Lesson 2.

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

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

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 OR AND 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 –

6. Operator precedence * , / precedes +, - • 5 + 6 * 3 = 23 (not 33) 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 –

8. Operator precedence * , / precedes +, - • 5 + 6 * 3 = 23 (not 33) 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 • -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 • my @files = glob “*.txt”; foreach my $f (@files) { print “$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 { my @params = @_; # do something... then... return $result; } Function call • my $result = foo($param1, $param2);

15. Subroutine parameters The @_ array is an alias to the original parameters • The original parameters will be changed if @_ is changed! Usually, @_ 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 = shift @_; my $marker = shift; #operates on @_ by default

16. CAVEAT! Subroutine parameters – multiple lists Function parameters such as: • foo(@x, @y) Don't work, because in the subroutine: • sub foo { my (@x, @y) = @_; All elements of @_ will be assigned to @x • Use listrefs (or hashrefs) in this case • foo(\@x, \@y) • sub foo { 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 in @INC @INC is populated by Perl at startup Changing @INC – – – • List of paths given in the environment variable $PERL5LIB is pre-pended to @INC –

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 • 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); }