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Marcs (bio)perl course


These are the lecture slides for the BITS training session "Introduction to programming in Bioperl". …

These are the lecture slides for the BITS training session "Introduction to programming in Bioperl".

See for more material: http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203793:bioperl-additional-material&catid=84&Itemid=610

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  • Remember to wear it !
  • Not often needed. Why might you need the braces ? String interpolation:$name = ‘Johnny’;Print “$name1”; # => nothing printedPrint “${name}1”; # => ‘Johnny1’
  • If there are more variables in the list than elements in the array, the extra variables are assigned the udefined value. If there are fewer variables than array elements, the extra elements are ignored.Distributiviteit: my ()
  • If there are more variables in the list than elements in the array, the extra variables are assigned the udefined value. If there are fewer variables than array elements, the extra elements are ignored.
  • Comma is operator: flattens (‘concatenates’) lists/arrays
  • Comma is operator: flattens (‘concatenates’) lists/arrays
  • No parens needed: comma operators produce list
  • main should have been called ‘our’ ;-)Not needed to use the family name when you are with your family. If you call John for dinner, John will know it’s him and you know who will come.But if your family has visitors of another family and they have a John in the family as well ...Family name + given name = fully qualified variable name


  • 1. Marc Logghe
  • 2. Perl
    “A script is what you give an actor, but a program is what you give an audience.”
  • 3. Goals
    Perl Positioning System: find your way in the Perl World
    Write Once, Use Many Times
    Object Oriented Perl
    Thou shalt not be afraid of the Bioperl Beast
  • 4.
  • 5. Agenda Day1
    Perl refresher
    Arrays and lists
    Subroutines and functions
    Creating and running a Perl script
    References and advanced data structures
    Packages and modules
    Objects, (multiple) inheritance, polymorphism
  • 6. Agenda Day 2
    What is bioperl ?
    Taming the Bioperl Beast
    Finding modules
    Finding methods
    Sequence processing
    One image says more than 1000 words
  • 7. Variables
    Data of any type may be stored within three basic types of variables:
    Scalar (strings, numbers, references)
    Array (aka list but not quite the same)
    Hash (aka associative array)
    Variable names are always preceded by a “dereferencing symbol” or prefix. If needed: {}
    $ - Scalar variables
    @ - List variables
    % - Associative array aka hash variables
  • 8. Variables
    You do NOT have to
    Declare the variable before using it
    Define the variable’s data type
    Allocate memory for new data values
  • 9. Scalar variables
    Scalar variable stores a string, a number, a character, a reference, undef
    $name, ${name}, ${‘name’}
    More magic: $_
  • 10. Array variables
    Array variable stores a list of scalars
    @name, @{name}, @{‘name’}
    Map: index => scalar value
    zero-indexed (distance from start)
  • 11. Array variables
    List assignment:
    Individual assignment: $count[2] = 42
    Individual acces: print $count[2]
    Special variable $#<array name>
    Scalar context
    @count = (1, 2, 3, 4, 5);
    @count = (‘apple’, ‘bat’, ‘cat’);
    @count2 = @count;
  • 12. Array variables
    Access multiple values via array slice:
    Assign multiple values via array slice:
    print @array[3,2,4,1,0,-1];
    @array[3,2,4,1,0,-1] = @new_values;
  • 13. Lists
    List = temporary sequence of comma separated values usually in () or result of qw operator
    Array = container for a list
    Array initialization
    Extract values from array
    my @array = qw/blood sweat tears/;
    my ($var1, $var2[42], $var3, @var4) = @args;
    my ($var5, $var6) = @args;
  • 14. Lists
    List flattening
    Remember: each element of list must be a scalar, not another list
    => NOT hierarchical list of 3 elements
    • FLATTENED list of scalar values
    Individual access and slicing cf. arrays
    my @vehicles = (‘truck’, @cars, (‘tank’,’jeep’));
    my @vehicles = (‘truck’, @cars, (‘tank’,’jeep’))[2,-1];
  • 15. Hash variables
    Hash variables are denoted by the % dereferencing symbol.
    Hash variables is a list of key-value pairs
    Both keys and values must be scalar
    Notice the ‘=>’ aka ‘quotifying comma’
    my %fruit_color = ("apple", "red", "banana", "yellow");
    my %fruit_color = (
    apple => "red",
    banana => "yellow",
  • 16. Hash variables
    Individual access: $hash{key}
    Access multiple values via slice:
    Assign multiple values via slice:
    @slice = @hash{‘key2’,’key23’,’key4’}
    @hash{‘key2’,’key23’,’key4’} = @new_values;
  • 17. Non data types
    There are several predefined filehandles, including STDIN, STDOUT, STDERR and DATA (default opened).
