Biopython README file

The Biopython Project 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.

For the impatient

To build and install Biopython, type: python setup.py build python setup.py test python setup.py install

System Requirements

• Python 2.0 or above

• mxTextTools

• Numerical Python 15.3 or above (optional) This is only required if you want to use the classification tools.

• Martel (now included in Biopython by default, so don't worry about adding this)

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.

For FreeBSD users, Johann Visagie has made Biopython available in the ports tree. According to Johann:

This means that a FreeBSD user with an up-to-date ports tree can now install BioPython as simply as:

cd /usr/ports/biology/py-biopython ; make install

Fetching of the package as well as installation of all dependencies (Python itself as well as Distutils) will be handled automagically.

Testing

Biopython includes a suite of regression tests to check if everything's running correctly. To do the tests, type: drevil:~biopython/> python setup.py test

If you have Tk installed, this will run a nice GUI that displays the results of the tests. Otherwise, you will see results on the command line.

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

If you wish to contribute a bug report, please submit them to the online bug reporting form

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...)

• clean up the directory tree

• make Registry for algorithms

• consolidate miscellaneous file handle code

• smoother handling of dependencies

• retrieval of search results

• connect DB stuff to Format stuff

• clean up the /etc/bioinformatics configuration files

If you see something here you would like to work on, please send mail to biopython@biopython.org!

Thanks