Introduction to bioperl

What is perl?

Production Engineering Research LaboratoryPractically Everything Really LikeablePre-positioned Equipment Requirement ListPrincipal Exchange Rate LinkedPathologically Eclectic Rubbish ListerPractical Extraction and Report Language

Perl is– Practical Extraction and Report Language (or

Pathologically Eclectic Rubbish Lister) (written by Larry Wall in 1986)

– An interpreted programming language that resembles both a real programming language and a shell

– A language for easily manipulating text, files, and processes

– Providing more concise and readable way to do jobs formerly accomplished using C or shells.

What is perl, really?

0’s and 1’sLow-level language, assemble

needed

High-level language, compilation needed

High-level language, compilation NOT needed

Why use Perl?

• Easy to use– Basic syntax is C-like– Lazy memory management– A small amount of code goes a long way

• Fast– Perl has numerous built-in optimization features which

makes it run faster than other scripting language.

• Portability– One script version runs everywhere (unmodified).

Why use Perl?

• Efficiency– More efficient than C to perform the same task

• Correctness– Perl fully parses and pre-”compiles” script before

execution.

• Free to use– Comes with source code

To learn perl

• Take a perl class!

• Reading books– “Learning Perl, 5th Edition” by Randal Schwartz, Tom

Phoenix, and brian d foy

– “Programming Perl (3rd Edition)” by Larry Wall, tom Christiansen, and Jon Orwant

• Reading perl documentations

• Practice, practice, practice……

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

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.

Bioperl Project

• It is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research

• Started in 1995 by a group of scientists tired of rewriting BLAST and sequence parsers for various formats

• Version 0.7 was released in 2000• Bioperl 1.0 was released in 2002• A paper about bioperl was published in October 2002 (Satjich

et al., 2002. The bioperl toolkit: perl modules for the life sciences. Genome Research 12: 1611-1618.)

• Current stable release 1.6.0 was made available in January 2009

Bioperl toolkit• Core package (bioperl-live)

– THE basic package and it’s required by all the other packages• Run package (bioperl-run)

– Providing wrappers for executing some 60 common bioinformatics applications

• DB package (bioperl-db)– Subproject to store sequence and annotation data in a BioSQL

relational database• Network package (bioperl-network)

– Parses and analyzes protein-protein interaction data• Dev package (bioperl-dev)

– New and exploratory bioperl development

Installing bioperl on a Windows computer

• On Windows– Install ActivePerl

– Install bioperl using PPM (Perl Package Manager)

• On cygwin (Linux-like environment in Windows)– Install cygwin

– Install required perl modules

– Install bioperl using source code

Route 1

Route 2

Installing bioperl on a Windows computer

• On Windows– Install ActivePerl

– Install bioperl using PPM (Perl Package Manager)

• On cygwin (Linux-like environment in Windows)– Install cygwin

– Install required perl modules

– Install bioperl using source code

Route 1

Route 2

Installing bioperl on Windowswww.bioperl.org

http://www.bioperl.org/wiki/Main_Page

Route 1

Downloads

Installing bioperl on WindowsRoute 1

Installing bioperl on WindowsRoute 1

Following the instructions

• Easy installation process

• Works well

• No good if to parse the results of other linux-base applications

• Not recommended

Installing bioperl on WindowsRoute 1

Installing bioperl on a Windows computer

• On Windows– Install ActivePerl

– Install bioperl using PPM (Perl Package Manager)

• On cygwin (Linux-like environment in Windows)– Install cygwin

– Install required perl modules

– Install bioperl using source code

Route 1

Route 2

Where to get bioperlwww.bioperl.org

http://www.bioperl.org

Small size

~ stands for the home directory(..) To move one level up to the parental

directoryThe parental directory is /home

There is one folder “XiaodongBai” in /home

Attributes :First position:- regular filed directory (folder)l link

Other positions:- not (readable|writeable|executable)r readablew writeablex executable

mkdir to make a directory called “programs”

Now there are 2 folders in /home

Change directory to “programs”

/cygdrive/c/Biodownloads/BioPerl-1.6.0.tar.gzLocation of the downloaded bioperl file

gunzip -c /cygdrive/f/Downloads/BioPerl-1.6.0.tar.gz | tar -xvf -

Commands to decompress and untar the bioperl file

Designate your drive (usually C) and directory

All Bioperl files are in this folder now

Change directory to “BioPerl-1.6.0” All the files in the

directory

Read “INSTALL” for detailed instructions when you have time

perl Makefile.PL

Check prerequisites required for bioperl installation

Press “return” to accept the default “yes” and continue.

Press “return” to accept the default “yes” and continue.

Prerequisites were installed successfully.Enter “a” and press “enter” to accept the default option and continue.

Press “enter” for all questions along with way

Information about the installation of prerequisites

Ignore the errors for now since these modules are optional

Press “return” to accept the default options [a] for all, and continue.

First step done!

Type “make” and press “enter” to start building

Second step done!

Type “make test” and press “enter” to start testing

Testing in progress…

All tests are passed!

Ignore any non-passed tests for now!

Type “make install” and press “enter” to start installing

Bioperl is successfully installed!

Congratulations!

Time to run a test to seewhether bioperl works

Type “clear” and press “return” to clear the screen

Use “cp” command to copy the test script “bioperl_installation_test.pl” to the current directory (.)

Check if the file is executable (x in fourth position).

If not,type “chmod +x bioperl_installation_test.pl” and press “enter”.

Check it again to make sure that it is executable.

To run a perl script, type$./bioperl_installation_test.pl

Or$perl bioperl_installation_test.pl

If you see “It works!!”, it works!

If you see something else, the installation failed in the sense that the modules are not being loaded correctly.See the instructors for troubleshooting individually.

Bioperl reading materials

• Bioperl tutorial: http://www.bioperl.org/wiki/Bptutorial.pl

• HOW-TOs http://www.bioperl.org/wiki/HOWTOs

• Example code, in the scripts/ and examples/ directories of a bioperl installation

• Online course written at the Pasteur Institute. http://www.pasteur.fr/recherche/unites/sis/formation/bioperl.

Troubleshooting:

If “FATAL ERROR” is encountered early in the installation through cygwin, double check the firewall settings on your computer (allow). If this does not permit installation, see www.bioperl.org “Installing BioPerl on Windows”

If you are running the WINDOWS VISTA OS, you will need to follow instructions for downloading at www.bioperl.org “Installing BioPerl on Windows”

MAC OS X users should also refer to instructions at www.bioperl.org

Make uses “build” not “make”