Background

Bioperl toolkit

• Bioperl is a collection of open source, object-oriented perl modules. Developped and maintained by hundreds of voluteers.
• Rapidly evolving.
• Many convenient tools for biologists:
  • Read in standard sequence data (FASTA, GenBank, EMBL, SwissProt,...)
  • Sequence format conversion
  • Process reports of programs (e.g. GenBank, BLAST, PAML)
  • Parse phylogenetic trees, outputs of molecular evolution softwares.
  • Population Genetic analysis
  • Manipulation and analysis of sequence data

Object oriented (OO) programing

Bioperl uses slightly different style of programming from what we have been using. We'll talk about object-oriented programming briefly, so you can start to use bioperl without knowing the details (the definition of OO here may be a little hackish, but it serves our purpose).

• Different approaches (styles) of programming
  • Declarative programming
    • You declare variables, functions, conditional tests, and other operations.

    • You have to manage the definition of variables and functions and how to use them exactly. You define that a function average() takes an array of floating-point numbers, and return floating point numbers. You have to know what the function expect and what it will return, and you have to manage your program so that you use it correctly. Otherwise, the program can misbehave.

    • Example: C, FORTRAN, BASIC, Perl (the way we used previously).

  • Object-oriented (OO) programming
    • Instead of variables, data structures called objects play the main roles in coding.
    • The objects contains data and associated subroutines which can manipulate the data.
    • Instead of accessing the data directly, we use these manipulation methods embedded in the objects.
    • Takes more effort to program in this way, but it's easier to reuse.
    • Example: Perl, C++, Java
• There are costs and benefits of each system, so OO programming is not necessarily better than declarative programming, or other styles.

Terminology

Object

• An object is a collection of data that naturally belongs together.
• Example: For a sequence object, this object may contain data about several attributes: DNA sequence, name of gene, taxon name, exon, intron etc.
• Programers group these several related data to be contained in a single object for convenience.
• Very similar to ``data structure'' you learned in C.

Method

• A method is an associated subroutine (function) which can manipulate the data included in the object. Each object can have many associated methods.

  e.g., ``calculateSequenceLength'', `` calculateBaseComposition'', ``tellMeTaxonName''.

• You do NOT directly manipulate the data. In C, you could directly manipulate the members of data structure (e.g. individual.phenotype = BIG;). Instead, you'll manipulate the data (or get what you want) by accessing the methods. (e.g. tell an object to use ``tellMeTaxonName'' method, which will retrieve the stored data, and give it back to you.

Class

• A class is the definition of the object and the associated methods.
• You can say that a specific object (say sequence object thisSeq) is an instance of a class.

analogy

• Class is like different types of robots: Gigantor-type robot, Aibo-type robot, roomba-type robot
  • Different types of robots are good for differnt task: e.g.,
    • Gigantor can fight crime around the world.
    • Aibo is good at fetching beer from the refrigerator (not really).
    • Roomba is good for cleaning mess.
  • Class defines what type of robots in this class can keep, and what commands it can understand. e.g. Gigantor doesn't understand ``cleanTheRoom'' command.

  

• Max and Molly are objects: specific instances of Class Aibo.

  You may use Max and Molly for different purposes. In C, you could declare double max, min;, and you use these two specific instances of double-type variables to store maximum and minimum values, respectively.

• Both Max and Molly understand same sets ofcommands: these commands are like methods.
  • If you ask Max, ``what's your name?'', it will say ``Max''.
  • Max accessed his internal data, and returned his name. You didn't have to know how or where the name data is stored.

Accessing documents

You can check perl related documentation by perldoc, similar to man pages.

# see some documentations about a topic
# Documentation for Bio::Seq Module
perldoc Bio::Seq

# to get documentation about Builtin Functions, use -f
perldoc -f splice

# Search FAQ with the keyword shuffle.  You can use reg. exp. for the keyword
perldoc -q shuffle

Additionally, these HOWTOs give you a good starrting point.