Introduction to Python for Bioinformatics

We will be using the Anaconda Python distribution, so download and install it from here.

Sometimes we will use the Visual Studio code text editor, which you can get here.

And we will be using the Python for Biologists book which you can get a copy of here. The exercise files for Python for Biologists are here.

We will be using this Etherpad for shared notes.

You can use the online Jupyter Lab environment if your laptop is not working.

Notebooks with Python code

Day 1: Chapter 2 of Python for Bioinformatics notebook.
Solutions for Chapter 2 problems: notebook.

Day 2: Chapter 3 of Python for Bioinformatics notebook.
Solutions for Chapter 3 problems: notebook.

Chapter 4 of Python for Biologists: notebook.
Solutions for Chapter 4 problems: notebook
For exercises, prepare the input files by running code in this notebook.

Chapter 5 of Python for Biologists notebook.
Solutions for Chapter 5 problems: notebook.

Chapter 6 of Python for Biologists notebook.
Chapter 6 problems: notebook.

Chapter 7 of Python for Biologists notebook.
Chapter 7 problems: notebook.

Chapter 8 of Python for Biologists notebook (which also contains exercise).

Chapter 9 of Python for Biologists notebook and chapter9.py script.

The pandas module: notebook and tutorial.

Additional Materials

The lessons from Software Carpentry on Python are useful:
1. Programming with Python
2. Plotting and programming with Python

Debuggex – for Regular Expression debugging is here

Argparse tutorials one and two.

Info on the conda package manager.