[Biopython-dev] Changed in C API

Dragoslav Zaric zaricdragoslav at gmail.com
Tue Oct 26 10:01:46 UTC 2010

Do not worry Peter,

I am writing from work, that is why I am using windows. At home I have
two lap tops
and both are Linux :) I do not have windows on any partition :)

I use and developo only on Linux outside of main job.

Ok, when I get home I will read


and start to work on


Kind regards

On Tue, Oct 26, 2010 at 1:47 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Oct 26, 2010 at 10:11 AM, Dragoslav Zaric
> <zaricdragoslav at gmail.com> wrote:
>> Ok Peter,
>> First it is my mistake that I was talking about python code upgrade.
>> I understand that you want me to do C code upgrade, but at the
>> end all should work together so this is why I looked at overall upgrade
>> process.
>> I have downloaded latest python source code and I have searched
>> for .c files and .h files and this is what I have found:
>> Bio\Cluster\cluster.c
>> Bio\Cluster\clustermodule.c
>> Bio\cMarkovModelmodule.c
>> Bio\cpairwise2module.c
>> Bio\csupport.c
>> Bio\KDTree\KDTree.c
>> Bio\KDTree\KDTreemodule.c
>> Bio\Motif\_pwm.c
>> Bio\Nexus\cnexus.c
>> Bio\PDB\mmCIF\lex.yy.c
>> Bio\PDB\mmCIF\mmcif_test.c
>> Bio\PDB\mmCIF\MMCIFlexmodule.c
>> Bio\trie.c
>> Bio\triemodule.c
>> Bio\Cluster\cluster.h
>> Bio\csupport.h
>> Bio\KDTree\KDTree.h
>> Bio\KDTree\Neighbor.h
>> Bio\trie.h
> What OS are you using? From the slashes I'd guess
> Windows (which may complicate things - getting the
> compilers all setup is more work).
>> Are these all files you want me to upgrade to python 3.1 ?
> Yes - but not all of them are equally important, and some
> will be more complicated to port.
> For example, the Nexus, MarkovModelmodule and
> cMarkovModelmodule C code have a Python fallback
> (i.e. the C code is not essential, just faster).
> Some of those (e.g. Bio.Cluster and Bio.KDTree) depend
> on NumPy, which may make things more complicated.
> You will need to install NumPy (for both Python 2 and 3).
> Some may have string encoding issues (bytes vs unicode),
> e.g. Nexus, Motif
> The mmCIF module is not urgent. This is a file parser for
> the Bio.PDB code, and we have discussed replacing this
> in C. One reason for this is it currently depends on the
> 3rd party library flex.
> I think Bio/Motif/_pwm.c would be a good module to start
> with. It is a short simple module exposing a single
> function to Python.
> You should read this:
> http://wiki.python.org/moin/PortingExtensionModulesToPy3k
> Peter

Dragoslav Zaric

Professional Programmer
MSc Astrophysics

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