Harvard:Biophysics 101/2007:Python: Difference between revisions
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*[http://diveintopython.org/installing_python/index.html alternative instructions] | *[http://diveintopython.org/installing_python/index.html alternative instructions] | ||
''' | '''Reading Material''' | ||
*[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/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.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://tinyurl.com/2mvzs7 Charming Python] (advanced topics) | |||
==BioPython== | ==BioPython== | ||
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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) | ||
*From the extracted directory, run the following commands: | *From the extracted directory, run the following commands: | ||
<pre> | <pre> | ||
| Line 55: | Line 56: | ||
'''Linux''' | '''Linux''' | ||
*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-2-2|Ubuntu]] | *[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-2-2|Ubuntu]] instructions from [[User:Denizkural|Deniz]] | ||
</div> | </div> | ||
Latest revision as of 17:37, 19 April 2007
Python
Installation
Reading Material
- Python Tutorial
- Python Style Guide
- Comparing Python to other languages
- Perl-to-Python
- Dive Into Python (for experienced programmers)
- Beginner's Guide (includes instructions for non-programmers)
- Learning Python (Online textbook for beginners)
- Py Reg Ex (regular expressions)
- Python Lib Ref
- Charming Python (advanced topics)
BioPython
Documentation
Pre-installation dependencies
- Python (see above)
- mxTextTools (direct link to Windows installer)
- Numeric 24.2 (direct link to Windows installer)
Windows Installation
OS X Installation
- Install xcode tools (either download ~1GB from the 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")
- 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:
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
