Python programming with applications to bioinformatics

Description

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

The course consists of a mix of presentations, demonstrations, and practical exercises (either in the lab with assistants or on your own). Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class.

Topics covered

• Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments
• Different ways to control program flow using loops and conditional tests
• Regular expressions and pattern matching
• Writing functions and best-practice ways of making them usable
• Reading from and writing to files
• Code packaging and Python libraries
• How to work with biological data using external libraries (if time allows).

Learning outcomes

Upon completion of this course, you will be able to:

• Describe and apply basic concepts in Python, such as:
  • Loops
  • If/else statements
  • Functions
  • Reading/writing to files
• Being able to edit and run Python code
• Write file-processing Python programs that produce output to the terminal and/or external files
• Create stand-alone python programs to process biological data
• Know how to develop your skills in Python after the course (including debugging)

Pre-requisites

The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises.

Level

beginner