UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits)

by Keith Bradnam , Ian Korf

• ISBN13: 9780521169820
• ISBN10: 0521169828
• Format: Paperback
• Copyright: 2012-08-27
• Publisher: Cambridge University Press

Summary

Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style.

Table of Contents

Introduction and Background:

Introduction

How to use this book

Installing Unix and Perl:

What do I need in order to learn Unix and Perl?

Installing Linux on a PC

Installing a code editor

Essential Unix:

Introduction to Unix

The Unix terminal

The Unix command prompt

Your first Unix command

The hierarchy of a Unix file system

Finding out where you are in the filesystem

How to navigate a Unix filesystem

Absolute and relative paths

Working with your home directory

The Unix shell

Environment variables

Introduction to command-line options

Main pages

Working with directories

The importance of saving keystrokes

Moving and renaming files

Moving and renaming directories

How to remove files

How to copy files and directories

Working with text files

Introduction to aliases

Editing text files

Automating Unix commands

How to hide files and find hidden files

Creating a configuration file

Programming with Unix

Unix file permissions

How to specify which directories contain programs

Creating useful shell scripts

Unix summary

Essential Perl:

Hello world

Scalar variables

Use warnings

Maths and functions

Perl vs perl

Conditional statements

Use strict

Stopping programs

Working with strings

Dealing with special characters

Matching operators

The transliteration operator

List context

Introduction to arrays

Array manipulation

The @ARGV array

Defined and undefined variables

Sorting

Introduction to loops

More loops

Loop control

Data input and output

Reading and writing files

Introduction to hashes

Working with hashes

Introduction to regular expressions

Regular expression metacharacters

Working with regular expressions

Interacting with other programs

Using functions and subroutines

Returning data from a subroutine

Part IV summary

Advanced Unix:

Introduction to advanced Unix

Introduction to process control

The grep command

Viewing, and controlling, program output

Redirecting input and output

Standard error

Connecting commands with pipelines

Advanced text manipulation

Advanced Perl:

Regular expressions revisited

Function libraries

References and 2-dimensional arrays

Records and other hash references

Using references with subroutines

Complex data structures

Adding command-line options

OOP basics

CPAN

Programming Topics:

Debugging strategies

Common error messages

Code beautification

Abstraction

Data management

Documentation

Revision control

Working with other peoples' data

Getting help

Appendix

Index

Table of Contents provided by Publisher. All Rights Reserved.