Mastering Perl for Bioinformatics

Chapter 4. Sequence Formats and Inheritance

This chapter applies concepts and techniques from previous chapters to a concrete project: handling sequence files. The chapter also introduces a few new techniques including a very important one called class inheritance. The code developed in this chapter will also be incorporated into later chapters.

Class inheritance allows you to define a new class by inheriting from other classes—altering or making additions as needed. It’s a style of software reuse that is particular to object-oriented design.

The first class developed in this chapter is a simple one: reading and writing files. Using inheritance, you can extend that class to a new one that can recognize, read, and write data in several different biological sequence datafile formats.

The goal is, as always, to learn enough about Perl to develop software for your own needs. The code in this chapter is designed with this goal in mind. In particular, the exercises at the end of the chapter will ask you to extend and improve the code in various ways.

Inheritance

You’ve seen the use of modules and how a Perl program can use all the code in a module by simply loading it with the use command. This is a simple and powerful method of software reuse , by which software can be written once but used many times by different programs.

You’ve also seen how object-oriented Perl defines classes in terms of modules, and how the use of classes, methods, and objects provides a more structured way to reuse ...