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Bio-perl Introduction

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					Introduction to bioperl
            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
          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.
 0’s and 1’s
Low-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.
Bioperl Modules

Perl Modules            Perls script    input



                     Perl Interpreter


                         output


                  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                                 Route 1
    – Install bioperl using PPM (Perl Package Manager)


 • On cygwin (Linux-like environment in Windows)
    – Install cygwin
    – Install required perl modules                      Route 2
    – Install bioperl using source code
Installing bioperl on a Windows computer
 • On Windows
    – Install ActivePerl                                 Route 1
    – Install bioperl using PPM (Perl Package Manager)


 • On cygwin (Linux-like environment in Windows)
    – Install cygwin
    – Install required perl modules                      Route 2
    – Install bioperl using source code
   Route 1   Installing bioperl on Windows
                     www.bioperl.org
        http://www.bioperl.org/wiki/Main_Page




Downloads
Route 1
          Installing bioperl on Windows
Route 1
          Installing bioperl on Windows



              Following the instructions
 Route 1
            Installing bioperl on Windows

• Easy installation process
• Works well
• No good if to parse the results of other linux-
  base applications
• Not recommended
Installing bioperl on a Windows computer
 • On Windows
    – Install ActivePerl                                 Route 1
    – Install bioperl using PPM (Perl Package Manager)


 • On cygwin (Linux-like environment in Windows)
    – Install cygwin
    – Install required perl modules                      Route 2
    – Install bioperl using source code
      Where to get bioperl
www.bioperl.org
             http://www.bioperl.org
Small size
     ~ stands for the home directory
(..) To move one level up to the parental directory
     The parental directory is /home
                               There is one folder “XiaodongBai” in /home

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

Other positions:
-      not (readable|writeable|executable)
r      readable
w      writeable
x      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.gz
Location 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
                                Read “INSTALL” for
                                detailed instructions
                                when you have time




Change directory to “BioPerl-1.6.0”
                                All the files in the
                                directory
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.
                     Press “enter” for all
                     questions along with
                     way


Prerequisites were installed successfully.
Enter “a” and press “enter” to accept the default
option and continue.
   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 see
 whether 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/form
  ation/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”

				
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posted:6/29/2012
language:English
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