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

ISBN-10: 0521169828
ISBN-13: 9780521169820
Edition: 2012
List price: $92.95 Buy it from $51.34
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Description: 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  More...

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Book details

List price: $92.95
Copyright year: 2012
Publisher: Cambridge University Press
Publication date: 7/19/2012
Binding: Paperback
Pages: 428
Size: 7.00" wide x 10.00" long x 1.00" tall
Weight: 2.178
Language: English

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.

Keith Bradnam is a project scientist in the Genome Center at the University of California, Davis. He has extensive experience working with model organism databases and spent four years as a project leader at WormBase, helping to develop this important bioinformatics resource.

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

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