Mastering Perl for Bioinformatics
Mastering Perl for Bioinformatics
ISBN: 0596003072
EAN: 2147483647
EAN: 2147483647
Year: 2003
Pages: 156
Pages: 156
Authors: James D. Tisdall
- Main Page
- Table of content
- 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
- 1.1 What Is a Module?
- 1.2 Why Perl Modules?
- 1.3 Namespaces
- 1.4 Packages
- 1.5 Defining Modules
- 1.6 Storing Modules
- 1.7 Writing Your First Perl Module
- 1.8 Using Modules
- 1.9 CPAN Modules
- 1.10 Exercises
- Chapter 2. Data Structures and String Algorithms
- 2.1 Basic Perl Data Types
- 2.2 References
- 2.3 Matrices
- 2.4 Complex Data Structures
- 2.5 Printing Complex Data Structures
- 2.6 Data Structures in Action
- 2.7 Dynamic Programming
- 2.8 Approximate String Matching
- 2.9 Resources
- 2.10 Exercises
- Chapter 3. Object-Oriented Programming in Perl
- 3.1 What Is Object-Oriented Programming?
- 3.2 Using Perl Classes (Without Writing Them)
- 3.3 Objects, Methods, and Classes in Perl
- 3.4 Arrow Notation (-)
- 3.5 Gene1: An Example of a Perl Class
- 3.6 Details of the Gene1 Class
- 3.7 Gene2.pm: A Second Example of a Perl Class
- 3.8 Gene3.pm: A Third Example of a Perl Class
- 3.9 How AUTOLOAD Works
- 3.10 Cleaning Up Unused Objects with DESTROY
- 3.11 Gene.pm: A Fourth Example of a Perl Class
- 3.12 How to Document a Perl Class with POD
- 3.13 Additional Topics
- 3.14 Resources
- 3.15 Exercises
- Chapter 4. Sequence Formats and Inheritance
- 4.1 Inheritance
- 4.2 FileIO.pm: A Class to Read and Write Files
- 4.3 SeqFileIO.pm: Sequence File Formats
- 4.4 Resources
- 4.5 Exercises
- Chapter 5. A Class for Restriction Enzymes
- 5.1 Envisioning an Object
- 5.2 Rebase.pm: A Class Module
- 5.3 Restriction.pm: Finding Recognition Sites
- 5.4 Drawing Restriction Maps
- 5.5 Resources
- 5.6 Exercises
- Part II: Perl and Bioinformatics
- Chapter 6. Perl and Relational Databases
- 6.1 One Perl, Many Databases
- 6.2 Popular Relational Databases
- 6.3 Relational Database Definitions
- 6.4 Structured Query Language
- 6.5 Administering Your Database
- 6.6 Relational Database Design
- 6.7 Perl DBI and DBD Interface Modules
- 6.8 A Rebase Database Implementation
- 6.9 Additional Topics
- 6.10 Resources
- 6.11 Exercises
- Chapter 7. Perl and the Web
- 7.1 How the Web Works
- 7.2 Web Servers and Browsers
- 7.3 The Common Gateway Interface
- 7.4 Rebase: Building Dynamic Web Pages
- 7.5 Exercises
- Chapter 8. Perl and Graphics
- 8.1 Computer Graphics
- 8.2 GD
- 8.3 Adding GD Graphics to Restrictionmap.pm
- 8.4 Making Graphs
- 8.5 Resources
- 8.6 Exercises
- Chapter 9. Introduction to Bioperl
- 9.1 The Growth of Bioperl
- 9.2 Installing Bioperl
- 9.3 Testing Bioperl
- 9.4 Bioperl Problems
- 9.5 Overview of Objects
- 9.6 bptutorial.pl
- 9.7 bptutorial.pl: sequence_manipulation Demo
- 9.8 Using Bioperl Modules
- Part III: Appendixes
- Appendix A. Perl Summary
- A.1 Command Interpretation
- A.2 Comments
- A.3 Scalar Values and Scalar Variables
- A.4 Assignment
- A.5 Statements and Blocks
- A.6 Arrays
- A.7 Hashes
- A.8 Complex Data Structures
- A.9 Operators
- A.10 Operator Precedence
- A.11 Basic Operators
- A.12 Conditionals and Logical Operators
- A.13 Binding Operators
- A.14 Loops
- A.15 InputOutput
- A.16 Regular Expressions
- A.17 Scalar and List Context
- A.18 Subroutines
- A.19 Modules and Packages
- A.20 Object-Oriented Programming
- A.21 Built-in Functions
- Appendix B. Installing Perl
- B.1 Installing Perl on Your Computer
- B.2 Versions of Perl
- B.3 Internet Access
- B.4 Downloading
- B.5 How to Run Perl Programs
- B.6 Finding Help
- Colophon
- Index
- Index SYMBOL
- Index A
- Index B
- Index C
- Index D
- Index E
- Index F
- Index G
- Index H
- Index I
- Index J
- Index K
- Index L
- Index M
- Index N
- Index O
- Index P
- Index Q
- Index R
- Index S
- Index T
- Index U
- Index V
- Index W
Mastering Perl for Bioinformatics
ISBN: 0596003072
EAN: 2147483647
EAN: 2147483647
Year: 2003
Pages: 156
Pages: 156
Authors: James D. Tisdall
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