[Bioperl-l] Bio::PopGen modules performance

[Albert Vilella]

El dt 08 de 11 del 2005 a les 08:05 -0500, en/na Kevin Thornton va
escriure:
> That is possible.  Although, like bioperl, the actual programs that  
> people may need/want do not exist yet.  The examples/ subdirectory in  
> the libsequence source package contains two example programs, ms--  
> and msbeta.  The former is a basic simulation with recombination, and  
> the latter a simulation with recombination where the shape of the  
> genetic map on the sequence is described by a Beta(a,b) density  
> sitting on top of the sequence.  For both programs, the demographic  
> model is the standard continuous approximation of a large Wright- 
> Fisher population.  One thing that would be quite quick to do is to  
> document those a little better at the top of their source files.

Yes, that sounds good. If you want I can open a bugzilla ticket with the
generic subject "libsequence wrapper" and then add this first
approximation as a first item to achieve.

Bests,

    Albert.

> 
> --Kevin
> On Nov 8, 2005, at 1:43 AM, Albert Vilella wrote:
> 
> > I would say that one way to have a Bioperl wrapper would be to have a
> > document in libsequence explaining how to call each binaries, with  
> > which
> > options. For example:
> >
> > ms-like-binary --option1 <accepted-values>
> >                --option2 <accepted-values>
> >                --option3 <accepted-values>
> >                [...]
> >
> > does-something-cool-binary --option1 <accepted-values>
> >                            --option2 <accepted-values>
> >                            [...]
> >
> > or with config files, along the lines of programs like PAML .ctl  
> > files.
> >
> > This is definitively a fantastic wrapper to implement,
> >
> > Cheers,
> >
> >     Albert.
> >
> >> This thread brings up something I've been meaning to post to this
> >> list for a while now.  Recent versions of libsequence now contain
> >> definitions for all the data types and functions necessary to do
> >> coalescent simulations with recombination.  The efficiency is quite
> >> good, easily on par with "ms", with a few extra nuts and bolts thrown
> >> in there that can lead to improved efficiency over ms.  Also, the
> >> resulting data structure (i.e. the ancestral recombination graph),
> >> can be accessed directly, and/or mutations can be thrown down on
> >> them, and objects are returned that are compatible with the summary-
> >> statistic calculation factories already in the library.
> >>
> >> Here's where bioperl may come in.  I have attempted to create a
> >> python wrapper for the library (using boost::python), with the
> >> ultimate goal of mentioning or submitting it to biopython.
> >> Unfortunately, there appears to be some limitations to boost::python
> >> that will prevent a full python interface to libsequence from
> >> appearing any time soon.  However, the code is all there for someone
> >> who's motivated to provide perl wrappers.  It is my understanding
> >> that a direct perl interface to a C++ API is not possible, or at
> >> least not easy.  If I'm wrong here, I'd be interested in hearing more
> >> about it.  However, some basic binaries could be provided which perl
> >> could call.  While this would be a pain in that it wouldn't be self-
> >> contained perl, it would be quite fast, and potentially quite  
> >> flexible.
> >
> >> If this sounds interesting to anybody, I'd be willing to discuss this
> >> further.
> >>
> >> --Kevin
> >> _________________________
> >> Kevin Thornton
> >> Molecular Biology and Genetics
> >> Cornell University
> >> http://www.molpopgen.org
> 
> _________________________
> Kevin Thornton
> Molecular Biology and Genetics
> Cornell University
> http://www.molpopgen.org
> 
>