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EMBRACE crash course in Perl


Textbooks:
Learning Perl, 4rd ed. by Randal Schwartz & Tom Christiansen (O'Reilly)
There is an online book on perl at http://learn.perl.org/library/beginning_perl, which can be used as an alternative source of wisdom.
If you are really keen on Perl, then the best book on the subject is the famous Camel Book Programming Perl, 3rd ed. by Larry Wall, Tom Christiansen & Jon Orwant (O'Reilly).

Course content:
Looping structure and control statements, regular expressions, tables (arrays and hashes) and more advanced data structures are covered. Exercises in these subjects attempts to have a bioinformatics aspect. It is important that participants set time off in between lectures to do the exercises, as programming is to a large extent "learning by doing".

Platform:
The course exercises will be run on a Unix system, and some familiarity with unix and a commmand line interface will be beneficial to the participants. Pure perl also runs under windows.

Necessary software:
Your machine must have a SSH (Secure SHell) client and and X-server installed. Linux has that as default. Mac is believed to have it as default. Windows has to install the the software, see this page for details.

PowerPoint for the course: perl.ppt
The course will skim through the PP presentation, however you would do well to look through this both before and after the course. It will not teach you to program, but it will cover the most basic perl syntax, structure and functions.

Goal:
You should understand how the following programs work, and be able to modify them.
http://www.cbs.dtu.dk/ws/GenomeAtlas/examples/getProt_simple.pl
http://www.cbs.dtu.dk/ws/RNAmmer/examples/RNAmmer.pl

Exercises: 18 exercises.
If you manage to do all, I will be extremely impressed.

A few possibly helpful pointers