Pygr README

Introduction

Pygr is an open source software project used to develop graph database interfaces for the popular Python language, with a strong emphasis on bioinformatics applications ranging from genome-wide analysis of alternative splicing patterns, to comparative genomics queries of multi-genome alignment data.

For more information see

http://pygr.org

Latest Release

http://code.google.com/p/pygr/downloads/list

Documentation

This distribution includes the full Pygr documentation source, but you will need the Sphinx documentation tool to build the formatted docs. You can get Sphinx via:

easy_install -U Sphinx

To build HTML versions of the docs using Sphinx: cd doc make html

The docs are also available online:

http://pygr.org/docs/latest-release/

Core Prerequisites

1. Python >= 2.3

To build Pygr from source code, you need Pyrex

Apps Prerequiites

MySQL-python >= 1.2.0 MySQL >= 3.23.x

Note: While pygr's core functionality is solely dependent on a sane python environment, the aformentioned apps requirements must be installed if one wishes to utilize the apps modules and test code.

Supported Platforms

In theory, pygr should work on any platform that adequately supports python.

Here are the OS's we've successfully tested on:

o Linux 2.2.x/2.4.x o OS X o OpenBSD o Windows XP

Installation

Installing pygr is quite simple.

1. tar -xzvf pygr-0.3.tar.gz
2. cd pygr
3. python setup.py install

Once the test framework has completed successfully, the setup script will install pygr into python's respective site-packages directory. If you don't want to install pygr into your system-wide site-packages, replace the "python setup.py install" command with "python setup.py build". This will build pygr but not install it in site-packages.

Using Pygr

Check out the tutorials in the online docs!

Pygr contains several modules imported as follows: from pygr import seqdb # IMPORT SEQUENCE DATABASE MODULE

If you did not install pygr in your system-wide site-packages, you must set your PYTHONPATH to the location of your pygr build. For example, if your top-level pygr source directory is PYGRDIR then you'd type something like: setenv PYTHONPATH PYGRDIR/build/lib.linux-i686-2.3 where the last directory name depends on your specific architecture.

License

New BSD license.

Author

Chris Lee leec@chem.ucla.edu and the rest of the Pygr developer team. Please see http://code.google.com/p/pygr for a current list of the participating developers.

Also see http://github.com/cjlee112/pygr/ for a list of other developers who have created their own branches of the Pygr git repository.