Harvard:Biophysics 101/2009:Python

Python

Installation

• Main download page
  • direct link to Windows installer
  • direct link to MacOS X dmg
• alternative instructions

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

• BioPython documentation
• Tutorial & Cookbook

Pre-installation dependencies

• Python (see above)
• mxTextTools (direct link to Windows installer)
• Numeric 24.2 (direct link to Windows installer)

Windows Installation

• Download & Install BioPython
  • direct link to BioPython Windows installer

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")
  • 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:

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

• Ubuntu instructions from Deniz