PYTHON Quick Links

I write a lot of code using the PYTHON Programing Language.  I just gave a very brief overview to a friend who has to learn it this summer. In the course of this lesson, it occurred to me that a lot of the bioinformatic resources that I use every day are not collected in one place.  So I’ve listed a couple of the most useful modules/packages below:

  • BioPython
    • This package lets you interface with NCBI, parse datafiles (e.g. fastas, Genbank, blast output etc.), run blast queries, run clustalw, etc.
  • SciPy
    • N-dimensional array manipulation
  • MatPlotLib
    • Graphing.
  • Python DB API
    • Database integration
  • Google App Engine
    • Free webhosting of python cgi scripts.  It’s in beta.
  • Django
    • Python Web Application Development package. It can be used in conjunction with Google App Engine.

Here are a few addition sites that I find useful:

  • Python 2.5 Quick Reference
    • both html and PDF versions are available for free!
  • TextMate
    • OS X text editor. It’s not free, but there is a student discount available
  • Forklift
    • OS X ftp program. Also not free, but reasonably priced.

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