Python C Nu
Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Failed to load latest commit information.|
Biopython README file ===================== The Biopython Project (http://www.biopython.org/) 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. System Requirements ------------------- o Python 1.52 or above http://www.python.org/ o Distutils 0.8.2 http://www.python.org/sigs/distutils-sig/ 0.9 may not work, due to differences in specifying extension packages. o Numerical Python 15.3 (optional) http://numpy.sourceforge.net/ This is only required if you want to use the classification tools. 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. Testing ------- Biopython includes a suite of regression tests to check if everything's running correctly. To do the tests, go to the Tests/ die rectory in the distribution and run br_regrtest.py: drevil:~/biopython/Tests> python br_regrtest.py test_Enzyme test_Fasta test_Fasta2 test_File test_KeyWList 5 tests OK. drevil:~/biopython/Tests> XXX We need to get this more closely integrated with the installation process. 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. http://www.biopython.org/ http://www.biopython.org/MailList.shtml If you wish to contribute a bug report, please submit them to the online bug reporting form at: http://www.biopython.org/biopython-bugs/ 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...) - Annotations on sequences - BLAST additions o PSI-BLAST on WWW - parsers o Enzyme - add parsers, iterator, dictionary, etc. o PDB - needs to be done - build on Andrew's UPDB? o Genbank - Chris Fenton email@example.com - generalize parsers - bug database - regression tests - documentation(!!) - look into Zope-ifying the web site - deprecate Seq.py - microarray data - look into docstring browser If you see something here you would like to work on, please let me know! Thanks, Jeff (firstname.lastname@example.org)