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.Active perl notepad++ 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 $variable along 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 – #!/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) output

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 http://www.webbasedprogramming.com/Perl- Quick-Reference/ch3.htm This link covers all languages including perl