Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

• Table of Contents

• Index

• Reviews

• Reader Reviews

• Errata

Mastering Perl for Bioinformatics

By
Publisher: O''Reilly

Pub Date: September 2003

ISBN: 0-596-00307-2

Pages: 396

Copyright

Foreword

Preface

About This Book

What You Need to Know to Use This Book

Organization of This Book

Conventions Used in This Book

Comments and Questions

Acknowledgments

Part I:
Object-Oriented Programming in Perl

Chapter 1.
Modular Programming with Perl

Section 1.1.
What Is a Module?

Section 1.2.
Why Perl Modules?

Section 1.3.
Namespaces

Section 1.4.
Packages

Section 1.5.
Defining Modules

Section 1.6.
Storing Modules

Section 1.7.
Writing Your First Perl Module

Section 1.8.
Using Modules

Section 1.9.
CPAN Modules

Section 1.10.
Exercises

Chapter 2.
Data Structures and String Algorithms

Section 2.1.
Basic Perl Data Types

Section 2.2.
References

Section 2.3.
Matrices

Section 2.4.
Complex Data Structures

Section 2.5.
Printing Complex Data Structures

Section 2.6.
Data Structures in Action

Section 2.7.
Dynamic Programming

Section 2.8.
Approximate String Matching

Section 2.9.
Resources

Section 2.10.
Exercises

Chapter 3.
Object-Oriented Programming in Perl

Section 3.1.
What Is Object-Oriented Programming?

Section 3.2.
Using Perl Classes (Without Writing Them)

Section 3.3.
Objects, Methods, and Classes in Perl

Section 3.4.
Arrow Notation (->)

Section 3.5.
Gene1: An Example of a Perl Class

Section 3.6.
Details of the Gene1 Class

Section 3.7.
Gene2.pm: A Second Example of a Perl Class

Section 3.8.
Gene3.pm: A Third Example of a Perl Class

Section 3.9.
How AUTOLOAD Works

Section 3.10.
Cleaning Up Unused Objects with DESTROY

Section 3.11.
Gene.pm: A Fourth Example of a Perl Class

Section 3.12.
How to Document a Perl Class with POD

Section 3.13.
Additional Topics

Section 3.14.
Resources

Section 3.15.
Exercises

Chapter 4.
Sequence Formats and Inheritance

Section 4.1.
Inheritance

Section 4.2.
FileIO.pm: A Class to Read and Write Files

Section 4.3.
SeqFileIO.pm: Sequence File Formats

Section 4.4.
Resources

Section 4.5.
Exercises

Chapter 5.
A Class for Restriction Enzymes

Section 5.1.
Envisioning an Object

Section 5.2.
Rebase.pm: A Class Module

Section 5.3.
Restriction.pm: Finding Recognition Sites

Section 5.4.
Drawing Restriction Maps

Section 5.5.
Resources

Section 5.6.
Exercises

Part II:
Perl and Bioinformatics

Chapter 6.
Perl and Relational Databases

Section 6.1.
One Perl, Many Databases

Section 6.2.
Popular Relational Databases

Section 6.3.
Relational Database Definitions

Section 6.4.
Structured Query Language

Section 6.5.
Administering Your Database

Section 6.6.
Relational Database Design

Section 6.7.
Perl DBI and DBD Interface Modules

Section 6.8.
A Rebase Database Implementation

Section 6.9.
Additional Topics

Section 6.10.
Resources

Section 6.11.
Exercises

Chapter 7.
Perl and the Web

Section 7.1.
How the Web Works

Section 7.2.
Web Servers and Browsers

Section 7.3.
The Common Gateway Interface

Section 7.4.
Rebase: Building Dynamic Web Pages

Section 7.5.
Exercises

Chapter 8.
Perl and Graphics

Section 8.1.
Computer Graphics

Section 8.2.
GD

Section 8.3.
Adding GD Graphics to Restrictionmap.pm

Section 8.4.
Making Graphs

Section 8.5.
Resources

Section 8.6.
Exercises

Chapter 9.
Introduction to Bioperl

Section 9.1.
The Growth of Bioperl

Section 9.2.
Installing Bioperl

Section 9.3.
Testing Bioperl

Section 9.4.
Bioperl Problems

Section 9.5.
Overview of Objects

Section 9.6.
bptutorial.pl

Section 9.7.
bptutorial.pl: sequence_manipulation Demo

Section 9.8.
Using Bioperl Modules

Part III:
Appendixes

Appendix A.
Perl Summary

Section A.1.
Command Interpretation

Section A.2.
Comments

Section A.3.
Scalar Values and Scalar Variables

Section A.4.
Assignment

Section A.5.
Statements and Blocks

Section A.6.
Arrays

Section A.7.
Hashes

Section A.8.
Complex Data Structures

Section A.9.
Operators

Section A.10.
Operator Precedence

Section A.11.
Basic Operators

Section A.12.
Conditionals and Logical Operators

Section A.13.
Binding Operators

Section A.14.
Loops

Section A.15.
Input/Output

Section A.16.
Regular Expressions

Section A.17.
Scalar and List Context

Section A.18.
Subroutines

Section A.19.
Modules and Packages

Section A.20.
Object-Oriented Programming

Section A.21.
Built-in Functions

Appendix B.
Installing Perl

Section B.1.
Installing Perl on Your Computer

Section B.2.
Versions of Perl

Section B.3.
Internet Access

Section B.4.
Downloading

Section B.5.
How to Run Perl Programs

Section B.6.
Finding Help

Colophon

Index