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

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(Python: - charming python link)
 
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*[http://diveintopython.org/installing_python/index.html alternative instructions]
 
*[http://diveintopython.org/installing_python/index.html alternative instructions]
  
'''Documentation'''
+
'''Reading Material'''
*[http://proquest.safaribooksonline.com.ezp1.harvard.edu/0596002815 Learning Python] (for beginners)
 
*[http://diveintopython.org/toc/index.html Dive Into Python] (for experienced programmers)
 
 
*[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==
 
==BioPython==
 +
'''Documentation'''
 +
*[http://biopython.org/wiki/Documentation BioPython documentation]
 +
*[http://www.bioinformatics.org/bradstuff/bp/tut/index.html Tutorial & Cookbook]
 +
 
'''Pre-installation dependencies'''
 
'''Pre-installation dependencies'''
 
*Python (see above)
 
*Python (see above)
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python setup.py install
 
python setup.py install
 
</pre>
 
</pre>
*Download and extract [http://biopython.org/wiki/Download BioPython] source file
+
*Download and extract [http://biopython.org/wiki/Download BioPython] source file (latest tar.gz file)
**http://biopython.org/DIST/biopython-1.42.tar.gz
 
 
*From the extracted directory, run the following commands:
 
*From the extracted directory, run the following commands:
 
<pre>
 
<pre>
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</pre>
 
</pre>
  
'''Documentation'''
+
'''Linux'''
*[http://biopython.org/wiki/Documentation BioPython documentation]
+
*[[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 16:37, 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