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Mastering Perl for Bioinformatics - James D. Tisdall

Contents

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


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