Python For Bioinformatics

You are a biologist who wants to learn Python. But you are a busy person, don’t have much time.

Py4Bio is a good option for you! You can go through the chapters of this series in a couple of afternoon, and you’ll have a pretty good idea of programming in Bioinformatics.

What you have to do is manually type each commands in your Python terminal and get the output. Don’t just read or skim through the materials, reproduce them too!

And try to do the exercises. Learning to programming is like building muscle, you have to do exercise!

This is a work in progress. Please let me know any feedback you have in the comments! Cheers!

Section 1: Fundamentals of Python

• Chapter 1: Strings
• Chapter 2: List
• Chapter 3: The for loop
• Chapter 4: if and files
• Chapter 5: while, elif, and write
• Chapter 6: Dictionaries
• Chapter 7: Functions

Section 2: Essential Modules

• Chapter 8: NumPy
• Chapter 9: Pandas
• Chapter 10: Matplotlib and Seaborn
• Chapter 11: Intro to OOP and Seq objects in Biopython
• Chapter 12: Dealing with genomic feature in Biopython
• Chapter 13: Manipulating GFF3, BED and other flat formats

Section 3: Advanced Topics

• Chapter 13: Advanced scripting with arguments
• Chapter 14: OOP introduction
• Chapter 15: Converting your script into a standalone command-line tool
• Chapter 16: Environment management with Conda