1. Lesson 2. Control structures File IO - reading and writing Subroutines
Modules
BioPerl

2. Comparisons and if statements
The if statement:
if (<condition>) {
# do something }
elsif (<another_condition>) {
# do something else
else {
# do yet another thing
a code block

3. comparators The result of a comparison is either true or false
Boolean algebra
Numeric values
Compare numbers
Is $a equal to $b? Larger? Smaller?
==, >, <, <=, >=, !=, <=>
if ($a > $b) { print “$a is larger than $b\n”; }
String values
eq, ne, gt (greater than), lt (less than)

4. Boolean algebra
AND OR
NOT

5. Boolean values in Perl Perl has no boolean type
Values that are “false”
0 (incl numerically assigned expressions that evaluate to zero)
“” (the empty string) (NB. “ “ (a string containing a space) is true)
undef (value of a variable that was declared but nothing assigned)
The empty list
The empty hash
True values
Everything else that is not true
Convention:
Assigning false: use 0. Assigning true: use 1.

6. Operator precedence * , / precedes +, - and, not precedes or
5 + (6 * 3)
(5 + 6) * 3
and, not precedes or
( $x < 2 or $x > 5 and $y < 100) ) vs.
( ( $x < 2 or $x > 5 ) and $y < 100)
See man perlop
See also de Morgan's law:
(! $x) and (! $y) = ! ( $x or $y )
(! $x) or (! $y) = ! ( $x and $y)

7. Boolean values in Perl Perl has no boolean type
Values that are “false”
0 (incl numerically assigned expressions that evaluate to zero)
“” (the empty string) (NB. “ “ (a string containing a space) is true)
undef (value of a variable that was declared but nothing assigned)
The empty list
The empty hash
True values
Everything else that is not true
Convention:
Assigning false: use 0. Assigning true: use 1.

8. Operator precedence * , / precedes +, - and, not precedes or
5 + (6 * 3)
(5 + 6) * 3
and, not precedes or
( $x < 2 or $x > 5 and $y < 100) ) vs.
( ( $x < 2 or $x > 5 ) and $y < 100)
See man perlop
See also de Morgan's law:
(! $x) and (! $y) = ! ( $x or $y )
(! $x) or (! $y) = ! ( $x and $y)

9. File I/O - Reading Opening a file
open(my $F, “<”, $filename); # “<”=reading
# “>”=writing
Reading from a file
while (<$F>) { # reads into default var $_
chomp(); # removes newline
my ($firstname, $lastname) = split /\t/; }
Closing a file
close($F);

10. File I/O - Writing Opening a file
open(my $F, “>”, $filename); # “<”=reading
# “>”=writing
Writing to a file
print $F “Hello World!\n”;
Closing a file
close($F);

11. File checks File check flags Check of the form if (-f $myfile) {
-d directory
-f plain file
-l symbolic link
-T text file
Check of the form
if (-f $myfile) {
open ($F, “<”, $myfile) # etc....
See also

12. The open or die construct
open (my $F, “<”, $myfile) or die “Can't open file $myfile”;
The open() call returns true on success, false otherwise.
The or operator evaluates the second operand only if the first operand is false (if the first operand is true, or will always be true!)

13. Reading directory listings
The glob function
= glob “*.txt”;
foreach my $f {
print “$f\n” }

14. Subroutines
Code that is duplicated in a script may be better in a subroutine
Subroutines are called like other Perl functions
Declaration and basic structure
sub foo {
# do something... then...
return $result; }
Function call
my $result = foo($param1, $param2);

15. Subroutine parameters
array is an alias to the original parameters
The original parameters will be changed is changed!
is assigned to more descriptive variables
Once assigned, the variables are not aliases anymore
Changing their values does not change the originals
Examples
sub foo {
my $chromosome =
my $marker = shift; #operates by default
my ($surface, $diameter)

16. CAVEAT! Subroutine parameters – multiple lists
Function parameters such as:
@y)
Don't work, because in the subroutine:
sub foo {
my @y)
All elements will be assigned
Use listrefs (or hashrefs) in this case
my ($xref, $yref)

17. Subroutine return values
Subroutines that return values are sometimes called functions
It is better for a function to return a value than to change the function parameters
Return values can be scalars, lists, or hashes.
Be careful with returning multiple lists or hashes.
Need to return listrefs or hashrefs!

18. Modules Create re-usable code that scripts can load and use
A module is a namespace
Subroutines that are used from different scripts are better placed into modules
Easier to maintain
Documention
Bug fixes

19. Modules Declaration package Foo; Notes about naming:
Package names should be uppercase
Often, package names are in CamelCase
Mapping to filesystem:
package Foo should be a file called Foo.pm
package Foo::Bar is in Foo/Bar.pm
Using modules
use Foo::Bar;

20. @INC is like $PATH for modules
How does Perl know where to look for modules?
Perl looks in the current directory
Perl looks in the order of directories given
@INC is populated by Perl at startup
List of paths given in the environment variable $PERL5LIB is pre-pended

21. Accessing other packages
You are ALWAYS in a package in Perl
The default package is called “main”.
The “main” package identifier can be omitted.
You can access all global variables declared in main by
our $example=100;
print $main::example.”\n”;
You can access globals in other packages by
print $MyOtherPackage::example;
print $Foo::Bar::example;

22. Some standard modules Math File Getopt::Std Test Math::Complex
Math::BigInt
File
File::Temp
File::Basename
File::Spec
Getopt::Std
Test

23. Bio::SeqIO Sequence input/output Usage use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format=>'fastq', - file=>$file);
my $out = Bio::SeqIO->new(-format=>'fasta', - file=>”>$file.fasta”);
while (my $s = $in->next_seq()) {
$out->write_seq($s); }

24. Changing object properties
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format=>'fasta', - file=>$file);
my $out = Bio::SeqIO->new(-format=>'fasta', - file=>”>$file.fasta”);
while (my $s = $in->next_seq()) {
my $id = $s->id();
my $new_id = $new_ids{$id};
$s->id($new_id);
$out->write_seq($s); }