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S* Online Course

S* Tutorial

Perl in Bioinformatics

Version 1.1

Last Revised: 19

Feb 2004

S* Online Course

Perl Basics

1. Preface

This is a short tutorial to help you get started programming in Perl. We will go through

several examples in developing simple application used in the area of Bioinformatics. If

you would like to learn more, you can pick up books or visit website to learn more about

Perl (see Appendix for more). There are many well written tutorials on Perl so we suggest

that you go through those tutorials which will give you a thorough understanding of Perl.

In this tutorial, we will focus on how to use Perl and BioPerl and applying them to

bioinformatics. This tutorial assumes certain levels of background knowledge and

familiarity with the use of computer.

If you find any error in this tutorial, please email to us at

course@s-star.org.

We welcome

any feedback or comments in improving this tutorial. Thanks to Alan Wardroper for his

fabulous feedback.

Thank you.

Sincerely,

S* Team

2. Motivation

Before you begin this tutorial, you may want to read an interesting article on “How Perl

Saved The Human Genome Project” by Lincoln Stein

(http://www.bioperl.org/GetStarted/tpj_ls_bio.html)

Bioinformatics is the application of information technology to manage and analyse

biological data. As more and more researchers start to deploy computers to their everyday

tasks, learning an easy and simple to use programming language to assist in storing,

organizing, analyzing data will put you in great advantage. We have decided to choose

Perl to be taught to participants of S* because of its practicality and ease of use. Many

tasks that you encounter can be easily solved using subset of Perl and usually "there's

more than one way to do it" (TMTOWTDI, pronounced "tim toady").

3. Getting Perl

Perl (Practical Extraction and Report Language) is a language which offers you the

capability and flexibility to get your job done easily. It is easy to learn and can be easily

found installed on most UNIX or Linux machines. Its strength lies mainly in the area of

text processing. However, it has grown to become a rich and sophisticated programming

language.

Last Revised: 19

Feb 2004

S* Online Course

Perl is freely available and freely distributable. To get a copy of Perl to be installed on

your computer, please find it at

http://www.cpan.org/.

Click on “Perl

binary distributions

("ports")”

and find the corresponding installation package for the system installed on

your computer.

For installation instruction, please follow the readme file contained in the installation

package. The readme is well written. However, should you encounter problem please

post to the IVLE forum.

If you have are using Unix/Linux, you probably already have Perl installed.

Type

perl –v

at the shell prompt to find out the version installed.

For Windows users, please download “ActivePerl” from this link to install Perl On your

computer :

http://www.cpan.org/ports/index.html#win32

4. Language Basics

Like other programming languages, Perl has its way of expressing variables. In this

tutorial, we will learn the following :

Scalar – represented by $. Stores single value only (a string or number)

e.g.

$dna_sequence

Array – represented by @. Stores list of values in orderly manner and accessible

by specifying the numeric position in the list. The index starts from 0.

e.g. @taxonomy

Hash – represented by %. Stores pairs of key/value in random fashion and

accessible by specifying the key (string).

e.g. %dna_sequences

TIPS / NOTE:

I. All statements in the code should end with “;”. See the examples in the

following sections.

II. Good indentation makes reading and debugging (i.e. to locate and

correct error in code) easy.

III. White space(s) is ignored. Practise good spacing to make code readable.

Last Revised: 19

Feb 2004

S* Online Course

4.1 Strings

Strings are just sequence of characters. In Perl, strings are represented using either single

quote or double quote. e.g. ‘hello world’. “hello Perl”

#!/usr/bin/perl

$course_no = "4th";

print "Welcome to S* $course_no Course !\n";

So, you can set a variable using a single quotes or double quotes.

$course_no = "4th";

$course_no = ‘4th’;

However, when printing, using single quotes print literally the variable whereas double

quotes interpolates the content of the variable.

print ‘Welcome to S* $course_no Course !\n’;

merely prints out

Welcome to S* $course_no Course !\n.

But substituting the code with

double quotes gives us

Welcome to S* 4th Course !.

In the simple code above, you notice that there is the special character “\n” at the end of

the line. By including this special character, it forces a new line in the results. There are

several other commonly used special characters.

Character

\xhh

Description

new line

tab

carriage return (CR)

Character with

hexadecimal code

4.2 Comments

Comment is denoted by the symbol ‘#’ and is frequently used in programs to allow the

author/programmer to document the code. When it is written at the beginning of a file, it

is a directive to tell the machine where to look for the perl program. For Windows users,

it not required to write the directive code, however, it’s usually a good practice to do so

since this is required in other machines installed with Unix/Linux.

Last Revised: 19

Feb 2004

S* Online Course

Example Program 4.2.1: Copy and paste the code into a new file. Then type perl

<filename> to execute the program.

#!/usr/bin/perl -w

use strict;

The line “#!/usr/bin/perl” tells the machine to

run Perl from that installed location. The “-w”

indicates that any warnings should be displayed.

“use strict” asserts that all the variables in the

programs should be properly declared

# Initialize a scalar and then print the value

my $sequence = "ATGCCAGGATCGCCC";

print $sequence;

# Initialize an array of strings and then print the 1

value

my @taxonomy = ("archaea", "eubacteria", "eukaryota", "virus");

print $taxonomy[0], "\n";

# Initialize a hash with key/value pairs and then print the value

my %dna_sequences = (

"AY258503" => "E.coli hemolysin plasmid pO113",

"AY131333" => "E.coli 16S ribosomal RNA gene",

"AY319289" => "E.coli strain K12 transposon Tn10.10"

);

print $dna_sequences{"AY258503"}, "\n";

exit;

4.3 Operators

4.3.1 Arithmetic Operators

Operator

Description

Addition

Subtraction

Division

Multiplication

Modulus

Exponential

4.3.2 String Operators

Given two strings, Perl allow concatenation of the two by using the dot operator ‘.’.

$s1 = ‘Homo’;

$s2 = ‘Sapien’;

print $s1. " ".$s2;

# prints out Homo Sapien

Last Revised: 19

Feb 2004

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