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An Introduction to Perl for Bioinformatics Part
2

• Will Hsiao
• Simon Fraser University
• Department of Molecular Biology and Biochemistry
• wwhsiao_at_sfu.ca
• www.pathogenomics.sfu.ca/brinkman

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Outline

• Session 1
• Review of the previous day
• Perl historical perspective
• Expand on Regular Expression
• General Use of Perl
• Expand on Perl Functions and introduce Modules
• Interactive demo on Modules
• Break
• Session 2
• Use of Perl in Bioinformatics
• Object Oriented Perl
• Bioperl Overview
• Interactive demo on Bioperl
• Introduction to the Perl assignment

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Perl in Bioinformatics

• Case to point 1 Human Genome data exchange
• How Perl saved the Human Genome Project
• Lincoln Stein (1996) www.perl.org
• Different sequencing centres all have different
  data format
• Perl allowed various genome centres to exchange
  and communicate data with each other
• Introduces a project to produce modules to
  process all known forms of biological data
  (Bioperl)

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Perl in Bioinformatics

• Case to point 2 Ensembl
• Much of Ensembl is written in Perl
• Ensembl has an extensive Perl API - allow you to
  access Ensembl database directly from your perl
  code
• Case to point 3 GMOD Generic Model Organism
  Database
• www.gmod.org
• a joint effort by model organism system databases
  (worm, fly, corn, rat, yeast, E. coli,
  arabidopsis, rice) to develop reusable components
  suitable to be adapted for other biological
  databases
• Written mostly in Java and Perl

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Bioinformatics Spectrum
JAVA
Perl
Math
Biology
Computer Science
Software/ data analysis
C/C
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Perl for bioinformatics in your lab

• Scripting
• automation of repetitive analyses
• parse results obtained from other programs
• Wrapping
• accessing others programs (e.g. BLAST) through
  Perl
• Web CGIing
• Develop an interactive web page to your lab
• Create web forms

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Bioperl Overview

• The Bioperl project www.bioperl.org
• Comprehensive, well documented set of Perl
  modules
• Last stable release 1.4.0 (developer 1.5.1)
• A bioinformatics toolkit for
• Format conversion
• Report processing
• Data manipulation
• Sequence analyses
• and more!
• Written in object-oriented Perl

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What are objects?

• Examples of objects in real life
• Cars, dogs, dishwashers
• Objects have ATTRIBUTES and ACTIONS

• Some attributes of a dog
• Color of fur
• Height
• Owners Name
• Weight
• Tail position
• Some actions of a dog
• Bark
• Walk
• Run
• Eat
• Wag tail

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What are programming objects?

• Borrows from the concept of real life objects

A Program Dog Object
Attributes are stored as variables Actions are
implemented as functions
sub dye_fur
fur_color weight tail_position
sub eat
sub wag_tail
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Object Exercise

• Pair up with your neighbour (2-3 people)
• In the next 2-3 minutes, come up with as many
  attributes and actions (aka methods) of a DNA
  sequence object
• E.g. attributes of a DNA sequence object
• length300, percent_GC50
• E.g. methods of a DNA sequence object
• Translate_to_protein, remove_polyA_tail
• Share with the class

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Objects belong to Classes

• If we take all your suggestions and design a
  generic template. We can then use this template
  to create objects.
• This template is called a Class
• An instance of a class is called an object

DNA sequence object 1 DNA sequence object 2 DNA
sequence object 3 DNA sequence object 4
DNA Sequence Class
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How do we interact with an object?

• We have to refer to an object by its name

WOOF
POLO
Polo is the name of my dog
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Interact with a program object
WOOF
A Program Dog Object
Polo
sub dye_fur
fur_color weight tail_position
sub eat
sub wag_tail
Polo is the name of a program dog object
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A name is a reference

• Objects have unique names (labels)
• You refer to an object by its unique name
• This unique name that you give to an object is
  called a reference

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Reference in Perl

• A reference is a scalar (simple) variable that
  refers to a chunk of memory
• Stored in that memory can be another variable or
  an object

Memory
My Program
array_ref
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Reference to an object
Memory
My Program
my_protein is called a reference to an object
(in this case a protein object) To access the
attributes and methods of the protein object, you
have to go through its reference (i.e.
my_protein) Objects have inherent functions
that are useful These inherent functions also
have specific names
my_protein
A protein object
varSwissProt_ID varname varlength varso
uce var_at_journal_articles vardomain_location
sub new sub return_ID sub get_domain
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Object Oriented Programming

