[BioPython] Changes to SubsMat

[Iddo Friedberg]

Hi,

I commited a new SubsMat ot the CVS. Changes that will cause code break
are:

1) relative entropy is now in SeqMat.relative_entropy. It is calculated
using the methods SeqMat.make_relative_entropy(obs_freq_mat), where
obs_freq_mat is the observed frequency matrix.

2) Absolute entropy is kept in SeqMat.entropy. It is calculated using
SeqMat.make_entropy()

If this really bugs someone, let me know. I changed the attributes names
as I gather that SubsMat is not being widely used for now, and the current
names reflect better on what they actually do and hold.

Bugfixes:
---------

A zero value in the observed substitutions matrix doesn't crash the
code. That happened because log(0) is undetermined. I'll elaborate on what
I do with a zero value in wiki. Or you can look through the code
documentation for now.


Other changes:
--------------

* Methods for subtraction, addition and multiplication of matrices

* Generation of an expected frequency table from an observed frequency
matrix

* Calculation of linear correlation coefficient between two matrices.
Actually, I commented this out until Bio.Tools.Statistics materializes.
(See Brad's post today on biopython-dev).

* Jensen-Shannon distance between the distributions from which the
matrices are derived. This is a distance function based on the
distribution's entropies.

* Calculates the relative entropy between the distributions of two
matrices. This is a sort of a distance function, only it's not symmetric.

* Can print a full or a half matrix now, formatted.

* Can read a text file with a matrix. More info on Wiki once I get it up.

I'll wiki up some more useful documentation soon.


Iddo

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/