Beginning Perl for Bioinformatics

Chapter 5. Motifs and Loops

This chapter continues demonstrating the basics of the Perl language begun in Chapter 4. By the end of the chapter, you will know how to:

• Search for motifs in DNA or protein

• Interact with users at the keyboard

• Write data to files

• Use loops

• Use basic regular expressions

• Take different actions depending on the outcome of conditional tests

• Examine sequence data in detail by operating on strings and arrays

These topics, in addition to what you learned in Chapter 4, will give you the skills necessary to begin to write useful bioinformatics programs; in this chapter, you will learn to write a program that looks for motifs in sequence data.

Flow Control

Flow control is the order in which the statements of a program are executed. A program executes from the first statement at the top of the program to the last statement at the bottom, in order, unless told to do otherwise. There are two ways to tell a program to do otherwise: conditional statements and loops. A conditional statement executes a group of statements only if the conditional test succeeds; otherwise, it just skips the group of statements. A loop repeats a group of statements until an associated test fails.

Conditional Statements

Let’s take another look at the open statement. Recall that if you try to open a nonexistent file, you get error messages. You can test for the existence of a file explicitly, before trying to open it. In fact, such tests are among the most powerful features of computer languages. ...