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Mastering Perl for Bioinformatics
Mastering Perl for Bioinformatics
ISBN: 0596003072
EAN: 2147483647
Year: 2003
Pages: 156
Authors:
James D. Tisdall
BUY ON AMAZON
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
Year: 2003
Pages: 156
Authors:
James D. Tisdall
BUY ON AMAZON
Lotus Notes and Domino 6 Development (2nd Edition)
Working with Fields
Setting View Properties
Real-World Example 1: Importing a Delimited Text File
Whats New in Designer 6
Applying Field-Level Security
Cisco IP Telephony (CIPT) (Authorized Self-Study) (2nd Edition)
Review Questions
Restricting External Transfers
Bandwidth Management
CAR Overview
Visual C# 2005 How to Program (2nd Edition)
Exercises
Labels, TextBoxes and Buttons
ListView Control
Exercises
Simple-Type structs, Boxing and Unboxing
Twisted Network Programming Essentials
Adding Twisted Utilities to Your Path
Monitoring Download Progress
Managing a Hierarchy of Resources
Web Services and RPC
SSH
FileMaker 8 Functions and Scripts Desk Reference
Importing Data
Count()
GetAsNumber()
Let()
PMT()
Java All-In-One Desk Reference For Dummies
Using Abstract Classes and Interfaces
Using Inner Classes
Book IV - Strings, Arrays, and Collections
Using Regular Expressions
Database for $100, Please
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