1. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Perl Programming for Biologists, Second Edition Part 1: 9/11/2007 Yannick Pouliot, PhD Bioresearch Informationist Lane Medical Library & Knowledge Management Center

2. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 2 Class Requirements You must  have wireless access  have the admin password to your machine

3. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 3 To Do Please download all class materials from http://lane.stanford.edu/howto/index.html?id=_2796 http://lane.stanford.edu/howto/index.html?id=_2796 into C:\course

4. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 4 Class Focus 1. Creating, writing and reading Excel files 2. Reformatting data files for input to an analysis program 3. Writing and reading from a database such as MS Access or other locally installed relational database, as well as from databases available on the Internet And remember: Ask LOTS OF QUESTIONS

5. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 5 Cautions All examples pertain to MS Office 2003  Examples still work in MS Office 2007  However, Perl modules used here do not work with MS Office 2007-formatted documents All examples pertain to Perl 5.x, not 6.x  V.5 and 6 are NOT compatible  V.5 is far more common, so not much of an issue

6. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 6 So Why Perl? Perl = Practical Extraction and Reporting Language Perl Free Very widely used  Especially in biological community Very flexible and portable Not the only language of this type  E.g., Python Not the absolute easiest  … but pretty easy Not suited for everything  E.g., for ultra-fast mathematically-oriented code, C is still best

7. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 7 Today’s session: - Installing and understanding what is required to run Perl - Understanding the basics of a Perl program

8. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 8 Part 1: Installation

9. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 9 Components to Install & Configure 1. Perl itself  More accurately, the Perl interpreter  We’ll use ActiveState Perl 5.8x (ActivePerl) www.activestate.com/store/freedownload.aspx?prdGuid=81fbce82-6bd5-49bc-a915- 08d58c2648ca 2. Additional Perl modules  Module = extra functions not part of the interpreter  Described at Comprehensive Perl Archive Network (CPAN)CPAN 3. Open Perl IDE  IDE = integrated development environment: Editor  to write/edit your program Debugger  to find bugs A compiler/interpreter  to run your program from within the IDE  sourceforge.net/project/showfiles.php?group_id=23334&release_id=91440 sourceforge.net/project/showfiles.php?group_id=23334&release_id=91440 4. Configuring the ODBC manager (next week)  Part of Windows  Allows different programs to interact with databases on your machine or anywhere on the Web via single “doorway”

10. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 10 What is an Interpreter? = A program that translates an instruction into the computer’s language and executes it before proceeding to the next instruction  = compiled and executed once instruction at a time Perl is usually used in interpreted mode  Can also be compiled once (= faster)

11. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 11 Installing Perl from ActiveState 1. Go to www.activestate.com/store/freedownload.aspx ?prdGuid=81fbce82-6bd5-49bc-a915- 08d58c2648ca www.activestate.com/store/freedownload.aspx ?prdGuid=81fbce82-6bd5-49bc-a915- 08d58c2648ca We’ll be downloading Perl 5.8.x.x: 1. Select Windows MSI package for Windows X86 2. Run the installer 3. Install under c:\Perl

12. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 12 Installing Additional Perl Modules The fountain of all things Perl: CPAN  = Comprehensive Perl Archive Network  http://www.cpan.org/ http://www.cpan.org/ What does a module look like?look Why modules? PPM for downloading & installing modules PPM What modules are in MY Perl? What

13. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 13 Perl Modules We’ll Be Using NameFunction IncludedFile::Copymanipulating files IncludedFile::Findmanipulating files IncludedFile::Pathmanipulating files You do it!File::RenameManipulating files IncludedIO::Fileaccessing the insides of files IncludedSpreadsheet::WriteExcelwriting into an MS Excel spreadsheet IncludedSpreadsheet::ParseExcelparsing an MS Excel spreadsheet IncludedSpreadsheet::BasicReadreading the contents of an MS Excel spreadsheet IncludedWin32::OLEprovides easy access to Windows (e.g., launching Excel) IncludedDBIprovides access to relational databases IncludedDBD::ODBCprovides access to relational databases IncludedURIaccessing URLs IncludedLWP::Simpleinteracting with a Web site via http IncludedArray::Uniquereturns unique elements of an array IncludedList::Uniqreturns unique elements of a list IncludedData :: Dumperdumping data out of a data structure IncludedSwitchswitch function ("multiple if-else-then")

14. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 14 The PPM Module: Installing Perl Modules the Easy Way Perl modules can downloaded and installed manually from CPAN (hard) They can also be installed via the Perl Package Manager: PPM (easy)

15. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 15 Installing an environment to run and edit Perl: Integrated Development Environment (IDE)

16. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 16 Why an IDE? IDE = integrated development environment: Editor  to write/edit your program Debugger  to find bugs A “runner” (compiler/interpreter)  to run your program from within the IDE IDEs provide facilities to facilitate writing & debugging E.g., automatic code highlighting We’ll use Open Perl IDE  Free, open source, portable sourceforge.net/project/showfiles.php?group_id=23334&release_id= 91440 sourceforge.net/project/showfiles.php?group_id=23334&release_id= 91440 IDE: Definition, descriptionDefinition, description For our Mac friends: AffrusAffrus

17. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 17 Installing Open Perl IDE 1. Go to sourceforge.net/project/showfiles.php?group_id= 23334&release_id=91440 sourceforge.net/project/showfiles.php?group_id= 23334&release_id=91440 and download the code 2. Create folder Program Files/OpenPerlIDE 3. Unzip into Program Files/OpenPerlIDE 4. Update Path (under System Properties, Advanced, Environment Variables, System Variables) → this makes it possible to run Open Perl IDE from anywhere on your machine…

18. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 18 BREAK

19. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 19 Part 2: What does it all do?

20. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 20 Example Short Program 1. Start Open Perl IDE 2. Load Simple1.pl 3. Run Simple1.pl

21. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 21 Learning by Example Simple2.pl

22. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 22 Exploring Perl’s Major Language Elements Norman Matloff’s introduction to Perl: http://heather.cs.ucdavis.edu/~matloff/Perl/PerlIntro.pdf http://heather.cs.ucdavis.edu/~matloff/Perl/PerlIntro.pdf Perl language referencereference http://en.wikipedia.org/wiki/Perl#Data_types

23. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 23 Additional Key Books/Resources Learning by example: Perl CookbookPerl Cookbook Perl Programming for Biologists Perl Quick Reference Guide My favorite: Perl Quick ReferencePerl Quick Reference

24. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 24 Going Further: Programming Tips Plan your program  Write down how you intend to process the data in more-or-less plain language Goal: making sure that it really does make sense  Hacking doesn’t really pay… Have documentation handy  ActivePerl documentation (searchable)documentation  Perl language referencereference → eBooks: help served on a silver plattereBooks  Lane FAQsFAQ When you’re stuck: Search the Web  Google can answer almost any programming question … though quality documentation is still best

25. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 25 Toying with Excel3.pl, a “real” program

26. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 26 Excel3.pl: Introducing Object Programming Purpose: From an Excel worksheet that lists public identifiers for DNA sequences associated with genes, the program retrieves:  UniGene cluster ID UniGene  Gene symbol  NCBI Gene ID  … and writes the result into another Excel worksheet Mix of procedural and object programmingobject programming Relevant links:  http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&orig_ db=unigene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&orig_ db=unigene  Entrez Utilities Entrez Utilities

27. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 27 What Excel3.pl Does

28. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 28 Assignments Look at code for Example3.pl  Modify it, break it  Write down at least one question so we can talk about it next week

29. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 29

30. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 30 eBooks Rule

31. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 31 What Does A Module Look Like?