biopython 1.61

Biopython README file

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

Our website http://www.biopython.org provides an online resource for modules, scripts, and web links for developers of Python-based software for life science research. This is hosted by the Open Bioinformatics Foundation or O|B|F, http://www.open-bio.org, who also host BioPerl etc.

This Biopython package is made available under generous terms. Please see the LICENSE file for further details.

If you use Biopython in work contributing to a scientific publication, we ask that you cite our application note (below) or one of the module specific publications (listed on our website):

Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878

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 sudo python setup.py install

System Requirements

• Python 2.5, 2.6 or 2.7, see http://www.python.org See below for notes about testing with Python 3.

• NumPy, see http://numpy.scipy.org (optional, but strongly recommended) This package is only used in the computationally-oriented modules. It is required for Bio.Cluster, Bio.PDB and a few other modules. If you think you might need these modules, then please install NumPy first BEFORE installing Biopython. The older Numeric library is no longer supported in Biopython.

• ReportLab, see http://www.reportlab.com/software/opensource/ (optional) This package is only used in Bio.Graphics, so if you do not need this functionality, you will not need to install this package. You can install it later if needed.

• matplotlib, see http://matplotlib.org/ (optional) The Bio.Phylo uses this package to plot phylogenetic trees. As with ReportLab, you can install this at any time to enable the plotting functionality.

• networkx, see http://networkx.lanl.gov/ (optional) and pygraphviz or pydot, see http://networkx.lanl.gov/pygraphviz/ and http://code.google.com/p/pydot/ (optional) These packages are used for certain niche functions in Bio.Phylo. Again, they are only needed to enable these functions and can be installed later if needed.

• psycopg2, see http://initd.org/psycopg/ (optional) or PyGreSQL (pgdb), see http://www.pygresql.org/ (optional) These packages are used by BioSQL to access a PostgreSQL database.

• MySQLdb, see http://sourceforge.net/projects/mysql-python (optional) This package is used by BioSQL to access a MySQL database.

In addition there are a number of useful third party tools you may wish to install such as standalone NCBI BLAST, EMBOSS or ClustalW.

Python 3.x

Note we do not intend to support Python 3.0, please use Python 3.1 or later. Python 3 support is still incomplete (and we do not yet officially support using Biopython with Python 3), but the majority of modules are largely functional. In order to be able to run Biopython with Python 3 it is first converted using the 2to3 script. This is done automatically by the setup.py script. Use python3 setup.py build etc (see installation notes below).

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 build python setup.py test sudo 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.

Source Code Repository

Like most of the Open Bioinformatics Foundation (OBF) projects, Biopython currently uses git for distributed source code control, hosted by github at https://github.com/biopython/biopython

Until late September 2009, Biopython source code was kept in CVS running on the OBF servers. These will remain online for a while as “read only” static backups of everything up to and including Biopython 1.52.

Experimental code

Biopython 1.61 introduced a new warning, Bio.BiopythonExperimentalWarning, which will be used to mark any experimental code included in the otherwise stable Biopython releases. Such ‘beta’ level code is ready for wider testing, but still likely to change, and should only be tried by early adopters in order to give feedback via the biopython-dev mailing list.

We’d expect such experimental code to reach stable status within one or two releases, at which point our normal policies about trying to preserve backwards compatibility would apply.

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. Update to the latest release if you are not using it already, and retry. If the problem persists, please search our bug database at https://redmine.open-bio.org/projects/biopython and our mailing lists to see if it has already been reported (and hopefully fixed), and if not please do report the bug. We can’t fix problems we don’t know about ;)

If you suspect the problem lies within a parser, it is likely that the data format has changed and broken the parsing code. (The text BLAST and GenBank formats seem to be particularly fragile.) Thus, the parsing code in Biopython is sometimes 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) from our git repository. However, be careful when doing this, because the code in github 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 the mailing list at biopython@biopython.org. In the bug report, please let us know:

1. Which operating system and hardware (32 bit or 64 bit) you are using

2. Python version

3. Biopython version (or git version/date)

4. Traceback that occurs (the full error message)

   And also ideally:

5. Example code that breaks

6. A 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.

BioSQL/ – Code for using Biopython with BioSQL databases.

Doc/ – Documentation.

Scripts/ – Miscellaneous, possibly useful, standalone scripts

Tests/ – Regression testing code