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Using Perl for Bioinformatics Module 1 : Learning Perl

By Stajich, Jason

Excerpt
Perl has seen widespread use in bioinformatics because of its ease of use, extensiblity, and its ability to scale to complex tasks. Being a scripting language, new programmers do not have to wrestle with the complexity of a compiled language and can quickly write scripts to achieve the small - medium sized tasks that they need to accomplish quickly. Perl was built to provide easy string manipulation and has simple I/O mechanisms making it ideal for formatting, searching, and reorganizing data sets contained within les. The Practical Extraction and Reporting Language was built for simplifying system administration tasks like How many people logged in over the last week on Machine X? The problem space of much of bioinformatics is data manipulation, text processing, and simple summary calculation which perl is perfectly suited to handle.

Table of Contents
Contents 1 Introduction and FAQ 1 1.1 Course Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 This document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.3 Why use perl for bioinformatics ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.4 Help I'm stuck and I can't debug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 Perl Basics 2 2.1 Hello World . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 Variables, Literals, Strings and Quotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.3 Arrays and Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.4 Associative Arrays or Hashes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.5 A Brief Discussion of Truth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.6 Conditionals and Loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.7 Built-in perl functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.7.1 String functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.7.2 Array functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.8 Input/Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.9 Regular Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.10 Scope, \use strict . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 2.11 Subroutines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3 Advanced Perl 12 3.1 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 3.2 Special Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.3 Executing external programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.4 Object Oriented Perl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 4 Resources 16 4.1 Books . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.2 WWW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 ii

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Book Id: WPLBN0000170114
Format Type: PDF eBook
File Size: 0.2 MB
Reproduction Date: 2005
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Title: Using Perl for Bioinformatics Module 1 : Learning Perl  
Author: Stajich, Jason
Volume:
Language: English
Subject: Health., Medical research, Medical reports
Collection: Medical Library Collection
Subcollection:
Historic
Publication Date:
Publisher: Centers for Disease Control and Prevention
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