Introduction to bioperl

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4 Νοε 2013 (πριν από 3 χρόνια και 9 μήνες)

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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

Perl is


P
ractical
E
xtraction and
R
eport
L
anguage (or
P
athologically
E
clectic
R
ubbish
L
ister) (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’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.

Perls script

Perl Interpreter

Perl Modules

Bioperl Modules

output

input

Bioperl and Perl

Why bioperl for b
ioinformatics
?


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 Windows

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

Route 1

Downloads

Installing
bioperl

on Windows

Route 1

Installing
bioperl

on Windows

Route 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 Windows

Route 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 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

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 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”