1. 1 Using Perl Modules

2. 2 What are Perl modules?  Modules are collections of subroutines  Encapsulate code for a related set of processes  End in.pm so Foo.pm would be used as Foo  Can form basis for Objects in Object Oriented programming

3. 3 Using a simple module  List::Util is a set of List utilities functions  Read the perldoc to see what you can do  Follow the synopsis or individual function examples

4. 4 List::Util use List::Util; my @list = 10..20; my $sum = List::Util::sum(@list); print “sum (@list) is $sum\n”; use List::Util qw(shuffle sum); my $sum = sum(@list); my @list = (10,10,12,11,17,89); print “sum (@list) is $sum\n”; my @shuff = shuffle(@list); print “shuff is @shuff\n”;

5. 5 Module naming  Module naming is to help identify the purpose of the module  The symbol :: is used to further specify a directory name, these map directly to a directory structure  List::Util is therefore a module called Util.pm located in a directory called ‘List’

6. 6 Module Naming (contd.)  Does not require inheritance or specific relationship between modules that all start with the same directory name  Case MaTTerS! List::util will not work  Read more about a module by doing “perldoc Modulename”

7. 7 Modules as objects  Modules are collections of subroutines  Can also manage data  Multiple instances can be created (instantiated)  Can access module routines directly on object

8. 8 Object creation  To instantiate a module call ‘new’  Sometimes there are initialization values  Objects are registered for cleanup when they are set to undefined (or when they go out of scope)  Methods are called using -> because we are dereferencing object.

9. 9 Simple Module as Object example #!/usr/bin/perl -w use strict; use MyAdder; my $adder = new MyAdder; $adder->add(10); print $adder->value, “\n”; $adder->add(10); print $adder->value, “\n”; my $adder2 = new MyAdder(12); $adder2->add(17); print $adder2->value, “\n”; my $adder3 = MyAdder->new(75); $adder3->add(7); print $adder3->value, “\n”;

10. 10 Writing a module: instantiation Starts with package to define the module name multiple packages can be defined in a single module file - but this is not recommended at this stage The method name new is usually used for instantiation bless is used to associate a datastructre with an object

11. 11 Writing a module: subroutines The first argument to a subroutine from a module is always a reference to the object - we usually call it ‘$self’ in the code. This is an implicit aspect Object-Oriented Perl Write subroutines just like normal, but data associated with the object can be accessed through the $self reference.

12. Writing a module package MyAdder; use strict; sub new { my ($package, $val) = @_; $val ||= 0; my $obj = bless { ‘value’ => $val}, $package; return $obj; } sub add { my ($self,$val) = @_; $self->{’value’} += $val; } sub value { my $self = shift; return $self->{’value’}; }

13. Writing a module II (array) package MyAdder; use strict; sub new { my ($package, $val) = @_; $val ||= 0; my $obj = bless [$val], $package; return $obj; } sub add { my ($self,$val) = @_; $self->[0] += $val; } sub value { my $self = shift; return $self->[0]; }

14. 14 Using the module Perl has to know where to find the module Uses a set of include paths type perl -V and look at the @INC variable Can also add to this path with the PERL5LIB environment variable Can also specify an additional library path in script use lib ‘/path/to/lib’;

15. Your script using adder #!/usr/bin/perl -w use lib “$ENV{HOME}/lib/perl”; # can also do this using the Env # module to import all the # environmnet vars # use Env; # use lib “$HOME/lib/perl”; my $adder = MyAdder->new(18); print $adder->add(-7); # add returned the sum as well Assuming you put the module in your homedir/lib/perl

16. 16 Using a module as an object LWP is a perl library for WWW processing Will initialize an ‘agent’ to go out and retrieve web pages for you Can be used to process the content that it downloads

17. LWP::UserAgent #!/usr/bin/perl -w use strict; use LWP::UserAgent; my $url = 'http://us.expasy.org/uniprot/P42003.txt'; my $ua = LWP::UserAgent->new(); # initialize an object $ua->timeout(10); # set the timeout value my $response = $ua->get($url);http://us.expasy.org/uniprot/P42003.txt' if ($response->is_success) { # print $response->content; # or whatever if( $response->content =~ /DE\s+(.+)\n/ ) { print "description is '$1'\n"; } if( $response->content =~ /OS\s+(.+)\n/ ) { print "species is '$1'\n"; } } else { die $response->status_line; }