    No prefix
    Code value aka subroutine
    Dereferencing symbol “&”
  • 18.
  • 19. Subroutines
    We can reuse a segment of Perl code by placing it within a subroutine.
    The subroutine is defined using the sub keyword and a name (= variable name !!).
    The subroutine body is defined by placing code statements within the {} code block symbols.
    sub MySubroutine{
    #Perl code goes here.
    my @args = @_;
  • 20. Subroutines
    To call a subroutine, prepend the name with the & symbol:
    &MySubroutine; # w/o arguments
    MySubroutine(); # with or w/o arguments
  • 21. Subroutines
    Arguments in underscore array variable (@_)
    List flattening !!
    my @results = MySubroutine(@arg1, ‘arg2’, (‘arg3’, ‘arg4’));
    sub MySubroutine{
    #Perl code goes here.
    my ($thingy, @args) = @_;
  • 22. Subroutines
    Return value
    Scalar value
    List value
    Return value
    Explicit with return function
    Implicit: value of the last statement
    sub MySubroutine{
    #Perl code goes here.
    my ($thingy, @args) = @_;
  • 23. Subroutines
    Calling contexts
    wantarray function
    Void => undef
    Scalar => 0
    List => 1
    my $num = getFiles($dir);
    my @files = getFiles($dir);
  • 24. Functions and operators
    Built-in routines
    Arguments at right hand side
    Sensible name (defined, open, print, ...)
  • 25. Functions
    Perl provides a rich set of built-in functions to help you perform common tasks.
    Several categories of useful built-in function include
    Arithmetic functions (sqrt, sin, … )
    List functions (push, chomp, … )
    String functions (length, substr, … )
    Existance functions (defined, undef)
  • 26. Array functions
    Array as queue: push/shift (FIFO)
    Array as stack: push/pop (LIFO)
  • 27. List functions
    chomp: remove newline from every element in the list
    map: kind of loop without escape, every element ($_) is ‘processed’
    grep: kind of filter
  • 28. Hash functions
    keys: returns the hash keys in random order
    values: returns values of the hash in random order but same order as keys function call
    each: returns (key, value) pairs
    delete: remove a particular key (and associated value) from a hash
  • 29. Operators
    Complex and subtle (=,<>, <=>, ?:, ->,=>,...)
    Symbolic name (+,<,>,&,!, ...)
  • 30. Operators
    Calling context
    Eg. assignment operator ‘=‘
    ($item1, $item2) = @array;
    $item1 = @array;
  • 31.
  • 32. perldoc
    Access to Perl’s documentation system
    Command line
    Web: http://perldoc.perl.org/
    Documentation overview: perldoc perl
    Function info:
    perldoc perlfunc
    perldoc -f <function name>
    Operator info: perldoc perlop
    Searching the FAQs: perldoc -q <FAQ keyword>
  • 33. perldoc
    Looking up module info
    Documentation: perldoc <module>
    Installation path: perldoc -l <module>
    Source: perldoc -m <module>
    All installed modules: perldoc -q installed
  • 34. perldoc
    Move around
  • 35. perldoc
  • 36. Creating a script
    Text editor (vi, textpad, notepad++, ...)
    IDE (Komodo, Eclipse, EMACS, Geany, ...)
    See: www.perlide.org
    Shebang (not for modules)
  • 37. Executing a script
    Command line
    .pl extension
    Shebang line
    chmod +x script
  • 38. Executing a script
    Geany IDE
  • 39.
  • 40. References(and referents)
    A reference is a special scalar value which “refers to” or “points to” any value.
    A variable name is one kind of reference that you are already familiar with. It’s a given name.
    Reference is a kind of private, internal, computer generated name
    A referent is the value that the reference is pointing to
  • 41. Creating References
    Method 1: references to variables are created by using the backslash() operator.
    $name = ‘bioperl’;
    $reference = $name;
    $array_reference = @array_name;
    $hash_reference = %hash_name;
    $subroutine_ref = &sub_name;
  • 42. Creating References
    Method 2:
    [ ITEMS ] makes a new, anonymous array and returns a reference to that array.
    { ITEMS } makes a new, anonymous hash, and returns a reference to that hash
    my $array_ref = [ 1, ‘foo’, undef, 13 ];
    my $hash_ref = {one => 1, two => 2};
  • 43. Dereferencing a Reference
    Use the appropriate dereferencing symbol
    Scalar: $
    Array: @
    Hash: %
    Subroutine: &
  • 44. Dereferencing a Reference
    Remember $name, ${‘name’} ?
    Means: give me the scalar value where the variable ‘name’ is pointing to.
