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.

Documentation

Please see our PygrDocumentation page for tutorials, module documentation, recipes, and forum. Within the source code repository, you can build the documentation via cd doc;make, then point your browser at the file doc/html/pygr/index.html. You can also check out the older documentation page.

Prerequisites

• Python >= 2.2: Pygr uses Python generators.
• C compiler: Pygr includes several C extension modules (pygr.cnestedlist, pygr.cdict, pygr.seqfmt), coded in C for high performance. To install Pygr from source code, you need a C compiler. (If you don't have a C compiler, you may be able to find a binary installer for Pygr on your platform on this site). Pygr uses the Python distutils module to build its extension modules, so any C compiler that distutils knows how to find and use is fine.

• Pyrex: You do not need this if you are installing one of our source code releases, because these include the C source code compiled by Pyrex. However, if you are compiling from the git repository, you will need Pyrex, because (currently) the git repository does not include the Pyrex-compiled C files.

Optional, Recommended

While pygr's core functionality only requires a sane python environment, some specific features require additional software:

• MySQL support: allows Pygr to access MySQL databases using its pygr.sqlgraph module. Also needed for worldbase module support for storage of worldbase resource databases in MySQL. Requirements: MySQL-python (MySQLdb module) >= 1.2.0; works with any server MySQL >= 3.23.x

• NCBI tools: used by the pygr.seqdb.BlastDB class to provide convenient blast/megablast search. Requirements: formatdb, blastall, megablast, any recent version which you can download from NCBI; executables must be in your $PATH.

Supported Platforms

In theory, pygr should work on any platform that adequately supports python. Here are the OS's we've successfully tested on:

• Linux 2.2.x/2.4.x
• Mac OS X
• OpenBSD
• Windows XP, Vista: please see our page on PygrOnWindows.

Installation

Installing pygr is quite simple.

cd pygr
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

Pygr contains several modules imported as follows:

from pygr import seqdb

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.

Pygr has a myriad of applications, however, providing a comprehensive description of its utility is out of the scope of this document (see PygrDocumentation).