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Perl

Perl. Introduction. Why Perl?. Powerful text manipulation capabilities Has a wide range of libraries available Fast Good support for file and process operations Widely used scripting language Alternatives: Python, Ruby. Less suiteable for:. Building large and complex applications

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Perl

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  1. Perl Introduction

  2. Why Perl? • Powerful text manipulation capabilities • Has a wide range of libraries available • Fast • Good support for file and processoperations • Widely used scripting language Alternatives: Python, Ruby

  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. Scripting • Preheat oven to 350 degrees F (175 degrees C). • In a large bowl, mix together the cake and pudding mixes, sour cream, oil, beaten eggs and water. Stir in the chocolate chips and pour batter into a well greased 12 cup bundt pan. • Bake for 50 to 55 minutes, or until top is springy to the touch and a wooden toothpick inserted comes out clean. Cool cake thoroughly in pan at least an hour and a half before inverting onto a plate If desired, dust the cake with powdered sugar.

  5. Computers are not ‘smart’

  6. Learning to script Knowledge + Skills

  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

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