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README
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README
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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.
Our website 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, 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
doi: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**
o "Python 2.4, 2.5 or 2.6":http://www.python.org/
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, 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.
o "ReportLab":http://www.reportlab.org/downloads.html (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.
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.
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 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.
**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 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) 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
biopython@biopython.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 since deprecated and no longer
installed.
BioSQL/ -- Code for using Biopython with BioSQL databases.
Doc/ -- Documentation.
Scripts/ -- Miscellaneous, possibly useful, standalone scripts
Tests/ -- Regression testing code