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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 <email@example.com> 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.