Python for Bioinformatics

Contents

Preface

Chapter 1    Introduction

1.1    The Purpose of This Book

1.2    Use of Third-Party Software

1.3    Required Background of Readers

1.4    Object-Oriented Programming

1.5    Presentation Convention

1.6    Conversion from C/C++ to Python

1.6.1 Similarities

1.6.2 Fundamental Python Commands that Differ from C/C++

1.7    The Environment

1.8    Biopython

Bibliography

Chapter 2    NumPy and SciPy

2.1    Introduction to NumPy and SciPy

2.2    Basic Array Manipulations

2.3    Basic Math

2.4    More on Multiplication

2.5    More Math

2.5.1 Equals or Copy

2.5.2 Comparisons

2.5.3 More on Slicing

2.5.4 Sorting and Shaping

2.5.5 Random Numbers

2.5.6 Statistical Methods

2.6    Thinking About Problems

2.7    Array Conversions

2.8    SciPy