Lecture 9: Basic concepts of Perl Modules

Functions (Subs) In perl functions take the following format: – sub subname – { my $var1 = $_[0]; statements Return value – } – After all the subs are defined they are then called as required: my $variable = subname($name); The SubroutineExample.pl

Perl Modules (.pm) A perl module is a set of functions stored in a separate file (example.pm) which can be used by any perl script. (increase re-usability) It is sometimes referred to as a library (like stdio.h) or package There is two files assoicated with using modules. A.pm file and a.pl file

A Simple perl module #!/usr/bin/perl package Foo; – sub bar – { print "Hello $_[0]\n" – } – sub blat – { print "World $_[0]\n" – } 1;

Utilising a perl Module A perl module can be invoked (loaded) in a perl script by using – require and then :: function_name – use and qw( parameter list) Loading with require: – #!/usr/bin/perl – require Foo; # used to load the perl module – Foo::bar( "a" ); – Foo::blat( "b" );

Utilising a perl module A perl module can also be loaded with use and by passing parameters via qw; e.g. – #!/usr/bin/perl – use FooUse; – bar( "a" ); # no need to use :: – blat( "b" ); However must use qw to utilise the module – require Exporter; = qw(Exporter); = qw(bar blat);

Modified Perl module for “use” package FooUse; require = = qw(bar blat); sub bar { print "Hello $_[0]\n" } sub blat { print "World $_[0]\n" } sub splat { print "Not $_[0]\n" } # Not exported! 1;

Exercise Create and run the perl modules covered in class. Modify the use perl script to see What happens if I call the splat function? Re-write the “ByReference” subroutine in the pass by reference example (in the subroutine lecture) as a perl module and load it in a perl script. Re-write your assignment perl scripts in the form of a perl module and a perl script driver.

Class Exercise: Finding start and stop codons and potential ORF Download the file. (TUBAC3 gene complete sequence) (see last lecture)TUBAC3 gene complete sequence Using “your” perl module and perl script determine the location of the start and stop codons. Write a script that will “attempt” to find at least one ORF. Clearly state how, using your background knowledge of gene expression, you are going to try and resolve this problem. Using your program: determine the position of an (the) ORF(s) for this gene. Discuss How your findings compare with the results obtained in the genebank record file.