Freely available tools for computational molecular biology.
Project description
**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 2.0":http://www.python.org/ or above
o "mxTextTools":http://starship.python.net/~lemburg/mxTextTools.html
o "Numerical Python 15.3 or above":http://numpy.sourceforge.net/ (optional)
This is only required if you want to use the classification tools.
o "Martel":http://www.biopython.org/~dalke/Martel/
(now included in Biopython by default, so don't worry about adding this)
**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.
For FreeBSD users, "Johann Visagie", mailto:wjv@cityip.co.za has made
Biopython available in the ports tree. According to Johann:
This means that a FreeBSD user with an up-to-date ports tree can now
install BioPython as simply as:
'cd /usr/ports/biology/py-biopython ; make install'
Fetching of the package as well as installation of all dependencies
(Python itself as well as Distutils) will be handled automagically.
**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.
**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, 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://www.biopython.org/MailList.shtml
If you wish to contribute a bug report, please submit them to the
"online bug reporting form":http://www.biopython.org/biopython-bugs/
**Distribution Structure**
AUTHORS -- An (incomplete) list of people who have contributed.
Bio/ -- The python package that makes up biopython
Doc/ -- Documentation
LICENSE -- License information for this package
MANIFEST.in -- Tells distutils what files to distribute
NEWS -- Release notes and news
README -- This file
Scripts/ -- Miscellaneous, possibly useful, standalone scripts
Tests/ -- Regression testing code
setup.py -- Installation file.
**To Do**
(In no particular order...)
- PDB parser
- more regression tests
- microarray data
If you see something here you would like to work on, please send mail
to biopython@biopython.org!
Thanks
"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 2.0":http://www.python.org/ or above
o "mxTextTools":http://starship.python.net/~lemburg/mxTextTools.html
o "Numerical Python 15.3 or above":http://numpy.sourceforge.net/ (optional)
This is only required if you want to use the classification tools.
o "Martel":http://www.biopython.org/~dalke/Martel/
(now included in Biopython by default, so don't worry about adding this)
**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.
For FreeBSD users, "Johann Visagie", mailto:wjv@cityip.co.za has made
Biopython available in the ports tree. According to Johann:
This means that a FreeBSD user with an up-to-date ports tree can now
install BioPython as simply as:
'cd /usr/ports/biology/py-biopython ; make install'
Fetching of the package as well as installation of all dependencies
(Python itself as well as Distutils) will be handled automagically.
**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.
**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, 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://www.biopython.org/MailList.shtml
If you wish to contribute a bug report, please submit them to the
"online bug reporting form":http://www.biopython.org/biopython-bugs/
**Distribution Structure**
AUTHORS -- An (incomplete) list of people who have contributed.
Bio/ -- The python package that makes up biopython
Doc/ -- Documentation
LICENSE -- License information for this package
MANIFEST.in -- Tells distutils what files to distribute
NEWS -- Release notes and news
README -- This file
Scripts/ -- Miscellaneous, possibly useful, standalone scripts
Tests/ -- Regression testing code
setup.py -- Installation file.
**To Do**
(In no particular order...)
- PDB parser
- more regression tests
- microarray data
If you see something here you would like to work on, please send mail
to biopython@biopython.org!
Thanks
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