Perl

1. Perl Introduction

2. Why Perl? • Widely used scripting language • Powerful text manipulation capabilities • Relatively easy to use • Has a wide range of libraries available • Fast • Good support for file and process operations

3. Less suiteable for: • Building large and complex applications • Java, C\C++, C# • Applications with a GUI • Java, C\C++, C# • High performance/memory efficient applications • Java, C\C++, C#, Fortran • Statistics • R

4. Learning to script Knowledge + Skills

5. Exercise Determine the percentage GC-content of the human chromosome 22

6. open file read lines per line: skip if header line count Cs and Gs count all nucleotides report percentage Cs and Gs

7. Hello World

8. Hello World…. Simple line of Perl code: print "Hello World"; Run from a terminal: perl -e 'print "Hello World";' Now try this and notice the difference: perl -e 'print "Hello World\n";'

9. \n “backslash-n” newline character 'Enter'key

10. \t “backslash-t” 'Tab' key

11. Hello World (cont) To create a text file with this line of Perl code: echo 'print "Hello World\n";' > HelloWorld.pl perl HelloWorld.pl In the terminal window, type kate HelloWorld.pl and then hit the enter key. Now you can edit the Perl code.

12. Pythagoras' theorem a2 + b2 = c2 32 + 42 = 52

13. Pythagoras.pl $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a2 + $b2; $c = sqrt($c2); print $c;

14. $a a single value or scalarvariable starts with a $ followed by its name

15. Pythagoras.pl $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a2 + $b2; $c = sqrt($c2); print $c;

16. 5

17. Perl scripts Add these lines at the top of each Perl script: #!/usr/bin/perl # author: # description: use strict; use warnings;

18. perl Pythagoras.pl Global symbol "$a2" requires explicit package name at Pythagoras.pl line 8. Global symbol "$b2" requires explicit package name at Pythagoras.pl line 9. Global symbol "$c2" requires explicit package name at Pythagoras.pl line 10. Global symbol "$a2" requires explicit package name at Pythagoras.pl line 10. Global symbol "$b2" requires explicit package name at Pythagoras.pl line 10. Global symbol "$c" requires explicit package name at Pythagoras.pl line 11. Global symbol "$c2" requires explicit package name at Pythagoras.pl line 11. Global symbol "$c" requires explicit package name at Pythagoras.pl line 12. Execution of Pythagoras.pl aborted due to compilation errors.

19. Pythagoras.pl $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a2 + $b2; $c = sqrt($c2); print $c;

20. Pythagoras.pl my $a = 3; my $b = 4; my $a2 = $a * $a; my $b2 = $b * $b; my $c2 = $a2 + $b2; my $c = sqrt($c2); print $c;

21. my The first time a variable appears in the script, it should be claimed using ‘my’. Only the first time...

22. Pythagoras.pl my($a,$b,$c,$a2,$b2,$c2); $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a2 + $b2; $c = sqrt($c2); print $c;

23. Pythagoras.pl $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a3 + $b2; $c = sqrt($c2); print $c;

24. 4

25. Pythagoras.pl $a = 3; $b = 4; $a2 = $a * $a; $b2 = $b * $b; $c2 = $a3 + $b2; $c = sqrt($c2); print $c;

26. Pythagoras.pl my $a = 3; my $b = 4; my $a2 = $a * $a; my $b2 = $b * $b; my $c2 = $a3 + $b2; my $c = sqrt($c2); print $c;

27. perl Pythagoras.pl Global symbol "$a3" requires explicit package name at Pythagoras.pl line 10. Execution of Pythagoras.pl aborted due to compilation errors.

28. Text or number Variables can contain text (strings) or numbers my $var1 = 1; my $var2 = "2"; my $var3 = "three"; Try these four statements: print $var1 + $var2; print $var2 + $var3; print $var1.$var2; print $var2.$var3;

29. Text or number Variables can contain text (strings) or numbers my $var1 = 1; my $var2 = "2"; my $var3 = "three"; Try these four statements: print $var1 + $var2; => 3 print $var2 + $var3; => 2 print $var1.$var2; => 12 print $var2.$var3; => 2three

30. variables can be added, subtracted, multiplied, divided and modulo’d with: + - * / % variables can be concatenated with: .

