Harvard:Biophysics 101/2009:Python
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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
