Introduction to Perl Bio Perl Dr G P

Introduction to Perl & Bio. Perl Dr G. P. S. Raghava Bioinformatics Centre IMTECH, Chandigarh Email: raghava@imtech. res. in Web: http: //imtech. res. in/raghava/

Perl • Practical Extraction and Report Language • Created by Larry Wall • Runs on just about every platform • Most popular on Unix/Linux systems • Excellent language for file and data processing

Simple Program On Unix, this is the location of the Perl interpreter #!/usr/local/bin/perl # This is a comment line. This program prints “Hello World. ” # to the screen. print “Hello world. n”; Newline character Program statements are terminated with semicolons Comments start with # and end with the end of the line

Control Structures #!/usr/local/bin/perl # Print out 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 # in this case, $x is local only to the loop because my is used for (my $x = 0; $x < 10; $x++) { print “$x”; if ($x < 9) { print “, ”; } } print “n”;

Control Structures #!/usr/local/bin/perl # Demonstrate the foreach loop, which goes through elements # in an array. my @users = (“bonzo”, “gorgon”, “pluto”, “sting”); foreach $user (@users) { print “$user is alright. n”; }

Functions • Use sub to create a function. • No named formal parameters, assign @_ to local subroutine variables. #!/usr/local/bin/perl # Subroutine for calculating the maximum sub max { my $max = shift(@_); # shift removes the first value from @_ foreach $val (@_) { $max = $val if $max < $val; # Notice perl allows post ifs } return $max; } $high = max(1, 5, 6, 7, 8, 2, 4, 9, 3, 4); print “High value is $highn”;

Files • File handles are used to access files • open and close functions #!/usr/local/bin/perl # Open a file and print its contents to copy. txt my $filename = $ARGV[0]; open(MYFILE, “<$filename”); # < indicates read, > indicates write open(OUTPUT, “>copy. txt”); while ($line = <MYFILE>) { # The <> operator reads a line print OUTPUT $line; # no newline is needed, read from file } close MYFILE; # Parenthesis are optional

Regular Expressions • One of Perl’s strengths is pattern matching • Perl’s regular expression language is extremely powerful, but can be challenging to learn • Some examples follow…

Comma Separated Value Files #!/usr/local/bin/perl # Some simple code demonstrating how to use split and regular # expressions. This code extracts out values in a CSV file. my $filename = $ARGV[0]; open(INPUT, “<$filename”); while (<INPUT>) { chomp; # Remove terminating newline my @values = split /, /; # Split string in $_ where , exists print “The first value is: “. $values[0]. “n”; } close INPUT;

Objects • Perl supports object oriented programming • Constructor name is new • A class is really a special kind of package. • Objects are created with bless

Example Class Definition package Critter; # constructor sub new { my $objref = {}; bless $objref; return $objref; } # reference to an empty hash # make it an object in Critter class # return the reference # Instance method, first parameter is object reference sub display { my $self = shift; # just to demonstrate print “I’m a critter. n”; } 1; # must end class with a true value Store in Critter. pm

Example Object Usage #!/usr/local/bin/perl use Critter; my $critter = new Critter; $critter->display; display $critter; # create an object # display the object # alternative notation

Bio. Perl (http: //www. bioperl. org/) Defnition : It is a collection of perl modules that facilitate the development of perl script for bioinformatics. FACTS • Started in 1995 by open Bioinformatics Foundation • These are reusable codes (subroutine) • It does not include any ready to use program • It need basic knowledge of perl programming • Bioperl is an open source software that is still under active development • Biojava, Biophython, Biocorba, EMBOSS

What is Bio. Perl? • An ‘open source’ project • http: //bio. perl. org or http: //www. cpan. org • A loose international collaboration of biologist/programmers • Nobody (that I know of) gets paid for this • A collection of PERL modules and methods for doing a number of bioinformatics tasks • Think of it as subroutines to do biology • Consider it a ‘tool-box’: • If you need a hammer, it is in there. • If you need a 7/16” hex-head wrench, you might need to code that yourself.

