Mastering Perl for Bioinformatics

Chapter 5. A Class for Restriction Enzymes

In this chapter, you’ll learn how to write an object-oriented class that handles restriction enzymes using the modules from the previous chapter as part of an interface to the Restriction Enzyme Database (Rebase). I’ll develop a class that finds restriction sites in DNA sequence data. In my book Beginning Perl for Bioinformatics, I presented code that extracts information from Rebase and uses it to make restriction maps of DNA sequence data. In this chapter, I’ll adapt and extend that software (or ideas from the accompanying exercises) in an object-oriented fashion. (All code is shown here and is available from this book’s web site.)

Envisioning an Object

The Rebase project provides a set of files that specify restriction enzymes, their cut sites, and a great deal more information. Consider the problem of designing an object-oriented version of code that uses this data. What will be the objects and the methods?

Each restriction enzyme has a name; associated with its name are the definition of its recognition site (which I’ll translate into a Perl regular expression), information about the chemistry of the restriction enzyme, vendors of the enzyme, and other annotation. This information is all part of the Rebase database.

Perhaps I should consider each restriction enzyme as a suitable candidate for my basic object. I can then read in the Rebase database, creating objects for each restriction enzyme that includes such attributes as ...