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Python graph database framework for bioinformatics
Python C Other




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

Latest Release


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:

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


Installing pygr is quite simple. 

1) tar -xzvf pygr-0.3.tar.gz 
2) cd pygr
3) python 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 install" command with
"python 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.


New BSD license.

Chris Lee <> and the rest of the Pygr developer team.
Please see for a current list
of the participating developers.

Also see for a list of other
developers who have created their own branches of the Pygr
git repository.

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