tutorials:learning_perl
Table of Contents
Learning Perl
Objectives
- Read and understand chapters 1-13 in Learning Perl.
- Know how to write some simple scripts. For example, solve all (or at least most) of the problems in the perl exercise page.
- Know how to use standard modules. For example,
File::BasenameandGetopt::Longare some of the most useful ones. - Know how to use BioPerl. This may not be necessary for simple scripting but is extremely useful if you need to work on sequence data (e.g., BLAST output).
- See the big picture: using perl scripts to solve real-world research problem.
- Example: download a list of GenBank records (Batch Download Entrez)
- Know how to read other people's scripts. See scripts in the perl example page.
- Can you describe, conceptually, how each script solves a particular problem?
- Do you understand how they work? Can you explain every line in a script?
- If someone accidentally (or purposely) introduces a bug in a script, can you fix it?
References
Books
- Learning Perl, Schwartz et al., O'Reilly. The Chinese version is Perl 學習手冊 第五版. This is the book to read when you want to get started with perl. Full text here.
- Perl Cookbook, Christiansen et al, O'Reilly. The Chinese version is in two parts: Perl 食譜 (上) and Perl 食譜（下冊）. Provides lots of useful tips. Useful as a reference book to find some quick solutions (but not as a systematic guide). Full text here.
- Programming Perl, Wall et al., O'Reilly. The Chinese version is Perl 程式設計 第三版. Written by the the creator of perl (Larry Wall), a must read if you really want to know perl. However, not an easy read for someone who just got started with perl. Full text here.
- Beginning Perl for Bioinformatics, Tisdall, O'Reilly.
- Mastering Perl for Bioinformatics, Tisdall, O'Reilly.
Web
Style
- Perltidy: A handy tool for re-formatting codes
tutorials/learning_perl.txt · Last modified: 2010/10/07 00:43 by chkuo