[Biopython-dev] Oligopython page

[Harry Zuzan]

Hi,

Originally the parser was in Python but it was too slow.  I could have
written it in C instead of C++ but I have a lot of other code related
to this that is written in C++.

If I write a class in Python that is too slow because of the amount of
data it has to handle I often solve the problem by converting the
Python class to a C++ class.  Then I write a thin wrapper in Python
around the C++ class.  So in my Python scripts nothing changes.  This
is where the C++ code comes from.

I'll read up on install scripts myself.  In the meantime I'm grateful
for any help.

Harry


> Hi,
> 
> Thanks for writing oligopython! I had a look at your package to see
> if I could 
> write a setup.py for it, and I noticed that the file parser makes use
> of C++ 
> rather than C. If I'm not mistaken, the only C++ code currently in
> Biopython is 
> Bio.KDTree, which is not installed by default because of problems
> building it on 
> some platforms. Is there some Biopython policy on C++ code? It may
> also be 
> possible to use Martel for the file parsing. I am not familiar with
> Martel 
> myself, so I cannot give much guidance there, but maybe somebody can.
> 
> --Michiel.
> 
> Harry Zuzan wrote:
> 
> > Hi,
> > 
> > I can't get dyndns to update www.oligopython.org.
> > 
> > For the time being, anyone interested can get the same pages from
> > oligopython.dyndns.org.
> > 
> > Sorry about any confusion.
> > 
> > Also, there is not a lot of code at this point so I just attached
> it.
> > 
> > Harry
> > 
> > 
> >
>
------------------------------------------------------------------------
> > 
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at biopython.org
> > http://biopython.org/mailman/listinfo/biopython-dev
> 
> -- 
> Michiel de Hoon, Assistant Professor
> University of Tokyo, Institute of Medical Science
> Human Genome Center
> 4-6-1 Shirokane-dai, Minato-ku
> Tokyo 108-8639
> Japan
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon
> 
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