Harvard:Biophysics 101/2007:Python: Difference between revisions

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**[http://python.org/ftp/python/2.5/python-2.5.msi direct link to Windows installer]
**[http://python.org/ftp/python/2.5/python-2.5.msi direct link to Windows installer]
**[http://www.python.org/ftp/python/2.5/python-2.5-macosx.dmg direct link to MacOS X dmg]
**[http://www.python.org/ftp/python/2.5/python-2.5-macosx.dmg direct link to MacOS X dmg]
*[http://diveintopython.org/installing_python/index.html alternative instructions]


'''Documentation'''
'''Reading Material'''
*[http://diveintopython.org/toc/index.html Dive Into Python]
*[http://docs.python.org/tut/tut.html Python Tutorial]
*[http://docs.python.org/tut/tut.html Python Tutorial]
*[http://www.python.org/dev/peps/pep-0008/ Python Style Guide]
*[http://www.python.org/doc/essays/comparisons/ Comparing Python to other languages]
*[http://wiki.python.org/moin/PerlPhrasebook Perl-to-Python]
*[http://wiki.python.org/moin/PerlPhrasebook Perl-to-Python]
*[http://diveintopython.org/toc/index.html Dive Into Python] (for experienced programmers)
*[http://wiki.python.org/moin/BeginnersGuide Beginner's Guide] (includes instructions for non-programmers)
*[http://proquest.safaribooksonline.com.ezp1.harvard.edu/0596002815 Learning Python] (Online textbook for beginners)
*[http://www.amk.ca/python/howto/regex/ Py Reg Ex] (regular expressions)
*[http://www.python.org/doc/2.4.1/lib/lib.html Python Lib Ref]
*[http://www.python.org/doc/2.4.1/lib/lib.html Python Lib Ref]
*[http://www.amk.ca/python/howto/regex/ Py Reg Ex]
*[http://tinyurl.com/2mvzs7 Charming Python] (advanced topics)


==BioPython==
'''Documentation'''
*[http://biopython.org/wiki/Documentation BioPython documentation]
*[http://www.bioinformatics.org/bradstuff/bp/tut/index.html Tutorial & Cookbook]


==BioPython==
'''Pre-installation dependencies'''
'''Pre-installation dependencies'''
*Python (see above)
*Python (see above)
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*[http://numpy.scipy.org/#older_array Numeric 24.2] ([http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe direct link to Windows installer])
*[http://numpy.scipy.org/#older_array Numeric 24.2] ([http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe direct link to Windows installer])


'''Installation'''
'''Windows Installation'''
*[http://biopython.org/wiki/Download Download & Install]
*[http://biopython.org/wiki/Download Download & Install BioPython]
**[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to Windows installer]
**[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to BioPython Windows installer]
 
'''OS X Installation'''
*Install xcode tools (either download ~1GB from the [http://developer.apple.com/tools/download/ developer site]) or install from the OS X installation DVD.
*Download the three dependencies and extract them (double click on the file, or use "tar -xzf filename.tar.gz" for tar.gz files, or "tar -xf filename.tar")
**http://www.egenix.com/files/python/egenix-mx-base-2.0.6.tar.gz
**http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz                                         
**http://www.reportlab.org/ftp/ReportLab_2_0.tgz
*For each of the three packages, use a terminal window (/Applications/Utilities/Terminal) to enter the package directory (created when you extracted the files) and run the following commands:
<pre>
python setup.py build
python setup.py install
</pre>
*Download and extract [http://biopython.org/wiki/Download BioPython] source file (latest tar.gz file)
*From the extracted directory, run the following commands:
<pre>
python setup.py build
python setup.py test
python setup.py install
</pre>


'''Documentation'''
'''Linux'''
*[http://biopython.org/wiki/Documentation Main page]
*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-2-2|Ubuntu]] instructions from [[User:Denizkural|Deniz]]
*[http://www.bioinformatics.org/bradstuff/bp/tut/index.html Tutorial & Cookbook]
</div>
</div>

Latest revision as of 17:37, 19 April 2007

Biophysics 101: Genomics, Computing, and Economics

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Python

Installation

Reading Material

BioPython

Documentation

Pre-installation dependencies

Windows Installation

OS X Installation 

python setup.py build
python setup.py install
  • Download and extract BioPython source file (latest tar.gz file)
  • From the extracted directory, run the following commands:
python setup.py build
python setup.py test
python setup.py install

Linux

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