1 An Introduction to Perl Part 1 CSC8304 – Computing Environments for Bioinformatics - Lecture 7.

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An Introduction to PerlPart 1

CSC8304 – Computing Environments for Bioinformatics - Lecture 7

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Objectives

To introduce the Perl programming language• Why Perl in bioinformatics?

To Examine Perl syntax, operators and constructions Recommended Books:

• SAMS – Teach yourself Perl in 24 hours – Clinton Pierce

• Beginning Perl for Bioinformatics – James Tisdall

The Best way to learn Perl is to read the books, numerous tutorials and to Practice.

These notes are not a comprehensive tutorial – reading extra material is essential


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Why Perl

Benefits• Ease of Programming

• Rapid Prototyping

• Portability speed and Maintenance

Compared to Java• No compilation

• A scripting language, object oriented concepts not required

• Less rigorous in promoting ‘good’ software engineering

• No exception handling

• Perl is much less strongly typed


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Perl for Bioinformatics

Wealth of existing code

Perl is good at:• Handling strings

• Detecting patterns in data

Easy for biologists to learn

Many books and tutorials

Own specialists flavours e.g. BioPerl see http://bio.perl.org/


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Installing Perl Perl is available for a variety of operating systems including windows

and unix Visit http://www.perl.com

Writing Perl program:

• Formulate program using an editor

• Save the program as xxx.pl

• Run using perl xxx.pl

• Perl is interpreted no compilation necessary


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First Perl Program – Hello World

#!/usr/bin/perl –w

#Say Hello

print “Hello, World! \n”;

Shebang Line:Tells Computer is a PerlProgram

Comments prefixed with #

Lines terminated with ;

Inserts a carriage return

Prints a string to output


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Print

Used to generate to a “file handle”

Default file handle is STDOUT

Takes a comma separated list of parameters as input


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Print - Examples

> print “Hello”,”out”,”there”;

Hellooutthere>

print “Hello out there\n”;

Hello out there

>

print STDOUT “Hello out there\n”;

Hello out there

>


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Numbers and Strings

Literals:• Integers (6), Floating Points (15.4), Scientific notation (6.6E-33)

Strings:• Strings of characters e.g.

• “foo”

• “Fourscore and seven\n years ago”

• ‘I don’t like writing lectures\n’

• “MRes Bioinformatics is too easy… \n”

A backslash (\) insideA string tells Perl that the next character is special

In single quoting strings are Taken literally. In doublequotes perl checks for escapesequences


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Sample String Escape Sequences

\n Newline

\r Carriage Return

\t Tab

\b Backspace

\u Change next character to upper case

\l Change next character to lowercase


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Scalar Variables

• To store scalar data in Perl requires the use of scalar variables in Perl

• A scalar variable is a variable that allows the definition of one piece of data for later use.

• A scalar variable in a program always starts with a dollar sign $

• For example: •$name•$a•$Date•$serial_number•$cat450


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Scalar Variables

• Variable names can contain alphabetic characters, numbers, or an underscore character

• The first character of a variable name can’t be a number though

• Variable names are case sensitive

• Single character names that do not start with an alphabetic character or underscore are special variables in Perl and should not be used as normal variables

• e.g. $_ $” $/ $2 $$

• More on these later


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Expressions and Operators

• Expressions

$title = “Gone with the wind”;$pi = 3.14159;$area = 3.14159 * ($radius ** 2);

• Numeric Operators:

5 + $t Addition Sum of 5 and $t$y - $x Subtraction Difference between $y and $x$e * $pi Multiplication Product of $e and $pi$f / 6 Division Quotient of $f divided by 624 % 5 Modulus Remainder of 24 divided by 5 (4)4 ** 2 Exponential 4 raised to the 2nd Power


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• String Operators:

• Strings can also be manipulated using operators

• The concatenation operator ‘.’ joins two strings:

$a=“Hello, World!”;$b=“Nice to meet you”;$c=$a.$b;

• If Perl finds a variable inside a string it is interpolated

$name=“Fred”;print “I went to the pictures with $name”;


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Expressions and Operators• To prevent interpolation put a backslash in front of the variable identifier or

put the string in single quotes:

$name=“Fred”;print “I went to the pictures with \$name”;print ‘I went to the pictures with \$name’;

• Many more operators – see Perl reference book for details:

• e.g. int, length, lc, uc, cos etc….

