Introduction to bioperl

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Introduction to bioperl
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What is perl?

• Production Engineering Research Laboratory
• Practically Everything Really Likeable
• Pre-positioned Equipment Requirement List
• Principal Exchange Rate Linked
• Pathologically Eclectic Rubbish Lister
• Practical Extraction and Report Language

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What is perl, really?

• 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.

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0s and 1s
Low-level language, assemble needed
High-level language, compilation needed
High-level language, compilation NOT needed
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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).

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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

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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

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Whats Bioperl?

• Bioperl is not a new language
• It is a collection of Perl modules that
  facilitate the development of Perl scripts for
  bioinformatics applications.

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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.

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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

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Bioperl toolkit

• Core package (bioperl-live)
• THE basic package and its 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

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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
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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
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Installing bioperl on Windowswww.bioperl.org
http//www.bioperl.org/wiki/Main_Page
Route 1
Downloads
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Installing bioperl on Windows
Route 1
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Installing bioperl on Windows
Route 1
Following the instructions
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Installing bioperl on Windows
Route 1

• Easy installation process
• Works well
• No good if to parse the results of other
  linux-base applications
• Not recommended

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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
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Where to get bioperl

• www.bioperl.org

http//www.bioperl.org
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Small size
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stands for the home directory
(..) To move one level up to the parental
directory
The parental directory is /home
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There is one folder XiaodongBai in /home
Attributes First position - regular
file d directory (folder) l link Other
positions - not (readablewriteableexecutable) r
readable w writeable x executable
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mkdir to make a directory called programs
Now there are 2 folders in /home
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Change directory to programs
/cygdrive/c/Biodownloads/BioPerl-1.6.0.tar.gz Loca
tion of the downloaded bioperl file
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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
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All Bioperl files are in this folder now
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Read INSTALL for detailed instructions when you
have time
Change directory to BioPerl-1.6.0
All the files in the directory
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perl Makefile.PL
Check prerequisites required for bioperl
installation
Press return to accept the default yes and
continue.
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Press return to accept the default yes and
continue.
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Press enter for all questions along with way
Prerequisites were installed successfully. Enter
a and press enter to accept the default
option and continue.
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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.
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First step done! Type make and press enter
to start building
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Second step done! Type make test and press
enter to start testing
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Testing in progress
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All tests are passed! Ignore any non-passed
tests for now! Type make install and press
enter to start installing
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Bioperl is successfully installed! Congratulation
s!
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Time to run a test to seewhether bioperl works
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Type clear and press return to clear the
screen
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Use cp command to copy the test script
bioperl_installation_test.pl to the current
directory (.)
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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.
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To run a perl script, type ./bioperl_installatio
n_test.pl Or perl bioperl_installation_test.pl
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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.
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Bioperl reading materials

• Bioperl tutorial http//www.bioperl.org/wiki/Bptu
  torial.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/formati
  on/bioperl.

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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