• What is O-O Programming?
• Simple answer a way to organize code so it
  interacts in certain ways and follows certain
  rules
• Long answer to be found in books on O-O
• Why O-O Programming?
• Provides well defined framework
• Promotes certain good practice such as code
  reuse, abstraction, cleaner design, etc.
• Does have certain trade-offs (e.g. O-O Perl is
  usually slower than declarative Perl)
• Designing good object classes requires
  forethoughts and skills

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To use an object

• Find out which class you need and learn about the
  class by reading its documentation
• Make the class available to your program
• Create a new object of the class
• Start using the object by modifying its
  attributes and calling its methods

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Example of using objects

• Task
• I have a sequence file in Genbank format that I
  want to convert to EMBL format
• How many objects do you think we need to
  accomplish the task above?

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1. Find the Objects you need

• Objects that we need
• an object that read in sequences from a file
• an object that represents a sequence record
• an object that write sequences to a file

Memory
EMBL
Genbank
Sequence File Input Object
Sequence Object
Sequence File Output Object
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Example of using objects

• Solution
• I remember that Bioperl provides this
  functionality. So first Ill take a look at the
  Bioperl documentation
• Website http//www.bioperl.org

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Bioperl Documentation demo

• Go to the webpage and navigate to SeqIO doc
• Pay attention to
• 1) the name of the module
• 2) Synopsis (code examples)
• 3) Description
• 4) list of methods

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Click
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List of Modules by Class
Complete List of Modules by Name
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2. Make the object class available

• In perl, classes are implemented as
  object-oriented modules
• To include a class, simply use the module
• E.g. use BioSeqIO
• Note the name of the module is case sensitive
• By using BioSeqIO, my program automatically
  gain access to any modules included in BioSeqIO

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3. Create an object

• Make up a name for my object reference (e.g.
  seq_input)
• Create the object by calling the object classs
  new method
• every class has a constructor method to create
  an object of that class
• constructor method is often called new
• use single arrow operator to call methods
• Assign the object to the object reference
• You can give the object you are about to create
  some initial attributes (e.g. the file name of my
  sequence record, the format of the record)

my seq_in
BioSeqIO-gtnew

( -file gt myGBrecord, -format gt
genbank)
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4. Call objects methods?

• Weve seen the -gt (single arrow) operator for
  calling a class method (e.g. new)
• The same operator is used for calling an object
  method
• E.g. to ask seq_in object to get a sequence
  record from your Genbank sequence file
• my seq_record seq_in-gtnext_seq()

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Putting it all together

• !/usr/bin/perl w
• use strict
• use BioSeqIO
• my seq_in BioSeqIO-gtnew(
• -file gt myGBrecord,
• -format gt genbank)
• my seq_out BioSeqIO-gtnew(
• -file gt gtmyEMBLrec,
• -format gt EMBL)
• my seq_record seq_in-gtnext_seq()
• seq_out-gtwrite_seq(seq_record)

Create a new BioSeqIO object and initialize
some attributes
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More Bioperl modules

• BioSeqIO Sequence Input/Output
• Retrieve sequence records and write to files
• Converting sequence records from one format to
  another
• BioSeq Manipulating sequences
• Get subsequences (seq-gtsubseq(start, end))
• Find the length of the object (seq-gtlength)
• Reverse complement a DNA sequence
• Translate a DNA sequence .etc.
• BioAnnotation Annotate a sequence
• Assign journal references to a sequence, etc.
• BioAnnotation is associated with an entire
  sequence record and not just part of a sequence
  (see also BioSeqFeature)

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Some more Bioperl modules

• BioSeqFeature Associate feature annotation to
  a sequence
• features describe specific locations in the
  sequence
• E.g. 5 UTR, 3 UTR, CDS, SNP, etc
• Using this object, you can add feature
  annotations to your sequences
• When you parse a genbank file using Bioperl, the
  features of a record are stored as SeqFeature
  objects
• BioDBGenBank, GenPept, EMBL and Swissprot
  Remote Database Access
• You can retrieve a sequence from remote databases
  (through the Internet) using these objects

