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] | ||
| + | *[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/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:// | + | *[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) | ||
| Line 23: | Line 32: | ||
*[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''' |
| - | *[http:// | + | *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> | ||
| + | |||
| + | '''Linux''' | ||
| + | *[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-2-2|Ubuntu]] instructions from [[User:Denizkural|Deniz]] | ||
</div> | </div> | ||
Current revision
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
