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Acknowledgments

My editor, Lorrie LeJeune, deserves special thanks for her work in developing the bioinformatics titles at O'Reilly. Her level of expertise is rare in any field. I thank Lorrie, Tim O'Reilly, and their colleagues for making it possible to bring these books to the public. I thank my technical reviewers for their invaluable expert help: Joel Greshock, Joe Johnston, Andrew Martin, and Sean Quinlan. I also thank Dr. Michael Caudy for his helpful suggestions in Chapter 3. I thank again those individuals mentioned in the first volume, especially those friends who have supported me during the writing of this book. I am also grateful to all those readers of the first volume who took the time and trouble to point out errors and weaknesses; their comments have substantially improved this volume as well. I thank Eamon Grennan and Jay Parini for their patient help with my writing. And I especially thank my much-loved children Rose, Eamon, and Joe, who are my most sincere teachers .

Part I: Object-Oriented Programming in Perl

Chapter 1. Modular Programming with Perl

Perl modules are essential to any Perl programmer. They are a great way to organize code into logical collections of interacting parts . They collect useful Perl subroutines and provide them to other programs (and programmers) in an organized and convenient fashion.

This chapter begins with a discussion of the reasons for organizing Perl code into modules. Modules are comparable to subroutines: both organize Perl code in convenient, reusable " chunks ."

Later in this chapter, I'll introduce a small module, GeneticCode.pm . This example shows how to create simple modules, and I'll give examples of programs that use this module.

I'll also demonstrate how to find, install, and use modules taken from the all-important CPAN collection. A familiarity with searching and using CPAN is an essential skill for Perl programmers; it will help you avoid lots of unnecessary work. With CPAN, you can easily find and use code written by excellent programmers and road- tested by the Perl community. Using proven code and writing less of your own, you'll save time, money, and headaches .