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

Book Description

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

Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You’ll learn the latest Python features and tools–such as linters, formatters, type checkers, and tests–to write documented and tested programs.

• Create command-line Python programs that document and validate parameters
• Write tests to verify refactor programs and confirm they’re correct
• Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython
• Create reproducible shortcuts and workflows using makefiles
• Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt
• Find patterns of text using regular expressions
• Use higher-order functions in Python like filter() and map()

中文：

书名：掌握用于生物信息学的Python：如何为研究计算编写灵活的、有文档记录的、经过测试的Python代码

今天的生命科学家迫切需要生物信息学技能方面的培训。太多的生物信息学程序写得很差，几乎没有维护，通常是由学生和博士后研究人员编写的，他们从未学习过基本的编程技能。这本实用指南展示了如何利用Python最好的部分来解决生物学中的问题，同时也创建了有文档记录的、经过测试的、可重现的软件。

肯·尤恩斯-克拉克，《生活》一书的作者微小的巨型巨蟒项目他(Manning)，演示了如何编写有效的Python代码，以及如何使用测试来编写和重构科学程序。您将学习最新的Python特性和工具，如索引器、格式化程序、类型检查器和测试，以编写有文档记录和测试的程序。

• 创建用于记录和验证参数的命令行Python程序
• Write tests to verify refactor programs and confirm they’re correct
• 使用Python数据结构(字符串、列表和集合)和诸如Biopython之类的模块解决生物信息学思想
• 使用生成文件创建可复制的快捷方式和工作流
• 解析基本的生物信息学文件格式，如FASTA、FASTQ和SwissProt
• 使用正则表达式查找文本模式
• 在Python中使用高阶函数，如Filter()和map()