    A reference $reference ìs a name, so $$reference, ${$reference}
    Means: give me the scalar value where the reference $reference is pointing to
  • 45. Dereferencing a Reference
    The arrow operator: ->
    Arrays and hashes
    my $array_ref = [ 1, ‘foo’, undef, 13 ];
    my $hash_ref = {one => 1, two => 2};
    ${$array_ref}[1] = ${$hash_ref}{‘two’}
    # can be written as:
    $array_ref->[1] = $hash_ref->{two}
    # can be written as:
    $sub_ref->($arg1, $arg2)
  • 46. Identifying a referent
    ref function
  • 47. References
    Why do we need references ???
    Create complex data structures
    !! Arrays and hashes can only store scalar values
    Pass arrays, hashes, subroutines, ... as arguments to subroutines and functions
    !! List flattening
  • 48. Complex data structures
    Reference is a scalar value
    Arrays and hashes are sets of scalar values
    In one go:
    my $array_ref = [ 1, 2, 3 ];
    my $hash_ref = {one => 1, two => 2};
    my %data = ( arrayref => $array_ref,
    hash_ref => $hash_ref);
    my %data = ( arrayref => [ 1, 2, 3 ],
    hash_ref => {one => 1, two => 2}
  • 49. Complex data structures
    Individual access
    my %data = ( arrayref => [ 1, 2, 3 ],
    hash_ref => {one => 1,
    two => [‘a’,’b’]});
    How to access this value ?
    my $wanted_value = $data{hash_ref}->{two}->[1];
  • 50. Complex data structures
    my @row1 = (1..3);
    my @row2 = (2,4,6);
    my @row3 = (3,6,9);
    my @rows = (@row1,@row2,@row3);
    my $table = @rows;
  • 51. Complex data structures
    my $table = [
    [1, 2, 3],
    [2, 4, 6],
    [3, 6, 9]
  • 52. Complex data structures
    Individual access
    my $wanted_value = $table->[1]->[2];
    # shorter form:
    $wanted_value = $table->[1][2]
  • 53. Packages and modules
    2 types of variables:
    Global aka package variables
    Lexical variables
  • 54. Packages and modules
    Global / package variables
    Visible everywhere in every program
    You get the if you don’t say otherwise
    !! Autovivification
    Name has 2 parts: family name + given name
    Default family name is ‘main’. $John is actually $main::John
    $Cleese::John has nothing to do with $Wayne::John
    Family name = package name
    $var1 = 42;
    print “$var1, “, ++$var2;
    # results in:
    42, 1
  • 55.
  • 56. Packages and modules
    Lexical / private variables
    Explicitely declared as
    Only visible within the boundaries of a code block or file.
    They cease to exist as soon as the program leaves the code block or the program ends
    The do not have a family name aka they do not belong to a package
    (except for subroutines ...)
    my $var1 = 42;
    use strict;
    my $var1 = 42;
  • 57. Packages
    Family where the (global!) variables (incl. subroutines) live (remember $John)
    In general, a namespace is a container that provides context for the identifiers (variable names) it holds, and allows the disambiguation of homonym identifiers residing in different namespaces.
  • 58. Packages
    Family has a:
    name, defined via package declaration
    House, block or blocks of code that follow the package declaration
    package Bio::SeqIO::genbank;
    # welcome to the Bio::SeqIO::genbank family
    sub write_seq{}
    package Bio::SeqIO::fasta;
    # welcome to the Bio::SeqIO::fasta family
    sub write_seq{}
  • 59. Packages
    Why do we need packages ???
    To organize code
    To improve maintainability
    To avoid name space collisions
  • 60. Modules
    What ?
    A text file(with a .pm suffix) containing Perl source code, that can contain any number of namespaces. It must evaluate to a true value.
    At compile time: use <module>
    At run time: require <expr>
    <expr> and <module>:compiler translates each double-colon '::' into a path separator and appends '.pm'.
    E.g. Data::Dumper yields Data/Dumper.pm
    use Data::Dumper;
    require Data::Dumper;
    require ‘my_file.pl’;
    require $class;
  • 61. Modules
    A module can contain multiple packages, but convention dictates that each module contains a package of the same name.
    easy to quickly locate the code in any given package (perldoc –m <module>)
    not obligatory !!
    A module name is unique
    1 to 1 mapping to file system !!
    Should start with capital letter
  • 62. Module files
    Module files are stored in a subdirectory hierarchy that parallels the module name hierarchy.
    All module files must have an extension of .pm.
  • 63. Modules
    Module path is relative. So, where is Perl searching for that module ?
