Chapter 25 First Perl Program

Scripting languages, like Perl, are very commonly used in bioinformatics. As a generous scripting language, Perl have many advantages: easy to use, free for all operating systems like Linux, designed for working with text files (tab-delimited files). It’s one of the most popular language in bioinformatics. Moreover there are many scripts and modules available. Additionally, there are a lot of resource on Internet.

25.1 First Program

As all other programming books, we begin with a “Hello world” program.

#!/usr/bin/perl
#Printing a line of text “Hello, Bioinformatics”
print "Hello, Bioinformatics!\n";

This program show how to display a line a text in Perl. It have several features. We go through each line in detail.

Line 1 is what we call shebang line. This line starts with shebang construct (#!). /usr/bin/perl indicates the path of the Perl interpreter.

Line 3 shows how to print a line of text in Perl. Nearly all programming language use print to display texts on the screen. Here, print is a built-in function in Perl. It print the string of characters (its arguments) between quotation marks (“” or ’’).

perl code_perl/hello_bioinfor.pl

## Hello, Bioinformatics!

However the characters \n are not displayed. Here backslash \ is a start of an escape sequence. It changes the meaning of the character after it. The backslash \ and n together (\n) form an escape sequence and signify a newline. Other examples are \t (tab) or \$ (= print an actual dollar sign, normally a dollar sign has a special meaning). We’ll see more escape sequences in 7.1.

You can try to remove \n in the program to see what will happen. This will give you a dee per understanding of the program.