31. sequence.pl print "Please type a DNA sequence: "; #this is a comment line #Read a line from the standard input (keyboard) my $DNAseq = <STDIN>; #Remove the newline (Enter) from the typed text chomp($DNAseq); #Get the length of the text(DNA sequence) my $length = length($DNAseq); print "It has $length nucleotides\n";

32. Program flow is top - down sequence.pl print "Please type a DNA sequence: "; #this is a comment line #Read a line from the standard input (keyboard) my $DNAseq = <STDIN>; #Remove the newline (Enter) from the typed text chomp($DNAseq); #Get the length of the text(DNA sequence) my $length = length($DNAseq); print "It has $length nucleotides\n";

33. <STDIN> read characters that are typed on the keyboard. Stop after the Enter key is pressed

34. <> same, STDIN is the default and can be left out. This is a recurring and confusing theme in Perl...

35. sequence.pl print "Please type a DNA sequence: "; #this is a comment line #Read a line from the standard input (keyboard) my $DNAseq = <>; #Remove the newline (Enter) from the typed text chomp($DNAseq); #Get the length of the text(DNA sequence) my $length = length($DNAseq); print "It has $length nucleotides\n";

36. $output = function($input) input and output can be left out parentheses are optional

37. $coffee = function($beans,$water)

38. sequence2.pl print "Please type a DNA sequence: "; my $DNAseq = <>; chomp($DNAseq); #Get the first three characters of $DNAseq my $first3bases = substr($DNAseq,0,3); print "The first 3 bases: $first3bases\n";

39. $frag = substr($text, $start, $num) Extract a fragment of string $text starting at $start and with $num characters. The first letter is at position 0!

40. perldoc perldoc -f substr substr EXPR,OFFSET,LENGTH,REPLACEMENT substr EXPR,OFFSET,LENGTH substr EXPR,OFFSET Extracts a substring out of EXPR and returns it. First character is at offset 0, .....

41. print perldoc -f print print FILEHANDLE LIST print LIST print Prints a string or a list of strings. If you leave out the FILEHANDLE, STDOUT is the destination: your terminal window.

42. print In Perl items in a list are separated by commas print "Hello World","\n"; Is the same as: print "Hello World\n";

43. sequence3.pl print "Please type a DNA sequence: "; my $DNAseq = <>; chomp($DNAseq); #Get the second codon of $DNAseq my $codon2 = substr($DNAseq,3,3); print "The second codon: $codon2\n";

44. if, else, unless

45. sequence4.pl print "Please type a DNA sequence: "; my $DNAseq = <>; chomp($DNAseq); #Get the first three characters of $DNAseq my $codon = substr($DNAseq,0,3); if($codon eq "ATG") { print "Found a start codon\n"; }

46. Conditional execution if ( condition ) { do something } if ( condition ) { do something } else { do something else }

47. Conditional execution if ( $number > 10 ) { print "larger than 10"; } elsif ( $number < 10 ) { print "smaller less than 10"; } else { print "number equals 10"; } unless ( $door eq "locked" ) { openDoor(); }

48. Conditions are true or false 1 < 10 : true 21 < 10 : false

49. Comparison operators

50. Examples if ( 1 == 1 ) { # TRUE if ( 1 == 2 ) { # FALSE if ( 1 != 2 ) { # TRUE if ( -1 > 10 ) { # FALSE if ( "hi" eq "dag" ) { # FALSE if ( "hi" gt "dag" ) { # TRUE if ( "hi" == "dag" ) { # TRUE !!! The last example may surprise you, as "hi" is not equal to "dag" and therefore should evaluate to FALSE. But for a numerical comparison they are both 0.