perl programming for biologists, second edition part 1: 9/11/2007

Lane Medical Library & Knowledge Management Centerhttp://lane.stanford.edu

Perl Programming for Biologists, Second EditionPart 1: 9/11/2007

Yannick Pouliot, PhDBioresearch Informationist

Lane Medical Library & Knowledge Management Center

Lane Medical Library &Knowledge Management Centerhttp://lane.stanford.edu

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Class Requirements You must

have wireless access have the admin password to your machine


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To Do

Please download all class materials fromhttp://lane.stanford.edu/howto/index.html?id=_2796

into C:\course


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Class Focus

1. Creating, writing and reading Excel files2. Reformatting data files for input to an

analysis program3. 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


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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


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So Why Perl? Perl = Practical Extraction and Reporting Language 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


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Today’s session:

- Installing and understanding what is required to run Perl

- Understanding the basics of a Perl program


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Part 1: Installation


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Components to Install & Configure1. 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)

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=914404. 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”


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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)


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Installing Perl from ActiveState

1. Go to 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


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Installing Additional Perl ModulesThe fountain of all things Perl: CPAN

= Comprehensive Perl Archive Network http://www.cpan.org/

What does a module look like?

Why modules?

PPM for downloading & installing modules

What modules are in MY Perl?


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Perl Modules We’ll Be Using

Name Function

Included File::Copy manipulating files

Included File::Find manipulating files

Included File::Path manipulating files

You do it! File::Rename Manipulating files

Included IO::File accessing the insides of files

Included Spreadsheet::WriteExcel writing into an MS Excel spreadsheet

Included Spreadsheet::ParseExcel parsing an MS Excel spreadsheet

Included Spreadsheet::BasicRead reading the contents of an MS Excel spreadsheet

Included Win32::OLE provides easy access to Windows (e.g., launching Excel)

Included DBI provides access to relational databases

Included DBD::ODBC provides access to relational databases

Included URI accessing URLs

Included LWP::Simple interacting with a Web site via http

Included Array::Unique returns unique elements of an array

Included List::Uniq returns unique elements of a list

Included Data :: Dumper dumping data out of a data structure

Included Switch switch function ("multiple if-else-then")


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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)


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Installing an environment to run and edit Perl:

Integrated Development

Environment (IDE)


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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

IDE: Definition, description For our Mac friends: Affrus


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Installing Open Perl IDE

1. Go to sourceforge.net/project/showfiles.php?group_id=23334&release_id=91440and download the code

2. Create folder Program Files/OpenPerlIDE3. Unzip into Program Files/OpenPerlIDE4. Update Path (under System Properties,

Advanced, Environment Variables, System Variables)→ this makes it possible to run Open Perl IDE from anywhere on your machine…


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BREAK


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Part 2: What does it all do?


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Example Short Program

1. Start Open Perl IDE

2. Load Simple1.pl

3. Run Simple1.pl


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Learning by Example

Simple2.pl


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Exploring Perl’s Major Language Elements

Norman Matloff’s introduction to Perl: http://heather.cs.ucdavis.edu/~matloff/Perl/PerlIntro.pdf

Perl language reference http://en.wikipedia.org/wiki/Perl#Data_types


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Additional Key Books/Resources

Learning by example: Perl Cookbook Perl Programming for Biologists Perl Quick Reference Guide My favorite: Perl Quick Reference


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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) Perl language reference→ eBooks: help served on a silver platter Lane FAQs

When you’re stuck: Search the Web Google can answer almost any programming question

… though quality documentation is still best


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Toying with Excel3.pl, a “real” program


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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 Gene symbol NCBI Gene ID … and writes the result into another Excel worksheet

Mix of procedural and object programming Relevant links:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&orig_db=unigene

Entrez Utilities


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Search UniGene for

cluster ID UniGene

Gene

ESearch

Sequence identifier

Retrieve UniGene description for that

cluster

Result ID

Search Gene with Gene

ESearch

Cluster ID

Result ID

Gene symbols & descriptions

Excel report

UniGeneESummary

GeneESummary

Retrieve Gene

description for that gene

write

Excel reportwrite

What Excel3.pl Does


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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


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eBooks Rule


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What Does A Module Look Like?

perl programming for biologists, second edition part 1: 9/11/2007

Documents

things perl

perl programpart

fasterinstalling perl

fb perl modulesmodule

ms office

ms access

moduleswhat modules

windows x86