Bioinformatics

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 neutrophilelastase gene) • TTGTCAGAGCCCCAGCTGGTGTCCAGGGACTGACCGTGAGCCTGGGTGAAAGTGAGTTCCCCGTTGGAGGCACCAGACGAGGAGAGGATGGAAGGCCTGGCCCCCAAGAATGAGCCCTGAGGTTCAGGAGCGGCTGGAGTGAGCCGCCCCCAGATCTCCGTCCAGCTGCGGGTCCCAGAGGCCTGGGTTACACTCGGAGCTCCTGGGGGAGGCCCTTGACGTGCTCAGTTCCCAAACAGGAACCCTGGGAAGGACCAGAGAAGTGCCTATTGCGCAGTGAGTGCCCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACAGGGCCCTGGGTAAACTGAGGCAGGCGACACAGCTGCATGTGGCCGGTATCACGGGGCCCTGGATAAACAGAGGCAGGCGAGGCCACCCCCATCAAG…… • 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 blablabla …’ • 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 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)

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 • This link covers all languages including perl