Programming Course for Bioinformatics and Internet

Editing Perl scripts
Perl scripts are plain text files that the Perl interpreter reads, understand and executes. As such, you may code Perl scripts on any plain text editor, like Notepad on Windows, vi on Unix/Linux/Mac OS X.

If you work on a Mac, consider using TextWrangler, a free powerful text editor able to perform several tasks, including Perl syntax coloring and the ability to open and save text files located on remote FTP and SFTP servers.

On Windows, you might consider one of many good 'editor for programmers', able to perform syntax highlighting for Perl and other programming languajes, : EditPlus and : Crimson, ConTEXT and OPEN Perl IDE.

There're specialized editors for Perl (and other programming languages) that make the life easier, by keeping track of syntax and definitions and offering debugging functions. They're called IDE (integrated development environment). Here some examples:

  • Komodo, an integrated development environment (IDE) for dynamic languages, like Perl, PHP, Python, Tcl and XSLT.
  • Affrus, an integrated Perl editing and debugging environment for Mac OS X.
  • OptiPerl, a Windows integrated visual developing environment and editor for creating, testing, debugging and running perl scripts.
We have installed Komodo on the computers of our Practices room. Komodo provides workspace for editing, debugging and testing the programs. It includes a Rx (regular expression) Toolkit that can be handy at the time of building and testing regular expressions.
More info on Komodo is available at the ActiveState site.
A full documentation and tutorial is avalable on the Computer Room PCs.


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Dr Jaime Prilusky, course@weizmann.ac.il.