This week, you'll learn how to write python programs that run under the command line. You'll also get more experience working with the BED file format.
The term scripting refers to writing programs designed to run as a series of steps, like a script in a play.
Most scripts are written to do a very specific, simple task, and often we link scripts into workflows, also called pipelines.
To write good scripts, you''ll continue to use the python interpreter, but when you run the scripts, you'll treat them just like any other UNIX command line utility.
Reading and references
- What makes an awesome commandline application
- BED format described: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
- Handout describing gene models and the bed format: gene_models.pdf
- How to make a file executable after checking it into subversion