PERL by Example Book

Preface xxvii

Chapter 1: The Practical Extraction and Report Language 1

1.1 What Is Perl? 1

1.2 What Is an Interpreted Language? 2

1.3 Who Uses Perl? 3

1.4 Where to Get Perl 5

1.5 What Is CPAN? 9

1.6 Perl Documentation 10

1.7 What You Should Know 12

1.8 What’s Next? 12

Chapter 2: Perl Quick Start 13

2.1 Quick Start, Quick Reference 13

2.2 Chapter Summary 29

2.3 What’s Next? 29

Chapter 3: Perl Scripts 31

3.1 Script Setup 31

3.2 The Script 32

3.3 Perl at the Command Line 39

3.4 What You Should Know 43

3.5 What’s Next? 43

Chapter 4: Getting a Handle on Printing 45

4.1 The Filehandle 45

4.2 Words 45

4.3 The print Function 46

4.4 The printf Function 59

4.5 What You Should Know 66

4.6 What’s Next? 66

Chapter 5: What’s in a Name 69

5.1 About Perl Variables 69

5.2 Scalars, Arrays, and Hashes 77

5.3 Reading from STDIN 94

5.4 Array Functions 100

5.5 Hash (Associative Array) Functions 118

5.6 More Hashes 128

5.7 What You Should Know 132

5.8 What’s Next? 133

Chapter 6: Where’s the Operator? 137

6.1 About Perl Operators 137

6.2 Mixing Data Types 138

6.3 Precedence and Associativity 139

6.4 What You Should Know 168

6.5 What’s Next? 168

Chapter 7: If Only, Unconditionally, Forever 171

7.1 Control Structures, Blocks, and Compound Statements 171

7.2 Repetition with Loops 177

7.3 What You Should Know 200

7.4 What’s Next? 200

Chapter 8: Regular Expressions–Pattern Matching 203

8.1 What Is a Regular Expression? 203

8.2 Expression Modifiers and Simple Statements 204

8.3 Regular Expression Operators 210

8.4 What You Should Know 232

8.5 What’s Next? 232

Chapter 9: Getting Control–Regular Expression Metacharacters 235

9.1 Regular Expression Metacharacters 235

9.2 Unicode 281

9.3 What You Should Know 283

9.4 What’s Next? 283

Chapter 10: Getting a Handle on Files 285

10.1 The User-Defined Filehandle 285

10.2 Passing Arguments 310

10.3 File Testing 319

10.4 What You Should Know 321

10.5 What’s Next? 322

Chapter 11: How Do Subroutines Function? 325

11.1 Subroutines/Functions 325

11.2 Passing Arguments 330

11.3 Call-by-Reference 344

11.4 What You Should Know 358

11.5 What’s Next? 359

Chapter 12: Modularize It, Package It, and Send It to the Library! 363

12.1 Packages and Modules 363

12.2 The Standard Perl Library 370

12.3 Modules from CPAN 390

12.4 What You Should Know 398

12.5 What’s Next? 398

Chapter 13: Does This Job Require a Reference? 401

13.1 What Is a Reference? What Is a Pointer? 401

13.2 What You Should Know 420

13.3 What’s Next? 420

Chapter 14: Bless Those Things! (Object-Oriented Perl) 423

14.1 The OOP Paradigm 423

14.2 Classes, Objects, and Methods 425

14.3 Anonymous Subroutines, Closures, and Privacy 453

14.4 Inheritance 460

14.5 Public User Interface–Documenting Classes 474

14.6 Using Objects from the Perl Library 479

14.7 What You Should Know 484

14.8 What’s Next? 485

Chapter 15: Those Magic Ties and DBM Stuff 493

15.1 Tying Variables to a Class 493

15.2 DBM Files 505

15.3 What You Should Know 512

15.4 What’s Next? 512

Chapter 16: CGI and Perl: The Hyper Dynamic Duo 513

16.1 Static and Dynamic Web Pages 513

16.2 How It all Works 516

16.3 Creating a Web Page with HTML 522

16.4 How HTML and CGI Work Together 526

16.5 Getting Information Into and Out of the CGI Script 531

16.6 CGI and Forms 535

16.7 The CGI.pm Module 559

Chapter 17: Perl Meets MySQL–A Perfect Connection 603

17.1 Introduction 603

17.2 What Is a Relational Database? 604

17.3 Getting Started with MySQL 613

17.4 What Is the Perl DBI? 638

17.5 Statements that Don’t Return Anything 666

17.6 Transactions 670

17.7 Using CGI and the DBI to Select and Display Entries 672

17.8 What’s Left? 678

17.9 What You Should Know 679

17.10What’s Next? 679

Chapter 18: Interfacing with the System 685

18.1 System Calls 685

18.2 Processes 721

18.3 Other Ways to Interface with the Operating System 747

18.4 Error Handling 755

18.5 Signals 760

18.6 What You Should Know 764

18.7 What’s Next? 765

Chapter 19: Report Writing with Pictures 767

19.1 The Template 767

19.2 What You Should Know 783

19.3 What’s Next? 783

Chapter 20: Send It Over the Net and Sock It to ’Em! 785

20.1 Networking and Perl 785

20.2 Client /Server Model 785

20.3 Network Protocols (TCP/IP) 785

20.4 Network Addressing 787

20.5 Sockets 794

20.6 Client /Server Programs 800

20.7 The Socket.pm Module 808

20.8 What You Should Know 813

Appendix A: Perl Built-ins, Pragmas, Modules, and the Debugger 815

A.1 Perl Functions 815

A.2 Special Variables 845

A.3 Perl Pragmas 848

A.4 Perl Modules 850

A.5 Command-Line Switches 856

A.6 Debugger 858

Appendix B: SQL Language Tutorial 863

B.1 What Is SQL? 863

B.2 SQL Data Manipulation Language (DML) 871

B.3 SQL Data Definition Language 888

B.4 SQL Functions 901

B.5 Appendix Summary 910

B.6 What You Should Know 910

Appendix C: Perl and Biology 915

C.1 What Is Bioinformatics? 915

C.2 A Little Background on DNA 915

C.3 Some Perl Examples 917

C.4 What Is BioPerl? 919

C.5 Resources 923

Appendix D: Power and Speed: CGI and mod_perl 925

D.1 What Is mod_perl? 925

D.2 The mod_perl Web Site 927

D.3 Installing mod_perl 928

D.4 Resources 938

Index 939