To: "Rouilly, Vincent" <vincent.rouilly03 at imperial.ac.uk>
> Cc: "biopython at lists.open-bio.org" <biopython at lists.open-bio.org>
> Date: Wednesday, June 17, 2009, 6:38 AM
> 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
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