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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

Code Review with AI

One of the most important jobs of a software engineer is to review the code of other engineers. This is typically done at modern companies to ensure code quality and can be as important and demanding as writing the code itself.Typically, one or more engineers, often someone more senior, may review your code and make comments to improve the code further, add more tests, or “nits” that can be just small format improvements. You will be expected to address these comments before the code is ready.Here is an example of a typical pull request in GitHub, where someone has requested additional changes to the code:

Figure 3.9 – An example of the code review process in Github

In this recipe, we will use AI to help us simulate a typical Code Review process and get a feel for how we would use it to improve our code further.

How to do it...

Here are the steps to try this recipe:

  1. Let’s use ChatGPT to simulate a Pull Request process. First, grab the...
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