Mastering Python for Bioinformatics pdf

肯·尤恩斯·克拉克 在关键路径研究所担任数据工程师，他帮助工业界、学术界和政府的合作伙伴为从癌症和肺结核到数千种罕见疾病的疾病寻找新的药物疗法。 他的生物信息学职业生涯始于 2001 年，当时他加入冷泉港实验室的植物基因组学项目，在林肯斯坦博士的指导下，他是 Perl 书籍和模块的著名作者，也是开放软件、数据和科学的早期倡导者。 2014 年，Ken 搬到亚利桑那州图森市，在亚利桑那大学担任高级科学程序员，并于 2019 年完成了生物系统工程硕士学位。在 UA 期间，Ken 喜欢教授编程和生物信息学技能，并运用了其中的一些想法 在他的第一本书 Tiny Python Projects（Manning，2020 年）中，该书使用测试驱动的开发方法来教授 Python。

Mastering Python for Bioinformatics pdf 肯·尤恩斯·克拉克

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.
• learn the latest Python features and tools including linters, formatters, type checkers, and tests to create documented and tested programs.
• 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().