[BioPython] Some proposed code-cleanup

[Andreas Kuntzagk]

Hi,

> I don't understand the subtle differences with UserDict with the dict 
> type.  

I think, UserDict, UserList, UserString was introduced, because before
python2.2. you could not directly inherit from the builtin types.
This was changed and the documentation for this modules read to me like
they will be deprecated and can be exchanged for the builtin type (now
classes).

> However, it does cause some problems.  For example, if you apply 
> the patches to SubsMat/__init__.py and FreqTable.py, the regression 
> tests fail!  I don't think we should accept these fixes until we know 
> that they won't break current code.

I'm sorry. I tried the regression tests and all seemed fine. What I
didn't notice was, the tests used my already installed biopython and not
the code from the build-directory. Grr, why do I keep tripping over this
errors? Shouldn't the "python setup.py test" use the directory it is
positioned in? If it is required to set PYTHONPATH before test, it
should be mentioned in the README. I will look into the problems now to
see if I could find out.

Andreas