What Bio. Perl isn’t • ‘Out of the box’ solutions to problems • You will have to know a little perl, and you will have to read documentation • Particularly well documented • Yes, there is documentation, but it can be difficult to see the ‘big picture’ - or sometimes the small picture • Fast • Generally the overhead involved in making perl objects (complicated ones) and loading in dependencies tends to make bioperl slow. • My own blast parser takes a small fraction of the time of the bioperl parser.

Application of Bioperl • Accessing sequence data from local and remote databases • Transforming formats of database/ file records • Manipulating individual sequences • Searching for ``similar'' sequences • Creating and manipulating sequence alignments • Searching for genes and other structures on genomic DNA • Developing machine readable sequence annotation

Accessing sequence data from Databases • Accessing data from remote databases • Gen. Bank • Swissprot • EMBL • Indexing and accessing local databases • Create index for your file • Access the file by keyword

Transforming formats of database/ file records This allows to convert your sequence/alignment from one format to another format (eg. Readseq) • Change sequence format • From GCG, PIR, FASTA etc. • To FASTA, GCG. PIR etc. • Change format of multiple sequence a; ignment • FASTA, CLUSTAL-W, GCG etc. • GCG, FASTA CLUSTAL-w etc.

Manipulating sequence Bioperl contains many modules with functions for sequence analysis. • Sequence data manipulation: Display component, Reverse complement, Translate/Reverse translate from NT to Protein • Obtaining basic sequence statistics (Residues, MW, CODON) • Restriction enzyme mapping • Identifying amino acid cleavage sites • Manipulation by EMBOSS using Bio. Perl

Searching for ``similar'' sequences • Running BLAST locally (Standalone BLAST) • Running BLAST remotely • Parsing BLAST and FASTA reports • Parsing HMM reports

Creating and manipulating sequence alignments • Aligning 2 sequences with Smith -Waterman (p. SW) • Aligning 2 sequences with Blast using bl 2 seq and Align. IO • Aligning multiple sequences (Clustalw. pm, TCoffee. pm) • Manipulating / displaying alignments (Simple. Align)

Example 1 #!/usr/local/bin/perl # Collect documents from Pub. Med containing the term “Breast Cancer” # and print them. use Bio: : Biblio; my $biblio = new Bio: : Biblio; my $collection = $biblio->find(“breast cancer”); while ($collection->has_next) { print $collection->get_next; } # there are underlines before next

Example 2 #!/usr/local/bin/perl # Get a sequence from Ref. Seq by accession number use Bio: : DB: : Ref. Seq; $gb = new Bio: : DB: : Ref. Seq; $seq = $gb->get_Seq_by_acc(“NM_007304”); print $seq->seq();

A simple script #!/opt/perl/bin/perl -w #bioperl_gb_fetch. pl use strict; use Bio: : DB: : Gen. Bank; my $gb = Bio: : DB: : Gen. Bank->new(); my $seq_obj = $gb>get_Seq_by_acc(‘AF 303112’); print $seq_obj->display_id(), “n”; print $seq_obj->seq(), ”n”;

Changing Formats: #!/opt/perl/bin/perl -w #genbank_to_fasta. pl use Bio: : Seq. IO; my $input = Bio: : Seq. IO: : new->(‘-file’ => $ARGV[0], ‘-format’ => ‘Gen. Bank’); my $output = Bio: : Seq. IO: : new->(‘-file’ => ‘>output. fasta’, ‘-format’ => ‘Fasta’); while (my $seq = $input->next_seq()){ $output->write_seq($seq)

Parsing Blast Reports • One of the strengths of Bio. Perl is its ability to parse complex data structures. Like a blast report. • Unfortunately, there is a bit of arcane terminology. • Also, you have to ‘think like bioperl’, in order to figure out the syntax. • This next script might get you started

