Introduction to bioperl

1. Introduction to bioperl

2. 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

3. 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.

4. 0’s and 1’s Low-level language, assemble needed High-level language, compilation needed High-level language, compilation NOT needed

5. 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).

6. 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

7. To learn perl • Ian Holford’s 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……

8. 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.

9. Bioperl Modules Perl Modules Perls script input Perl Interpreter output Bioperl and Perl

10. 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.

11. 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

12. 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

13. 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

14. 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

15. Route 1 Installing bioperl on Windows

16. Route 1 Installing bioperl on Windows

17. Route 1 Installing bioperl on Windows Following the instructions

18. 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

19. 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

20. Where to get bioperl www.bioperl.org http://www.bioperl.org

24. Small size

25. ~ stands for the home directory To move one level up to the parental directory The parental directory is /home

26. 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

27. Make a directory called “programs” Now there are 2 folders in /home

28. Change directory to “programs” Location of the downloaded bioperl file

29. gunzip -c /cygdrive/f/Downloads/BioPerl-1.6.0.tar.gz | tar -xvf - Commands to decompress and untar the bioperl file

30. All bioperl files are in this folder now

31. Read “INSTALL” for detailed instructions when you have time Change directory to “BioPerl-1.6.0” All the files in the directory

32. perl Makefile.PL Check prerequisites required for bioperl installation Press “return” to accept the default “yes” and continue.

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

34. Press “enter” for all questions along with way Prerequisites were installed successfully. Enter “a” and press “enter” to accept the default option and continue.

35. Information about the installation of prerequisites Ignore the errors for now since these modules are optional Press “return” to accept the default options and continue.

36. First step done! Type “make” and press “enter” to start building

37. Second step done! Type “make test” and press “enter” to start testing

38. Testing in progress…

39. All tests are passed! Ignore any non-passed tests for now! Type “make install” and press “enter” to start installing

40. Bioperl is successfully installed! Congratulations!

41. Time to run a test to seewhether bioperl works

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

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

44. Check if the file is executable. If not, type “chmod +x bioperl_installation_test.pl” and press “enter”. Check it again to make sure that it is executable.

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

46. 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.

47. Bioperl reading materials • Bioperl tutorial: http://www.bioperl.org/wiki/Bptutorial.pl • HOW-TOshttp://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.