Python for Biologists

Learning objectives

• Ability to run Python scripts and work in interactive Python sessions
• Ability to understand and edit existing Python scripts
• Ability to manipulate numbers and text
• Ability to create reusable functions
• Basic understanding of Python’s built-in data types and structures
• Basic understanding of control flow and loops
• Ability to read in and write out files
• Ability to reuse functionality from Python’s built-in standard library
• Experience of creating a complex data analysis script

Contents

• Interacting with Python
  • What is Python?
  • The Python interpreter
  • The IPython interpreter
  • Running a Python script
  • Exercises
• Editing scripts
  • Finding a text editor
  • Whitespace matters!
  • Exercises
• Manipulating numbers
  • Mathematical operations
  • Variables
  • Exercises
• Manipulating strings
  • Creating strings
  • Useful string methods
  • Exercises
• Creating reusable functions
  • Exercises
• Data types
  • Background
  • Practical examples
  • Exercises
• Data structures
  • Lists
  • Tuples
  • Dictionaries
  • Exercises
• Control flow and loops
  • Conditional statements and boolean operators
  • Looping
  • Exercises
• Reading and writing files
  • Exercises
• Reusing code
  • Exercises
• Parsing FASTA files
  • The FASTA file format
  • Working with “big data”
  • Exercises
• Linking it all together
  • Getting input from the command line
  • Exercises
• Further reading
• Instructor notes