Programming with Python and Biopython

This lesson is an introduction to programming Python, using Biopython applications as motivation. It is designed to be used in Software Carpentry workshops. Like most Software Carpentry Python lessons, it references Jupyter Notebooks, but can be taught using a regular Python interpreter as well. Please note that this lesson uses Python 3 rather than Python 2.

Schedule

13:00	Running and Quitting	How can I run Python programs?
13:15	Variables and Assignment	How can I store data in programs?
13:25	Data Types and Type Conversion	What kinds of data do programs store? How can I convert one type to another?
13:35	Built-in Functions and Help	How can I use built-in functions? How can I find out what they do?
13:55	Error Messages	What kind of errors can occur in programs? How can I identify errors when they occur?
14:10	Libraries	How can I use software that other people have written? How can I find out what that software does?
14:20	Afternoon Coffee	Break
14:35	Lists and Indexing	How can I store multiple values?
14:55	For Loops	How can I make a program do many things?
15:15	Conditionals	How can programs do different things for different data?
15:30	Sets	What is a set, and how do I use it?
15:40	Night	Break
08:40	Biopython	How do I handle sequence files?
09:00	Writing Functions	How can I create my own functions?
09:25	Programming Style	How can I make my programs more readable? How do most programmers format their code?
09:50	Debugging	How can I debug my program?
10:15	Defensive Programming	What sorts of things frequently go wrong in programs? How can I make my programs more robust?
10:30	Morning Coffee	Break
10:45	Reading Tabular Data into Data Frames	How can I read tabular data?
11:00	Pandas Data Frames	How can I do statistical analysis of tabular data?
11:20	Next Steps	What else is out there and where do I find it?
11:35	Wrap-Up	What have we learned?
11:50	Finish

Programming with Python and Biopython

Prerequisites

Schedule