ToyokoLabs / Py4Bio

Public data for the book Python for Bioinformatics

Py4Bio

Public data for the book Python for Bioinformatics.

This repo has all source code, Jupyter notebooks and data needed to run all sample code from the book Python for Bioinformatics.

Directories:

• code: There are a directory per chapter, inside each directory there are all programs for each chapter.
• notebooks: Jupyter notebook, one per chapter. To run these notebooks, you need Jupyter.
• samples: Supplementary data needed for some of the programs.

Jupyter Notebook

• nbviewer: will show you the rendered Notebook
• Open in Colab: You can run the Notebook on the Google Colab.

Chapter	Title	nbviewer	Open in Colab
1	Introduction
2	First Steps with Python
3	Basic Programming - Data Types
4	Programming - Flow Control
5	Handling Files
6	Code Modularizing
7	Error Handling
8	Introduction to Object Orienting Programming (OOP)
9	Introduction to Biopython
10	Web Applications
11	XML
12	Python and Databases
13	Regular Expressions
14	Graphics in Python
15	Sequence Manipulation in Batch
16	Web Application for Filtering Vector Contamination
17	Searching for PCR Primers Using Primer3
18	Calculating Melting Temperature from a Set of Primers
19	Filtering Out Specific Fields from a GenBank File
20	Inferring Splicing Sites
21	Web Server for Multiple Alignment
22	Drawing Marker Positions Using Data Stored in a Database
23	Online Bonus chapter. DNA Mutations with Restrictions