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

Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software.

Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--including linters, formatters, type checkers, and tests--to create documented and tested programs. You'll also tackle 14 challenges at Rosalind, a problem-solving platform for learning bioinformatics and programming.

• Create command-line Python programs to document and validate parameters
• Write tests to verify refactor programs and confirm they're correct
• Address bioinformatics ideas using Python data structures and modules such as 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
• Use higher-order functions in Python like filter(), map(), and reduce()

現今的生命科學家迫切需要接受生物信息學技能的培訓。太多的生物信息學程式是寫得很差且幾乎沒有維護，通常是由從未學過基本程式設計技能的學生和研究人員所撰寫。這本實用指南向博士後生物信息學專業人員和學生展示如何利用Python的優勢來解決生物學問題，同時創建有文件、經過測試且可重現的軟體。

《Tiny Python Projects》（Manning）的作者Ken Youens-Clark不僅展示了如何撰寫有效的Python程式碼，還介紹了如何使用測試來撰寫和重構科學程式。您將學習最新的Python功能和工具，包括檢查器、格式化工具、類型檢查器和測試，以創建有文件且經過測試的程式。您還將在Rosalind這個用於學習生物信息學和程式設計的問題解決平台上解決14個挑戰。

本書內容包括：
- 創建命令行Python程式以記錄和驗證參數
- 撰寫測試以驗證重構的程式並確保其正確性
- 使用Python數據結構和模組（如Biopython）來處理生物信息學概念
- 使用makefile創建可重現的快捷方式和工作流程
- 解析重要的生物信息學文件格式，如FASTA和FASTQ
- 使用正則表達式尋找文本模式
- 在Python中使用高階函數，如filter()、map()和reduce()

Ken Youens-Clark works as a Data Engineer at The Critical Path Institute where he helps partners in industry, academia, and government find novel drug therapies for diseases ranging from cancer and tuberculosis to thousands of rare diseases. His career in bioinformatics began in 2001 when he joined a plant genomics project at Cold Spring Harbor Laboratory under the direction of Dr. Lincoln Stein, a prominent author of books and modules in Perl and an early advocate for open software, data, and science. In 2014 Ken moved to Tucson, AZ, to work as a Senior Scientific Programmer at the University of Arizona where he completed a MS in Biosystems Engineering in 2019. While at UA, Ken enjoyed teaching programming and bioinformatics skills, and used some of those ideas in his first book, Tiny Python Projects (Manning, 2020), which uses a test-driven development approach to teaching Python.

Ken Youens-Clark在The Critical Path Institute擔任數據工程師，協助工業、學術界和政府合作夥伴尋找從癌症和結核病到數千種罕見疾病的新型藥物療法。他的生物信息學職業生涯始於2001年，當時他加入了Cold Spring Harbor Laboratory的一個植物基因組學項目，由Perl的書籍和模塊的知名作者Dr. Lincoln Stein指導，他也是開放軟件、數據和科學的早期倡導者。2014年，Ken搬到亞利桑那州圖森市，在亞利桑那大學擔任高級科學程序員，並於2019年獲得生物系統工程碩士學位。在UA期間，Ken喜歡教授編程和生物信息學技能，並將其中一些想法應用於他的第一本書《Tiny Python Projects》（Manning，2020），該書使用測試驅動開發方法來教授Python。