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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Solve advanced computational biology problems and build production pipelines with Python & AI tools

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Product type Paperback
Published in Jan 2026
Last Updated in Oct 2025
Publisher Packt
ISBN-13 9781836642756
Length 617 pages
Edition 4th Edition
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Author (1):
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Shane Brubaker Shane Brubaker
Author Profile Icon Shane Brubaker
Shane Brubaker
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Table of Contents (14) Chapters Close

1. Bioinformatics with Python Cookbook, Fourth Edition: Solve advanced computational biology problems and build production pipelines with Python & AI tools FREE CHAPTER
2. Chapter 1: Computer Specifications and Python Setup 3. Chapter 2: Basics of Data Manipulation 4. Chapter 3: Modern Coding Practices and AI-generated coding 5. Chapter 4: Data Science and Graphing 6. Chapter 5: Alignment and Variant Calling 7. Chapter 6: Annotation and Biological Interpretation 8. Chapter 7: Genomes and Genome Assembly 9. Chapter 8: Accessing Public Databases 10. Chapter 9: Protein Structure and Proteomics 11. Chapter 10: Phylogenetics 12. Chapter 11: Population Genetics 13. Chapter 12: Mectabolic Modeling and Other Applications 14. Chapter 13: Genome Editing

Writing Tests with AI-assisted coding

In this recipe we will try out a really useful function of AI-Assisted coding: test writing. Tools like ChatGPT can help you write a variety of tests automatically for your code. This helps ensure completeness and accuracy. We will take the code from read alignment work in Recipe 3-3, Read Alignment and write some tests for it.Go into ChatGPT and get ready to write a prompt to add testing code for the alignment function that we just wrote in Recipe 3.3

How to do it...

Here are the steps to try this recipe:

  1. We’ll begin by writing a prompt to develop testing code for the alignment code we wrote in the previous recipe (make sure it is still available in ChatGPT, if it’s not then run the examples from the Sequence manipulation and Read alignment recipes first). Here’s the prompt: Write test code for the above

    Note

    We can be very generic with our instructions with ChatGPT. We could have said “write unit tests” or...

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