• Increment and decrement:

$counter = 10;$counter = $counter + 1;$counter++;$counter--;


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• For the most part Perl allows you to use numbers and strings interchangeably

• How a variable is interpreted depends on what Perl is looking for at the time

• If something looks like a number Perl can use it as a number when a number is needed:

$a=42; # A number

print $a+18; # Displays 60

$b=“50”;

print $b-10; # Displays 40


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Flow control

Up to now all statements have been executed in the order top to bottom

Perl’s control structures allow statements to be grouped in to statement blocks and run conditionally or repeatedly


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Blocks

The simplest grouping of statements is in a block

{statement_a;

statement_b;

statement_c;

}


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The if statement

Used to control whether statements are executed based on a condition

Syntax: if (expression) BLOCK e.g.

if ( $r == 5 )

{print ‘The value of $r is equal to 5.’;

}


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The if statement

Can also use else:

if ( $r == 5 )

{

print ‘The value of $r is equal to 5.’;

}

else

{

print ‘$r is something other than 5.’;

}


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Relational Operators

Perl, like Java, has operators for numerical conditions

OPERATOR EXAMPLE EXPLANATION

== $x == $y True if $x equals $y

> $x > $y True if $x is greater than $y

< $x < $y True if $x is less than $y

>= $x >= $y True if $x is greater than or equal to $y

<= $x <= $y True if $x is less than or equal to $y

!= $x != $y True if $x is not equal to $y


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Alphanumeric Relational Operators

Perl, like Java, has operators for numerical conditions

OPERATOR EXAMPLE EXPLANATION

eq $s eq $t True if $s is equal to $t

gt $s gt $t True if $s is greater to $t

lt $s lt $t True if $s is less than $t

ge $s ge $t True if $s is greater than or equal to $t

These operators decide “greater than” and “less than” by examining each character left to right and comparing them in ASCII order.

Strings therefore sort in ascending order: Most punctuation first, then number, then uppercase then lowercase.


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Looping Looping with while:

• while (expression) BLOCK

$counter=0;while ($counter < 10){

print “Still counting...$counter\n”;

$counter++;}


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Looping Looping with for:

• for (initialisation; test; increment) BLOCK

for ($counter=0; $counter< 10; $counter++){


}• The initialisation expression is evaluated• The test expression is evaluated; if is true the block of code is run• After the block is executed the increment is performed and the test is evaluated again• If the test is true the block is run again


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Looping Fine grained control with last:

• The last statement causes the innermost currently running loop block to be exited if the condition evaluates to true

$counter=0;while ($counter < 10){


last if ($counter==6);$counter++;

}


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Looping Fine grained control with next:

• The next statement causes control to be passed back to the top of the loop and the next iteration of the loop to begin if the loop isn’t finished

for ($i=0; $i<100; $i++){

next if (not $i % 2);print “An odd number=$i\n”;

}


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Summary

Numbers, strings, escape sequences Print, file handle Variables, expressions and operators Flow control:

• Blocks

• Looping: while, for, last, next


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Q & A – 1

Is it true that the default file handle is STDOUT ? Can we get as output: Hello out there

by typing and executing print “Hello”,”out”,”there”; ?

Is it true that the following are names of variables: $name, $a, $Date, $serial_number ?

What is the value of $c:$a=“Hello, World!”;$b=“Nice to meet you”;

$c=$a.$b; ?


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Q & A – 2

What do we get by executing$name=“Fred”;print “I went to the pictures with \$name”; ?

What do we get if we writeprint ‘I went to the pictures with \$name’; ?

Can we use ‘else’ in an if-statement ? Can we use ‘last’ in a for-statement ? What about

‘next’ ?


1 An Introduction to Perl Part 1 CSC8304 – Computing Environments for Bioinformatics - Lecture 7.

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