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 Perl is a high level [scripting] language Perl is an interpreted language Very good string handling [feature] functionality and other features [functionality] which we will cover later. This makes it suitable for bioinformatics

4. A typical bioinformatics file: FASTA format Name of the following file is: DNA_sequence.fasta >gi|34529|emb|Y00477.1| Human bone marrow serine protease gene (medullasin) (leukocyte neutrophil elastase gene) TTGTCAGAGCCCCAGCTGGTGTCCAGGGACTGACCGTGAGCCTGGGTGAAAGTGAGTTCCCCGTTGGAGGCA CCAGACGAGGAGAGGATGGAAGGCCTGGCCCCCAAGAATGAGCCCTGAGGTTCAGGAGCGGCTGGAGTGA GCCGCCCCCAGATCTCCGTCCAGCTGCGGGTCCCAGAGGCCTGGGTTACACTCGGAGCTCCTGGGGGAGGCC CTTGACGTGCTCAGTTCCCAAACAGGAACCCTGGGAAGGACCAGAGAAGTGCCTATTGCGCAGTGAGTGCCC GACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCC GGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGG TAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGAC ACAGCTGCATGTGGCCGGTATCACGGGGCCCTGGATAAACAGAGGCAGGCGAGGCCACCCCCATCAAG…… The line in Bold is the “descriptor line” The rest are nucleotides bases The Y00477.1 gene has over 5292 bp [most not shown here but can be found in file] Need to analyse such files and Perl as we will see is suited to manipulating such files. Note: FASTA files also exist for proteins

5. Variables: $variable_name A variable is a location in memory that can store a value – A Number: (1, 1.2) – A string (text) AATTAAGGA or ‘I like bla bla bla …’ In perl to use a “basic” variable use: – $variable_name The $variable_name [memory location] can be assigned a value – There is no distinction between basic data types. – $variable_name = ‘ my name is Denis’; ( = is the assign operator) – $variable_name = 5.1; –

6. “explicit” variable The &variable is referred to as a global variable and it may lead to problems; for example if I entered &varaible = 5; it would not change the value of &variable and nor would the compiler detect an error. It is better to use my &variable as it gives greater control if used with: use strict; and use warnings.

7. Using Strict 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; Example 2: #!/usr/bin/perl # using strict and my $variables my $variable = 5; print "the value of the variable is: ",$varaible;

8. Example 1 Example 2

9. Using Strict 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;

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

11. 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

12. 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 OutputExample.pl): – #!/usr/bin/perl – # formating output example – Print ’ ”the end justifies the means “ \n’; – $x = "I am from Cork "; #declare a string – $y = "my name is Denis"; #declare another string – print "the value of $x is $x\n"; – print "the value of \$x is $x\n"; # note the \$x – print "the value of \$y concatenated to \$x is $y$x\n";

13. Output from OutputExample.pl

14. Inputting Data (assign data to a variable) This is where data can be typed in from the keyboard, read from a file or “hardcode” into the program Perl reads text files – including FASTA files. Reads input one line at a time this includes the return key (carriage return/End of line ) Read data from the key board – #!/usr/bin/perl : This line must be at the start of each program. – $var = <> ; (input a line of characters and assign it to $var) – Chomp $var removes the return character from the line. – Use both of these statements together – Alternatively you can combine both statements together – chomp($var = <>);

15. display contents from a file 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 inputin g form the keyboard) At the Command line type – C:\directory> Input.pl text1.txt

16. 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

17. Exercise 2 Ask user to input a line of text from the keyboard and assign it to a variable Display the “value” that was assigned to the variable – Run the above with only the name on the command line – Re run the program with a text file as one of the arguments.

18. 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