Python for Bioinformatics, Second Edition

"In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author's extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development."--Provided by publisher Cover -- Half Title -- Chapman & Hall/crc -- Published Titles -- Title -- Copyright -- Contents -- List Of Figures -- List Of Tables -- Preface To The First Edition -- Preface To The Second Edition -- Acknowledgments -- Section I Programming -- Chapter 1 Introduction -- 1.1 Who Should Read This Book -- 1.1.1 What The Reader Should Already Know -- 1.2 Using This Book -- 1.2.1 Typographical Conventions -- 1.2.2 Python Versions -- 1.2.3 Code Style -- 1.2.4 Get The Most From This Book Without Reading It All -- 1.2.5 Online Resources Related To This Book -- 1.3 Why Learn To Program -- 1.4 Basic Programming Concepts -- 1.4.1 What Is A Program -- 1.5 Why Python -- 1.5.1 Main Features Of Python -- 1.5.2 Comparing Python With Other Languages -- 1.5.3 How Is It Used -- 1.5.4 Who Uses Python -- 1.5.5 Flavors Of Python -- 1.5.6 Special Python Distributions -- 1.6 Additional Resources -- Chapter 2 First Steps With Python -- 2.1 Installing Python -- 2.1.1 Learn Python By Using It -- 2.1.2 Install Python Locally -- 2.1.3 Using Python Online -- 2.1.4 Testing Python -- 2.1.5 First Use -- 2.2 Interactive Mode -- 2.2.1 Baby Steps -- 2.2.2 Basic Input And Output -- 2.2.3 More On The Interactive Mode -- 2.2.4 Mathematical Operations -- 2.2.5 Exit From The Python Shell -- 2.3 Batch Mode -- 2.3.1 Comments -- 2.3.2 Indentation -- 2.4 Choosing An Editor -- 2.4.1 Sublime Text -- 2.4.2 Atom -- 2.4.3 Pycharm -- 2.4.4 Spyder Ide -- 2.4.5 Final Words About Editors -- 2.5 Other Tools -- 2.6 Additional Resources -- 2.7 Self-evaluation -- Chapter 3 Basic Programming: Data Types -- 3.1 Strings -- 3.1.1 Strings Are Sequences Of Unicode Characters -- 3.1.2 String Manipulation -- 3.1.3 Methods Associated With Strings -- 3.2 Lists -- 3.2.1 Accessing List Elements Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. The book focuses on the easy-to-use, yet powerful, Python 3 computer language and explores NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.