Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing

Life scientists urgently need training in bioinformatics skills, and this practical guide shows how to exploit Python to solve biological problems while creating documented, tested, and reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and use tests to write and refactor scientific programs.

Format: Paperback / softback
Length: 350 pages
Publication date: 18 May 2021
Publisher: O'Reilly Media, Inc, USA

The demand for bioinformatics skills among life scientists is rapidly increasing, and there is a critical need for training in this field. Unfortunately, many bioinformatics programs are poorly written and barely maintained, often by students and researchers who lack basic programming skills. This practical guide aims to address this issue by providing postdoc bioinformatics professionals and students with the necessary skills to exploit the best parts of Python to solve problems in biology while creating documented, tested, and reproducible software.

The author of Tiny Python Projects (Manning), Ken Youens-Clark, takes the readers on a journey to write effective Python code and utilize tests to write and refactor scientific programs. He demonstrates how to use the latest Python features and tools, such as linters, formatters, type checkers, and tests, to create documented and tested programs. The guide also tackles 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming.

Through this guide, readers will learn how to create command-line Python programs to document and validate parameters, write tests to verify refactor programs and confirm their correctness, address bioinformatics ideas using Python data structures and modules like Biopython, create reproducible shortcuts and workflows using makefiles, parse essential bioinformatics file formats such as FASTA and FASTQ, find patterns of text using regular expressions, and use higher-order functions in Python like filter(), map(), and reduce().

By mastering these bioinformatics skills, life scientists can improve their productivity, accuracy, and reproducibility in their research, leading to groundbreaking discoveries in the field of biology.

Weight: 780g
Dimension: 179 x 233 x 27 (mm)
ISBN-13: 9781098100889