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Nick Matzke's git mirror of the Biopython CVS repository, for GSoC 2009 project: BioGeography module for biopython
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**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. **For the impatient** To build and install Biopython, download and unzip the source code, go to this directory at the command line, and type: python setup.py build python setup.py test python setup.py install **System Requirements** o "Python 2.3, 2.4, 2.5 or 2.6":http://www.python.org/ Note that support for Python 2.3 is likely to be dropped in a few releases time. Given that Python 2.6 is still very new, it would be prudent to opt for Python 2.5 or 2.4 at this time. o "NumPy":http://numpy.scipy.org/ (optional, but strongly recommended) This package is only used in the computationally-oriented modules. It is required for Bio.Cluster and a few other modules. If you think you might need these modules, then please install NumPy first. Also, please install if you are seeing error messages such as: ImportError: No module named numpy Please note that this is the current NumPy distribution. The older Numeric library is no longer supported in Biopython. o "ReportLab":http://www.reportlab.org/downloads.html (optional) This package is used in some code that generates graphical displays of chromosomes. If you do not need this functionality, you will not need to install this package. o "psycopg":http://initd.org/software/psycopg/ (optional) or "pgdb":http://www.druid.net/pygresql/ (optional) These packages are used by BioSQL to access a PostgreSQL database. o "MySQLdb":http://sourceforge.net/projects/mysql-python (optional) This package is used by BioSQL or Bio.GFF to access a MySQL database. o "mxTextTools":http://www.egenix.com/files/python/mxTextTools.html (unlikely) You probably won't need mxTextTools. This was used in some of Biopython's older parsers, and Martel/Mindy, but these have all been deprecated now. In addition there are a number of useful third party tools you may wish to install such as standalone NCBI BLAST or ClustalW. **Installation** *** Make sure that Python is installed correctly *** Installation should be as simple as going to the biopython source code 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 is running correctly. To do the tests, go to the biopython source code directory and type: 'python setup.py test' Do not panic if you see messages warning of skipped tests: test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL. This most likely means that a package is not installed. You can ignore this if it occurs in the tests for a module that you were not planning on using. If you did want to use that module, please install the required dependency and re-run the tests. **Bugs** While we try to ship a robust package, bugs inevitably pop up. If you are having problems that might be caused by a bug in Biopython, it is possible that it has already been identified. Search the "bug database":http://bugzilla.open-bio.org/ and mailing lists to see if it has already been reported (and hopefully fixed). If you suspect the problem lies within a parser, it is likely that the data format has changed and broken the parsing code. (The BLAST and GenBank formats seem to be particularly fragile.) Thus, the parsing code in Biopython is updated faster than we can build Biopython releases. You can get the most recent parser by pulling the relevant files (e.g. the ones in Bio.SeqIO or Bio.Blast) out of "anonymous cvs":http://cvs.biopython.org/ . However, be careful when doing this, because the code in CVS is not as well-tested as released code, and may contain new dependencies. Finally, you can send a bug report to the bug database or firstname.lastname@example.org. In the bug report, please let us know 1) which operating system and hardware you are using, 2) Python version, 3) Biopython version (or CVS version/date), 4) traceback that occurs, 5) offending code, and 6) data file that causes the problem. **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, documentation writing, technical administration, and whatever else comes up. If you wish to contribute, please visit the "web site":http://www.biopython.org and join our "mailing list":http://biopython.org/wiki/Mailing_lists **Distribution Structure** README -- This file. NEWS -- Release notes and news LICENSE -- What you can do with the code. CONTRIB -- An (incomplete) list of people who helped Biopython in one way or another. DEPRECATED -- Contains information about modules in Biopython that are removed or no longer recommended for use, and how to update code that uses those modules. MANIFEST.in -- Tells distutils what files to distribute setup.py -- Installation file. Bio/ -- The main code base code. Martel/ -- Code for the Martel parsing system, once used in many Biopython parsers but now deprecated. BioSQL/ -- Code for using Biopython with BioSQL databases. Doc/ -- Documentation. Scripts/ -- Miscellaneous, possibly useful, standalone scripts Tests/ -- Regression testing code