Introduction to Perl for Bioinformatics: Basic Concepts & Syntax \

1. Bioinformatics Introduction to Perl

2. Introduction • What is Perl • Basic concepts in Perl syntax: • variables, strings, • Use of strict (explicit variables) and warnings • Basic input and output • Read and writing to a File

3. Computer programming • This set of lectures will use the Active perl and notepad++ both of which are free. • Be aware: Some of the examples used in the perl lectures can be found in the accompanying zip file. • Perl is a scripting interpreter language that has: • good string handling functionality; • pattern matching functionality; • other features, which we will cover later, • This makes it suitable for bioinformatics

4. Variables: $variable_name • In perl to declare a variable use: • $variable_name • The $variable_name [memory location] can be assigned any value • There is no distinction between basic data types; the following are both valid: • $variable_name = “my name is Denis”; ( = is the assign operator) • $variable_name = 5.1;

5. “explicit” variable • The $variable is referred to as a global variable and it may lead to problems; • It is better to use an “explicit” variable using my $variablealong with use strict;and use warnings. • Consider the following examples:

6. Not using Strict and warnings • Example 1: • #!/usr/bin/perl • # not using strict and warnings • my $variable = 5; • print "the value of the variable is: ",$varaible;

7. Using strict with semantic error • Example 1: • #!/usr/bin/perl • # using strict and my $variables • use strict; • use warnings; • my $variable = 5; • print "the value of the variable is: ",$varaible;

8. Using Strict and no “semantic” error • Example 3: (Write and Run Program) • #!/usr/bin/perl • # using strict and my $variables • use strict; • use warnings; • my $variable = 5; • print "the value of the variable is: ",$variable;

9. Variables: $variable_name • The “value” associated with the variable can be assigned new values • $variable_name = 3.7; or $variable_name = “I like … “; • If the value of the variable is a number Arithmetic operators can be applied: • +, • -, • *, • / , • **( exponential or “to the power” ); • % modulus (the remainder after dividing; 3%2 is 1)

10. Arithmetic example Code output • #!/usr/bin/perl • #evaluating expressions in print (# comment line symbol) • $x = 15; • $y = 8; • print “the value of x is “, $x , “\n”; • print “the new value of x is “, $x + 3, “\n”; • print “the sum of x and y is “, $x + $y, “\n”; • print “the product of x and y is “, $x*$y, “\n”; • (ArithmeticExample.pl)

11. Format output • Double v single quotation marks • Sometimes we want to print a “ quotation“ so in perl it is done using ‘ ‘: • Print ’ ”the end justifies the means “ \n’; • More on output (refer to Output_Example.pl): • #!/usr/bin/perl • use strict; • use warnings • # formating output example • print ’ ”The secret to happiness is not doing what one likes to do but liking what one has to do “ \n’; • my $x = "I am from Cork "; #declare a string • my $y = "my name is Denis"; #declare another string • print "the value of \$x is $x\n"; # note the \$x • print "the value of $x is $x\n"; • print "the value of \$y concatenated to \$x is $y$x\n";

12. Output from OutputExample.pl

13. Inputting Data (assign data to a variable) • Data can be typed in from the keyboard, read from a file or “hardcoded” to the end of the program • Perl is good for reading text files – such as the Bioinfomatics “FASTA” file. • Reads input one line at a time inclusive of carriage return/end of line marker • Read data from the key board • #!/usr/bin/perl : This line must be at the start of each program. • use strict; use warnings; • $var = <> ; #(input a line of characters and assign it to $var) • chomp $var # removes the return character from the line. • Alternatively you can combine both statements together • chomp($var = <>);

14. Read data from a file (redirect input) • Normally you open a file and read/write to the file. However perl can put the name of the file as one of the “arguments” in the command line; let us consider a file called text1.txt • Perl code: • $variable = <> (same as that for inputting from the keyboard) • At the Command line type • C:\directory> Input.pl text1.txt

15. Exercise 1 • Declare 3 ($x, $y and $z) variables and assign them the following values: 12, 6, 8. • Perform and print the results of the following arithmetic operations • $x to the power of $y • $x modulus % $y • $x modulus $z • &x plus $y plus $z and assign it to a new variable ($a) • Perform one other simple arithmetic operation of your choice

16. Exercise 2 • Ask user to input a line of text from the keyboard and assign it to a variable then display the “value”. • Run the program • Re run the program but this time the input must come from a text file.

17. Useful link • http://www.perl.org/books/beginning-perl/ • perl tutorial book • http://www.webbasedprogramming.com/Perl-Quick-Reference/ch3.htm • This link covers all languages including perl