Mastering Perl for Bioinformatics

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.

What Is a Module?

A Perl module is a library file that uses package declarations to create its own namespace. Perl modules provide an extra level of protection from name collisions beyond that provided by my and use strict. They also serve as the basic mechanism for defining object-oriented classes.

Why Perl Modules?

Building a medium- to large-sized program usually requires you to divide ...