Subroutines in Perl. Jon-Michael Deldin. Dept. of Computer Science University of Montana September 12, 2011

Transcription

1 Subroutines in Perl Jon-Michael Deldin Dept. of Computer Science University of Montana September 12, 2011 Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

2 Outline 1 Overview 2 Elements of a subroutine 3 Example: fasta_to_array 4 Example: clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

3 Topic 1 Overview 2 Elements of a subroutine 3 Example: fasta_to_array 4 Example: clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

4 What is a subroutine? A subroutine is a function in Perl that can take 0 or more arguments. Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

5 Remember these? Functions (Math) f (x) = x 2 + 2x 1 f (3) = 14 Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

6 Remember these? Functions (Perl) Functions (Math) f (x) = x 2 + 2x 1 f (3) = 14 sub f { my $x = shift; return $x**2 + 2*$x - 1; } print "f(3) = ". f(3); Gives us f(3) = 14 Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

7 What can you do with them? Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

8 What can you do with them? Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

9 What can you do with them? Produce reusable code Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

10 What can you do with them? Produce reusable code Make your life easier Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

11 What can you do with them? Produce reusable code Make your life easier Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

12 What can you do with them? Produce reusable code Make your life easier fasta_to_string( sequence.fna ) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

13 What can you do with them? Produce reusable code Make your life easier fasta_to_string( sequence.fna ) fasta_to_array( sequence.fna ) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

14 What can you do with them? Produce reusable code Make your life easier fasta_to_string( sequence.fna ) fasta_to_array( sequence.fna ) clean_array(\@array) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

15 What can you do with them? Produce reusable code Make your life easier fasta_to_string( sequence.fna ) fasta_to_array( sequence.fna ) clean_array(\@array) sequence_genome_and_make_coffee() Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

16 Topic 1 Overview 2 Elements of a subroutine 3 Example: fasta_to_array 4 Example: clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

17 Declaration use the sub keyword assign a name (follows variable naming rules) Example definition sub fasta_to_string { # code goes here } Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

18 Arguments the x in f (x) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

19 Arguments the x in f (x) as many as you want (even none) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

20 Arguments the x in f (x) as many as you want (even none) passed in as an array with special Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

21 Arguments the x in f (x) as many as you want (even none) passed in as an array with special scalars only (there s a trick for arrays and hashes) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

22 Example: Receiving arguments Using shift sub fasta_to_string { # first element my $filename = shift; #... } Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

23 Example: Receiving arguments Using shift sub fasta_to_string { # first element my $filename = shift; #... } sub fasta_to_string { # inline list for vars my ($filename) #... } Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

24 Example: Receiving more than one argument If we needed two arguments, $x, $y, we would get args using multiple shift calls Multiple shift calls sub f { my $x = shift; my $y = shift; #... } Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

25 Example: Receiving more than one argument If we needed two arguments, $x, $y, we would get args using multiple shift calls Multiple shift calls sub f { my $x = shift; my $y = shift; #... } sub f { my ($x, $y) #... } Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

26 Passing an array as an argument You can pass the array like a scalar if only one argument Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

27 Passing an array as an argument You can pass the array like a scalar if only one argument Otherwise, pass the array as a reference (similar to file handles) Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

28 Passing an array as an argument You can pass the array like a scalar if only one argument Otherwise, pass the array as a reference (similar to file handles) When passing an array to a function, use \@my_array as an argument Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

29 Passing an array as an argument You can pass the array like a scalar if only one argument Otherwise, pass the array as a reference (similar to file handles) When passing an array to a function, use \@my_array as an argument When receiving an array in the function, convert back to an array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

30 Example: Passing arrays as arguments Example sub square_array { my ($arrref) } for (my $i = 0; $i $i++) { $arr[$i] = $arr[$i]**2; } return \@arr; = (0, 1, 2, 3, 4); print "ORIGINAL\n"; print Output ORIGINAL NEW print "\n\nnew\n"; print Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

31 Returning values You can return the result of an operation, but it s not required. Not returning sub f { my $x = shift; print "x was $x!\n"; } prints a value to screen, but unusable Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

