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Bio
Doc
Scripts
Tests
AUTHORS
LICENSE
MANIFEST.in
NEWS
README
setup.py

README

Biopython README file
=====================

The Biopython Project (http://www.biopython.org/) is an international
association of developers of freely available Python tools for
computational molecular biology.

biopython.org provides an online resource for modules, scripts, and
web links for developers of Python-based software for life science
research.  Thanks to bioperl, we can also provide web, FTP and CVS
space for individuals and organizations wishing to distribute or
otherwise make available standalone scripts & code.

This Biopython package is made available under generous terms.  Please
see the LICENSE file for further details.



System Requirements
-------------------

o Python 1.52 or above
  http://www.python.org/
o Distutils 0.8.2
  http://www.python.org/sigs/distutils-sig/
  0.9 may not work, due to differences in specifying extension packages.
o Numerical Python 15.3 (optional)
  http://numpy.sourceforge.net/
  This is only required if you want to use the classification tools.



Installation
------------

*** Make sure Python and Distutils are installed correctly ***

Installation should be as simple as going to the biopython directory,
and typing:
python setup.py install


If you need to do additional configuration, e.g. changing the base
directory, please type 'python setup.py', or see the documentation for
Distutils.



Testing
-------

Biopython includes a suite of regression tests to check if
everything's running correctly.  To do the tests, go to the Tests/
die
rectory in the distribution and run br_regrtest.py:

  drevil:~/biopython/Tests> python br_regrtest.py
  test_Enzyme
  test_Fasta
  test_Fasta2
  test_File
  test_KeyWList
  5 tests OK.
  drevil:~/biopython/Tests> 


XXX We need to get this more closely integrated with the installation
process.




Contributing, Bug Reports
-------------------------

Biopython is run by volunteers from all over the world, with many
types of backgrounds. We are always looking for people interested in
helping with code development, web-site management, technical
administration, and whatever else comes up.

If you wish to contribute, please visit the web site and join our
mailing list.
http://www.biopython.org/
http://www.biopython.org/MailList.shtml

If you wish to contribute a bug report, please submit them to the
online bug reporting form at:
http://www.biopython.org/biopython-bugs/



Distribution Structure
----------------------

AUTHORS       An (incomplete) list of people who have contributed.
Bio/          The python package that makes up biopython
Doc/          Documentation
LICENSE       License information for this package
MANIFEST.in   Tells distutils what files to distribute
NEWS          Release notes and news
README        This file
Scripts/      Miscellaneous, possibly useful, standalone scripts
Tests/        Regression testing code
setup.py      Installation file.



To Do
-----

(In no particular order...)

- Annotations on sequences
- BLAST additions
  o PSI-BLAST on WWW
- parsers
  o Enzyme
    - add parsers, iterator, dictionary, etc.
  o PDB
    - needs to be done
    - build on Andrew's UPDB?
  o Genbank
    - Chris Fenton chrisf@fagmed.uit.no
- generalize parsers
- bug database
- regression tests
- documentation(!!)
- look into Zope-ifying the web site
- deprecate Seq.py
- microarray data
- look into docstring browser

If you see something here you would like to work on, please let me
know!

Thanks,
Jeff (jchang@smi.stanford.edu)
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