Lecture 8:

1. Lecture 8: Basic concepts of subroutines

2. Functions • 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

3. Functions: passing more than one variable • Subroutines : pass one or more variables. • sub subname • { • my ($var1, $var2,….) = @_; • { alternatively uses subscripts $_[0], $_[2].…. • statements • Return value • } • After all the subs are defined they are then called as required: • my $variable = subname($name); • The SubroutineExample2.pl

4. Returning values • A basic return uses the “return $var1” / “return @sequences”…. • The values can also be returned if they are the last statement in the program. • Sub-routine biggest{ • My ($a, $b, $c) = @_; # the list of “local varaible” must correspond to the types that are passed. If you pass a hash table my(%hash) = @_ • use strict; use warnings; # this is for the local variable • My $temp; • $temp = ($a<$b ? $a : $b); #(An alternative if else statement) • # returning the value (last statement in the function) • if ($temp < $c ) • { &temp} # this is returned • Else • {$c} #this is returned • } • In main • print “The biggest of the three number is: biggest(5,2,4)”

5. Passing by reference • By using the \ in a function call you pass the pointer to the subroutine • The pointer can be de-referenced by using the $ value • sub ByReference (PassReference.pl) • { • print " In sub5: parms = @_ \n"; • my($val1) = $_[0]; • $arry_ptr = $_[1]; • $var2_ptr = $_[2]; • print " In sub5: \$val1 = ", $val1, " Address = ", \$val1, "\n"; • $val1 = $val1 - 1; • print " In sub5: Var1 = ", $val1, "\n"; • print " In sub5: Var2 = ", $var2_ptr, " Contents = ", $$var2_ptr, "\n"; • $$var2_ptr = $$var2_ptr - 1; • print " In sub5: Variable1 = ", $var2_ptr, " Contents = ", $$var2_ptr, "\n"; • chop(@$arry_ptr); • print " In sub5: Array1 = ", $arry_ptr, " Contents = ", @$arry_ptr, "\n"; • } • In main • ByReference($var1, \@arr1, \$var2); (what are the values of output)

6. Exercises • Write a program using subroutines that: • Confirms if the user has input the code in the following format: • Classcode_yearcode(papercode) • E.g dt249 4(w203c) • Modify the sequence size example (from “basic pattern matching” lecture) • Allow the user to input a file name and determine its length. • Write the script using one or more subroutines.

7. Exercises • Write a sub-routine that can find the reverse complement of an DNA sequence. Use this subroutine to print out the compliment of each sequence line of a DNA fastafile • write a subroutine to convert a DNA sequence to amino acid sequence; use this to translated all three reading frames in a fasta file.