HTTPS clone URL
Subversion checkout URL
Official git mirror of the Biopython CVS repository
Python C Nu
Nothing to show
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. **For the impatient** To build and install Biopython, type: python setup.py build python setup.py test python setup.py install **System Requirements** o "Python 2.2 or better":http://www.python.org/ o "mxTextTools":http://starship.python.net/~lemburg/mxTextTools.html This is used in many of the text handling routines in Biopython. Much of Biopython will not work without it. o "Numerical Python":http://numpy.sourceforge.net/ (optional) 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 Numeric Python first. Also, please install if you are seeing error messages such as: ImportError: No module named Numeric o ReportLab (optional) This package is used in some code that generates graphical displays of chromosomes. If you do not need this functoinality, 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 only used by Bio.GFF to access a MySQL database. **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, type: drevil:~/biopython> python setup.py test If you have Tk installed, this will run a nice GUI that displays the results of the tests. Otherwise, you will see results on the command line. Do not panic if you see messages warning of skipped tests: Skipping test because of import error: No module named reportlab.pdfgen 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. genbank_format.py) 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/maillists/ **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, used in many Biopython parsers. BioSQL/ -- Code for using Biopython with BioSQL databases. Doc/ -- Documentation. Scripts/ -- Miscellaneous, possibly useful, standalone scripts Tests/ -- Regression testing code