Parse BLAST output #!/opt/perl/bin/perl -w #bioperl_blast_parse. pl # program prints out query, and all hits with scores for each blast result use Bio: : Search. IO; my $record = Bio: : Search. IO->new(-format => ‘blast’, -file => $ARGV[0]); while (my $result = $record->next_result){ print “>”, $result->query_name, “ “, $result>query_description, “n”; my $seen = 0; while (my $hit = $result->next_hit){ print “t”, $hit->name, “t”, $hit->bits, “t”, $hit>significance, “n”; $seen++ }

Search. IO parsers: • Search. IO can parse (and reformat) several formats containing alignment or similarity data: • • blast xml formatted blast (still a little wonky) psi-blast exonerate WABA FASTA HMMER • The interface is the same for all of these, making your life a little easier.

Some advanced Bio. Perl • What if you want to draw pretty images of blast reports? Bio: : Graphics to the rescue: • Input - A blast report (single query): • Output: • Script in PERL 13/blast_to_png. Image. pl

Some really advanced • Bio. Perl What if you want to display an entire genome with annotation? Grow your own genome project • We can do that all in Bio. Perl (and a my. SQL or Oracle database): • GBrowse - the Generic Genome Browser • Allows any feature to be displayed on a reference sequence • Many different styles of ‘Glyphs’, so all features can be drawn in a different style • Allows user to zoom in and out on reference sequence • User can select which features to display • User can upload their own features to be displayed on your reference sequence • And more!!!

GBrowse (Generic Genome Browser)

Bio. Perl Pros and Cons • It can be a substantial investment in time to learn how to use bioperl properly • Once you get used to it, it is pretty simple to do some complicated things • There a lot of nice tools in there, and (usually) somebody else takes care of fixing parsers when they break • Bio. Perl code is portable - if you give somebody a script, it will probably work on their system • Bio. Perl, unfortunately, has high overhead. Sometimes it is quicker

So what is Bio. Perl? (continued…) • 551 modules (incl. 82 interface modules) • 37 module groups • 79, 582 lines of code (223, 310 lines total) • 144 lines of code per module • For More info: Bio. Perl Module Listing

Some statistics mean 144

Downloading modules Ø Modules can be obtained from: Øwww. CPAN. org (Perl Modules) Øwww. Bio. Perl. org (Bio. Perl Modules) Ø Downloading modules from CPAN ØInteractive mode Ø perl -MCPAN -e shell ØBatch mode Øuse CPAN; Øclean, install, make, recompile, test

Installing Modules Ø Steps for installing modules ØUncompress the module Ø Gunzip file. tar. gz Ø Tar –xvf file. tar Øperl Makefile. PL Ømake test Ømake install

Directory Structure • Bio. Perl directory structure organization: • • • Bio/ Bio. Perl modules models/ UML for Bio. Perl classes t/ Perl built-in tests t/data/ Data files used for the tests scripts/ Reusable scripts that use Bio. Perl • scripts/contributed/ Contributed scripts not necessarily integrated into Bio. Perl. • doc/ "How To" files and the FAQ as

Platforms • • • HP-UX / Itanium ('ia 64') 11. 0 HP-UX / PA-RISC 11. 0 Mac. OS X Cyg. Win NT_5 v. 1. 3. 10 on Windows 2000 5. 00 Win 32, Win. NT i 386 IRIX 64 6. 5 SGI Solaris 2. 8 Ultra. Sparc Open. BSD 2. 8 i 386 Red. Hat Linux 7. 2 i 686 Linux i 386

References • Programming Perl by Wall, Christiansen, and Schwartz (O’Reilly) • Learning Perl by Schwartz and Phoenix (O’Reilly) • Beginning Perl for Bioinformatics by Tisdall (O’Reilly) • http: //www. perl. com • http: //www. bioperl. org