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Official git repository for Biopython (converted from CVS)
Python TeX Parrot C HTML PLpgSQL Other
GSOC2010 bio.struct cif_fix endstatement_fix mangled-disordered master modeller-pirIO pdb-fixes pdb_enhancements
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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, 2.6 or 2.7":http://www.python.org/ We are phasing out support for Python 2.4. See below for notes about testing with Python 3. 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 "psycopg2":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, EMBOSS or ClustalW. **Python 3.x** Python 3 support is still incomplete, but the majority of modules are already functional. In order to be able to run Biopython with Python 3 you first need to convert the code. The conversion process is easy but it has to be done BEFORE running setup.py. To convert the code to Python 3, the 2to3 tool is required (this comes with Python 2.6+ and Python 3). On the top-level directory do: $ 2to3 --nofix=long --no-diffs -n -w Bio BioSQL Tests Scripts Doc/examples $ 2to3 --nofix=long --no-diffs -n -w -d Bio BioSQL Tests Scripts Doc/examples The first command converts the code, the second command converts the doctests (examples within the docstrings). You can in general ignore the output of 2to3. The tool takes some time to complete, please be patient (or use the -j option to set the number of threads used). After 2to3 execution the normal install from source process should be followed, i.e. "python3 setup.py build" etc (see below). To try Biopython on Python 3 on Windows, to call the 2to3 script you would use something like this (before compiling from source): C:\Python31\python.exe C:\Python31\Tools\Scripts\2to3.py --nofix=long ... **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 http://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. **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) 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 email@example.com. In the bug report, please let us know 1) which operating system and hardware you are using, 2) Python version, 3) Biopython version (or git 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. BioSQL/ -- Code for using Biopython with BioSQL databases. Doc/ -- Documentation. Scripts/ -- Miscellaneous, possibly useful, standalone scripts Tests/ -- Regression testing code