Bioperl

What’s Bioperl?

Bioperl is not a new language

It is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

Perls script

Perl Interpreter

Perl Modules

Bioperl Modules

output

input

Bioperl and Perl

Bioperl and perl

Why bioperl for bioinformatics?

Perl is good at file manipulation and text processing, which make up a large part of the routine tasks in bioinformatics.

Perl language, documentation and many Perl packages are freely available.

Perl is easy to get started in, to write small and medium-sized programs.

Where to get help

Type perldoc <modulename> in terminal

Search for particular module in https://metacpan.org

Bioperl Document

Object-oriented and Process-oriented programming

Process-oriented: Yuan Hao eats chicken

Name object: $name Food object: $foodAction method: eat

Object-oriented: $name->eat($food)

Modularize the program

Perl 5.6.1 or higher Version 5.8 or higher is highly recommended

make for Mac OS X, this requires installing the Xcode Developer Tools

Platform and Related Software Required

Installation On Linux or Max OS X

Install from cpanminus: perlbrew install-cpanm cpanm Bio::Perl

Install from source code: git clone https://github.com/bioperl/bioperl-live.gitcd bioperl-liveperl Build.PL./Build test (optional)./Build install

Install MinGW (MinGW is incorporated in Strawberry Perl, but must it be installed through PPM for ActivePerl) : ppm install MinGW

Install Module::Build, Test::Harness and Test::Most through CPAN: Type cpan to enter the CPAN shell. At the cpan> prompt, type install CPAN Quit (by typing ‘q’) and reload CPAN. You may be asked some configuration questions, accept defaults At the cpan> prompt, type o conf prefer_installer MB then type o conf commitAt the cpan> prompt, type install Module::Build. At the cpan> prompt, type install Test::Harness. At the cpan> prompt, type install Test::Most.

Installation On Windows

Finish install from source code: Go to GitHub and press the Download ZIP button. Extract the archive in the normal way. In a cmd window cd to the directory you extracted to. Eg. if you extracted to directory ‘bioperl-live’, cd bioperl-live Type perl Build.PL and answer the questions appropriately. Type perl Build test. All the tests should pass, but if they don’t, let us know. Your usage of Bioperl may not be affected by the failure, so you can choose to continue anyway. Type perl Build install to install Bioperl.

Installation On Windows

Finish install from cpan: type /d/bioperl/ .... Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz type install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

Show the capability of bioperl in following examples

Creating a sequence, and an Object

#!/usr/bin/perl -w

use Bio::Seq;

my $seq_obj = Bio::Seq->new(-seq => 'aaaatgggggggggggccccgtt', -alphabet => 'dna' );

object class method argument

Creating a sequence, and an Object

#!/usr/bin/perl -w

use Bio::Seq;

my $seq_obj = Bio::Seq->new(-seq => 'aaaatgggggggggggccccgtt', -alphabet => 'dna' );

print $seq_obj->seq . "\n"

#!/usr/bin/perl -w

use Bio::Seq;

my $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -display_id => "#12345", -desc => "example 1", -alphabet => "dna" );

print $seq_obj->seq();

More True-to-life example

Write Sequence to File

#!/usr/bin/perl -w

use Bio::Seq; use Bio::SeqIO;

my $seq_obj = Bio::Seq->new(-seq => 'aaaatgggggggggggccccgtt', -alphabet => 'dna' );

my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' );

Create object for IO from class Bio::SeqIO

#!/usr/bin/perl -w

use Bio::Seq; use Bio::SeqIO;

my $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -display_id => "#12345", -desc => "example 1", -alphabet => "dna" );

my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' );

$seqio_obj->write_seq($seq_obj);

Write Sequence to File

Write Sequence to File

#!/usr/bin/perl -w

use Bio::Seq; use Bio::SeqIO;

my $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -display_id => "#12345", -desc => "example 1", -alphabet => "dna" );

my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'Genbank' );

$seqio_obj->write_seq($seq_obj);

Unified Programming~~

Retrieving a Sequence from a File

#!/usr/bin/perl -w

use Bio::SeqIO;

my $seqio_obj = Bio::SeqIO->new(-file => "sequence.fasta", -format => "genbank" );

my $seq_obj = $seqio_obj->next_seq;

print $seq_obj->seq . "\n";

#!/usr/bin/perl -w

use Bio::Tools::Run::Alignment::Muscle; use Bio::AlignIO;

my @params = (quiet => 0, maxiters => '100');

my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params); my $inputfilename = "$ARGV[0]"; my $aln = $factory->align($inputfilename);

my $out = Bio::AlignIO->new(-file => ">$ARGV[1]", -format => 'fasta'); $out->write_aln($aln);

Multiple Sequences Alignment

Bioperl can incorporate with other software

Retrieving a Sequence from a Database

#!/usr/bin/perl -w

use strict; use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', -user => 'anonymous', );

my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); my $slice = $slice_adaptor->fetch_by_gene_stable_id('ENSG00000128573');

print $slice->seq . "\n";

Application Programming Interface (API)

Bioperl provides various kind of API to extract user-defined dataset from database efficiently even you aren’t familiar with data structure of them

Database

Obstacle in Learning OOP

Programming in a total different way

Familiar with different object, method and class

That’s worthwhile !!!

Thanks