Harvard:Biophysics 101/2007:Python

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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]
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*[http://diveintopython.org/installing_python/index.html alternative instructions]
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'''Documentation'''
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'''Reading Material'''
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*[http://proquest.safaribooksonline.com.ezp1.harvard.edu/0596002815 Learning Python] (for beginners)
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*[http://diveintopython.org/toc/index.html Dive Into Python] (for experienced programmers)
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*[http://docs.python.org/tut/tut.html Python Tutorial]
*[http://docs.python.org/tut/tut.html Python Tutorial]
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*[http://www.python.org/dev/peps/pep-0008/ Python Style Guide]
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*[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]
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*[http://diveintopython.org/toc/index.html Dive Into Python] (for experienced programmers)
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*[http://wiki.python.org/moin/BeginnersGuide Beginner's Guide] (includes instructions for non-programmers)
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*[http://proquest.safaribooksonline.com.ezp1.harvard.edu/0596002815 Learning Python] (Online textbook for beginners)
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*[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]
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*[http://www.amk.ca/python/howto/regex/ Py Reg Ex]
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*[http://tinyurl.com/2mvzs7 Charming Python] (advanced topics)
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==BioPython==
==BioPython==
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'''Documentation'''
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*[http://biopython.org/wiki/Documentation BioPython documentation]
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*[http://www.bioinformatics.org/bradstuff/bp/tut/index.html Tutorial & Cookbook]
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'''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])
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'''Installation'''
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'''Windows Installation'''
*[http://biopython.org/wiki/Download Download & Install BioPython]
*[http://biopython.org/wiki/Download Download & Install BioPython]
**[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to BioPython Windows installer]
**[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to BioPython Windows installer]
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'''Documentation'''
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'''OS X Installation'''
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*[http://biopython.org/wiki/Documentation BioPython documentation]
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*Install xcode tools (either download ~1GB from the [http://developer.apple.com/tools/download/ developer site]) or install from the OS X installation DVD.
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*[http://www.bioinformatics.org/bradstuff/bp/tut/index.html Tutorial & Cookbook]
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*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")
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**http://www.egenix.com/files/python/egenix-mx-base-2.0.6.tar.gz
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**http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz                                         
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**http://www.reportlab.org/ftp/ReportLab_2_0.tgz
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*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:
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<pre>
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python setup.py build
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python setup.py install
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</pre>
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*Download and extract [http://biopython.org/wiki/Download BioPython] source file (latest tar.gz file)
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*From the extracted directory, run the following commands:
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<pre>
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python setup.py build
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python setup.py test
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python setup.py install
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</pre>
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'''Linux'''
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*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-2-2|Ubuntu]] instructions from [[User:Denizkural|Deniz]]
</div>
</div>

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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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