[Bioperl-l] Bio::PopGen modules performance

Albert Vilella avilella at ub.edu
Tue Nov 8 01:43:00 EST 2005

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,



> 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

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