    Possible modules roots
    []$ perldoc –V

  • 64. Modules
    Alternative module roots (perldoc -q library)
    In script
    Command line
    use lib ‘/my/alternative/module/path’;
    []$ perl -I/my/alternative/module/path script.pl
    export PERL5LIB=$PERL5LIB:/my/alternative/module/path
  • 65. Modules
    package My::Package::Says::Hello;
    sub speak
    print __PACKAGE__, " says: 'Hello'n";
    package My::Package::Says::Blah;
    sub speak
    print __PACKAGE__, " says: 'Blah'n";
    use strict;
    use Test::Speak;
  • 66. Modules
    Why do we need modules???
    To organize packages into files/folders
    Code reuse (ne copy & paste !)
    Module repository: CPAN
    Special module that influences the code (compilation)
    Lexically scoped
  • 67. Modules
    Module information
    In standard distribution: perldoc perlmodlib
    Manually installed: perldoc perllocal
    All modules: perldoc –q installed
    Documentation: perldoc <module name>
    Location: perldoc –l <module name>
    Source: perldoc –m <module name>
  • 68. Packages and Modules - Summary
    A package is a separate namespace within Perl code.
    A module can have more than one package defined within it.
    The default package is main.
    We can get to variables (and subroutines) within packages by using the fully qualified name
    To write a package, just write package <package name> where you want the package to start.
    Package declarations last until the end of the enclosing block, file or until the next package statement
    The require and use keywords can be used to import the contents of other files for use in a program.
    Files which are included must end with a true value.
    Perl looks for modules in a list of directories stored in @INC
    Module names map to the file system
  • 69.
  • 70. Exercises
    Bioperl Training Exercise 1: perldoc
    Bioperl Training Exercise 2: thou shalt not forget
    Bioperl Training Exercise 3: arrays
    Bioperl Training Exercise 4: hashes
    Bioperl Training Exercise 5: packages and modules 1
    Bioperl Training Exercise 6: packages and modules 2
    Bioperl Training Exercise 7: complex data structures
  • 71.
  • 72. Object Oriented Programming in Perl
    Why do we need objects and OOP ?
    It’s fun
    Code reuse
  • 73. Object Oriented Programming in Perl
    What is an object ?
    An object is a (complex) data structure representing a new, user defined type with a collection of behaviors (functions aka methods)
    Collection of attributes
    Developer’s perspective: 3 little make rules
    To create a class, build a package
    To create a method, write a subroutine
    To create an object, bless a referent
  • 74. Rule 1: To create a class, build a package
    Defining a class
    A class is simply a package with subroutines that function as methods. Class name = type = label = namespace
    package Cat;
  • 75. Rule 2: To create a method, write a subroutine
    First argument of methods is always class name or object itself (or rather: reference)
    Subroutine call the OO way (method invocation arrow operator)
    package Cat;
    sub meow {
    my $self = shift;
    print __PACKAGE__ “ says: meow !n”;
  • 76. Rule 3: To create an object, bless a referent
    ‘Special’ method: constructor
    Any name will do, in most cases new
    Object can be anything, in most cases hash
    Reference to object is stored in variable
    Arguments: reference (+ class). Does not change !!
    Underlying referent is blessed (= typed, labelled)
    Returns reference
    package Cat;
    sub new {
    my ($class, @args) = @_;
    my $self = { _name => $_args[0] };
    bless $self, $class;
  • 77. Objects
    Perl objects are data structures ( a collection of attributes).
    To create an object we have to take 3 rules into account:
    Classes are just packages
    Methods are just subroutines
    Blessing a referent creates an object
  • 78. Objects
    Objects are passed around as references
    Calling an object method can be done using the method invocation arrow:
    Constructor functions in Perl are conventionally called new() and can be called by writing:
    $object_ref = ClassName->new()
  • 79. Inheritance
    Way to extend functionality of a class by deriving a (more specific) sub-class from it
    In Perl:
    Way of specifying where to look for methods
    store the name of 1 or more classes in the package variable @ISA
    Multiple inheritance !!
    package NorthAmericanCat;
    use Cat;
    @ISA = qw(Cat);
    package NorthAmericanCat;
    use Cat;
    use Animal;
    @ISA = qw(Cat Animal);
  • 80. Inheritance
    UNIVERSAL, parent of all classes
    Predifined methods
    isa(‘<class name>’): check if the object inherits from a particular class
    can(‘<method name>’): check if <method name> is a callable method
  • 81. Inheritance
    SUPER: superclass of the current package
    start looking in @ISA for a class that can() do_something
    explicitely call a method of a parental class
    often used by Bioperl to initialize object attributes
  • 82. Polymorphism
    methods defined in the base class will override methods defined in the parent classes
    same method has different behaviours
  • 83.
  • 84. Exercises
    Bioperl Training Exercise 8: OOP
    Bioperl Training Exercise 9: inheritance, polymorphism
    Bioperl Training Exercise 10: aggregation, delegation