Introduction to Perl

Researchers are using Perl for various scientific computations, such as biological data analysis (Bioinformatics) and other applications. By using Perl, you can quickly write programs which will run on a variety of computer platforms. If you are familiar with Perl, you can also edit programs written by other researchers or third-party providers.

Perl has powerful text processing and I/O capabilities, which you can easily use with the operators and functions built into the Perl language. You can also take advantage of Perl's numerous library extensions, which implement a wide variety of useful tools.

This class will provide an introduction to the Perl programming language. We will explore the elements of the language through interactive examples.

Time and Place

Location: Teague B013 (take elevator to basement)

Dates: Tuesday, February 19, 2013 to Thursday, February 21, 2013

Time: 3:00 p.m. - 5:00 p.m. each day

Agenda

Day 1 (Tuesday)
- What you can use Perl to do
- Executing your program
- Finding documentation
- Statement syntax
- Variables, constants, expressions
- Exercise 1: Executing sample Perl scripts
Day 2 (Wednesday)
- Control flow
- Understanding error messages
- Exercise 2: Conditionals and loops
- I/O
- Exercise 3: Reading and writing files
Day 3 (Thursday)
- Regular expressions (major component of Perl)
- Exercise 4: Searching for pattern matches
- Subroutines
- System calls
- Exercise 5: Processing input
- Modules and object-oriented programming (as time permits)

Course Materials

Presentation Slides
Laboratory Exercises (includes instructions on obtaining sample files used in slide presentation)

Resources

Laboratory Requirements

In order to participate in the lab exercises, you will need:

a NetId,
a laptop with wireless access,
and a Supercomputing account on eos or hydra.

If you are new to Unix or want a refresher, you should do the brief homework assignment before the fourth day of class to get (re)acquainted with Unix. These simple exercises should be enough for you to be able to do the laboratory exercises. To learn more about basic Unix commands, go to the New User Information page, and look under the Getting Started section for links to additional information. Read the Introduction to Unix and Basic Unix Commands pages. Experiment with the commands while you are logged into the system.