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Even more Bioperl modules

• BioSearchIO Parse sequence database search
  reports
• Parse BLAST reports (make custom report)
• Parse HMMer, FASTA, SIM4, WABA, etc.
• Custom reports can be output to various formats
  (HTML, Table, etc)
• BioToolsRunStandAloneBLAST Run Standalone
  BLAST through perl
• By combining this and SearchIO, you can automate
  and customize BLAST search
• BioGraphics Draw biological entities (e.g. a
  gene, an exon, BLAST alignments, etc)

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Bioperl Summary

• For Online documentation
• For this workshop http//doc.bioperl.org/releases
  /bioperl-1.4/
• Tutorial http//www.bioperl.org/wiki/HOWTOBeginn
  ers
• HOWTOs http//www.bioperl.org/wiki/HOWTOs
• Modules http//www.bioperl.org/wiki/CategoryCore
  _Modules
• Literature
• Stajich et al., The Bioperl toolkit Perl modules
  for the life sciences. Genome Res. 2002
  Oct12(10)1611-8.PMID 12368254
• Bioperl mailing list bioperl-l_at_bioperl.org
• Best way to get help using Bioperl
• Very active list (upwards of 10 messages a day)
• Use with caution things change fast and without
  warning (unless you are on the mailing list)

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Interactive demo on Bioperl

• Open your laptop!
• Open a terminal window
• Type cd /perl_two
• Type gedit ./bioperl_demo.pl
• Lets go over the example together

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Summary for Session 2

• Perl is a popular language in bioinformatics
  because
• it handles text well
• It has great user base and support (e.g. Bioperl)
• Bioperl is a large collection of object oriented
  perl modules for many biological data analyses
• an object is a collection of attributes and
  methods
• You have to access an object through its
  reference
• a reference is a name

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Perl Documents

• In-line documentation
• POD plain old documents
• Read POD by typing perldoc ltmodule namegt
• E.g. perldoc perl, perldoc BioSeqIO
• On-line documentation
• http//www.cpan.org
• http//www.perl.com
• http/www.bioperl.org
• Books
• Learning Perl (the best way to learn Perl if you
  know a bit about programming already)
• Beginning Perl for Bioinformatics (example based
  way to learn Perl for Bioinformatics)
• Programming Perl (THE Perl reference book not
  for the faint of heart)

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Additional Book References

• Perl Cookbook 2nd edition (quick solutions to 80
  of what you want to do)
• Learning Perl Objects, References Modules (for
  people who want to learn objects, references and
  modules in Perl)
• Perl in a Nutshell (an okay quick reference)
• Perl CD Bookshelf, Version 4.0 (electronic
  version of the above books best value,
  searchable, and kill fewer trees)
• Mastering Perl for Bioinformatics (more example
  based learning)
• CGI Programming with Perl (rather outdated
  treatment on the subject... Not really
  recommended)
• Perl Graphics Programming (if you want to
  generate graphics using Perl side note Perl is
  probably not the best tool for generating
  graphics)

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Introduction to the Assignment Part A

• Goals
• To convert passive knowledge to active skills
• To write some simple perl programs by yourself
• Consists of 2 modules
• Write a program to convert the temperature from F
  to C
• Write a program to count the frequencies of bases
  in a sequence (sequence MAN1.fasta can be
  downloaded from Day6 wiki)

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Introduction to the Assignment Part B

• Goals
• To see the power of Perl in bioinformatics
• To see how some common bioinformatics tasks are
  done using Perl
• Consists of 3 modules
• Download E. coli O157H7 proteins in FASTA format
• Use Regular Expression to find a protein motif
• Run BLAST on all proteins in the proteome (gt5000
  BLAST runs)

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Introduction to the Assignment Part B

• Most of the code is given to you, you just have
  to modify them (in total, no more than 15 lines
  of new code!!)
• You are not expected to know everything in the
  scripts. It takes time to learn a new language
• TAs and your CS team mates will help you, dont
  wait until last minute to ask for help
• Remember, you still have to hand in your own
  version of the assignment! No copying!

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Acknowledgements

• Thanks to Sohrab Shah and Sanja Rojic (CS, UBC)
  for a wonderful collaborative work on the
  lecture/lab material
• Some ideas of this lecture is borrowed from
  Lincoln Steins workshop (http//stein.cshl.org/ge
  nome_informatics/)