32 Returning values You can return the result of an operation, but it s not required. Returning a value Not returning sub f { my $x = shift; print "x was $x!\n"; } prints a value to screen, but unusable sub f { my $x = shift; my $result = $x * rand(10); return $result; } my $num = f(20); print $num; # optional... makes $num this value: Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

33 Topic 1 Overview 2 Elements of a subroutine 3 Example: fasta_to_array 4 Example: clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

34 Planning Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

35 Planning Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

36 Planning fasta_to_array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

37 Planning fasta_to_array input filename Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

38 Planning fasta_to_array input filename output array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

39 Planning fasta_to_array input filename output array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

40 Planning Process fasta_to_array input filename output array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

41 Planning Process fasta_to_array input filename output array 1 Open a file handle Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

42 Planning Process fasta_to_array input filename output array 1 Open a file handle 2 Read the contents as an array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

43 Planning Process fasta_to_array input filename output array 1 Open a file handle 2 Read the contents as an array 3 Close the file handle Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

44 Planning Process fasta_to_array input filename output array 1 Open a file handle 2 Read the contents as an array 3 Close the file handle 4 Return the array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

45 Build the stub Build functions iteratively! Example (sequence.fa) > very interesting sequence ACTG CCCC AAAAAAAA TTTT Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

46 Build the stub Build functions iteratively! function Example (sequence.fa) > very interesting sequence ACTG CCCC AAAAAAAA TTTT use warnings; use strict; sub fasta_to_array { my $filename = shift; } return (); # an empty list for now = fasta_to_array( sequence.fa ); Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

47 Add file handling Code use warnings; use strict; sub fasta_to_array { my $filename = shift; open my $fh, <, $filename or die("can t read $filename"); close $fh; } return (); = fasta_to_array( sequence.fa ); Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

48 Read in the file Code use warnings; use strict; sub fasta_to_array { my $filename = shift; open my $fh, <, $filename or die("can t read $filename"); = <$fh>; close $fh; return \@lines; # a reference } sequence.fa )}; Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

49 Read in the file Code use warnings; use strict; sub fasta_to_array { my $filename = shift; open my $fh, <, $filename or die("can t read $filename"); = <$fh>; close $fh; return \@lines; # a reference } Output > very interesting sequence ACTG CCCC AAAAAAAA TTTT sequence.fa )}; Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

50 Topic 1 Overview 2 Elements of a subroutine 3 Example: fasta_to_array 4 Example: clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

51 Planning Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

52 Planning Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

53 Planning clean_fasta Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

54 Planning clean_fasta input array reference from fasta_to_array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

55 Planning clean_fasta input array reference from fasta_to_array output array reference Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

56 Planning clean_fasta input array reference from fasta_to_array output array reference Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

57 Planning clean_fasta input array reference from fasta_to_array output array reference Process Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

58 Planning clean_fasta input array reference from fasta_to_array output array reference Process 1 Get the array reference Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

59 Planning clean_fasta input array reference from fasta_to_array output array reference Process 1 Get the array reference 2 Get rid of the header line Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

60 Planning clean_fasta input array reference from fasta_to_array output array reference Process 1 Get the array reference 2 Get rid of the header line 3 For each line, get rid of all whitespace Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

61 Planning clean_fasta input array reference from fasta_to_array output array reference Process 1 Get the array reference 2 Get rid of the header line 3 For each line, get rid of all whitespace 4 Return the cleaned array Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

62 Stub Code sub clean_fasta { my $ref = shift; } return \@arr; sequence.fa ))}; Output > very interesting sequence ACTG CCCC AAAAAAAA TTTT Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

63 Drop the header line Code sub clean_fasta { my $ref = shift; Output } return \@arr; ACTG CCCC AAAAAAAA TTTT sequence.fa ))}; Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24

64 Get rid of whitespace Code sub fasta_to_array { my $filename = shift; open my $fh, <, $filename or die("can t read $filename"); = <$fh>; close $fh; } return \@lines; # or a reference, \@lines sub clean_fasta { my $ref = shift; # remove header line Output - ACTG - CCCC - AAAAAAAA - TTTT # get rid of newlines, tabs, spaces for (my $i = 0; $i $i++) { $arr[$i] =~ s/[\t\n ]//g; } } return \@arr; sequence.fa ))}; print "- ". join("\n- Jon-Michael Deldin (UM) Subroutines in Perl September 12, / 24