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

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

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)

Boolean algebra AND OR NOT

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.

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)

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.

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)

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);

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);

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

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!)

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

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);

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 $marker = shift; #operates on @_ by default my ($surface, $diameter) = @_;

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) my ($xref, $yref) = @_;

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!

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

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;

@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

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;

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

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); }

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); }