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Learning Perl

Objectives

Read and understand chapters 1-13 in Learning Perl.
- Perl quick reference
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::Basename and Getopt::Long are 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?

Learning Perl, Schwartz et al., O'Reilly. This is the book to read when you want to get started with perl. Full text here. The Chinese version is Perl 學習手冊第五版
Perl Cookbook, Christiansen et al, O'Reilly. Provides lots of useful tips. Useful as a reference book to find some quick solutions (but not as a systematic guide). Full text here. The Chinese version is in two parts: Perl 食譜 (上) and Perl 食譜（下冊）
Programming Perl, Wall et al., O'Reilly. 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. The Chinese version is Perl 程式設計第三版
Beginning Perl for Bioinformatics, Tisdall, O'Reilly.
Mastering Perl for Bioinformatics, Tisdall, O'Reilly.