UNIX and Perl to the Rescue A Field Guide for the Life Sciences and Other Data rich Pursuits 1st Edition by Keith Bradnam, Ian Korf – Ebook PDF Instant Download/Delivery: 1107000688, 9781107000681
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ISBN 10: 1107000688
ISBN 13: 9781107000681
Author: Keith Bradnam; Ian Korf
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.
UNIX and Perl to the Rescue A Field Guide for the Life Sciences and Other Data rich Pursuits 1st Table of contents:
Introduction and background
1.1 Introduction
Why this book?
Why Unix?
Why Perl?
About the authors
Acknowledgments
1.2 How to use this book
Or rather, how not to use this book
Organization
Style conventions
Installing Unix and Perl
2.1 What do I need in order to learn Unix and Perl?
In addition to time, patience, and a beverage of your choice…
What computers can run Perl?
What computers can run Unix?
Linux
Unix vs. Linux: part 1
Unix vs. Linux: part 2
Learning Perl without learning Unix?
2.2 Installing Linux on a PC
There are virtually a dozen solutions
Linux distributions
Installing Cygwin
Running from a CD-ROM or flash drive
Install Linux
Virtualization software
2.3 Installing a code editor
So I installed Perl and Linux, can I start writing code yet?
Essential Unix
3.1 Introduction to Unix
3.2 The Unix terminal
3.3 The Unix command prompt
3.4 Your first Unix command
3.5 The hierarchy of a Unix filesystem
3.6 Finding out where you are in the filesystem
3.7 How to navigate a Unix filesystem
3.8 Absolute and relative paths
3.9 Working with your home directory
3.10 The Unix shell
3.11 Environment variables
3.12 Introduction to command-line options
3.13 Man pages
3.14 Working with directories
3.15 The importance of saving keystrokes
3.16 Moving and renaming files
3.17 Moving and renaming directories
3.18 How to remove files
3.19 How to copy files and directories
3.20 Working with text files
3.21 Introduction to aliases
3.22 Editing text files
3.23 Automating Unix commands
3.24 How to hide files and find hidden files
3.25 Creating a configuration file
3.26 Programming with Unix
3.27 Unix file permissions
3.28 How to specify which directories contain programs
3.29 Creating useful shell scripts
3.30 Unix summary
Essential Perl
4.1 Hello World
4.2 Scalar variables
4.3 Use warnings
4.4 Maths and functions
4.5 Perl vs. perl
4.6 Conditional statements
4.7 Use strict
4.8 Stopping programs
4.9 Working with strings
4.10 Dealing with special characters
4.11 Matching operators
4.12 The transliteration operator
4.13 List context
4.14 Introduction to Arrays
4.15 Array manipulation
4.16 The @ARGV array
4.17 Defined and undefined variables
4.18 Sorting
4.19 Introduction to loops
4.20 More loops
4.21 Loop control
4.22 Data input and output
4.23 Reading and writing files
4.24 Introduction to hashes
4.25 Working with hashes
4.26 Introduction to regular expressions
4.27 Regular expression metacharacters
4.28 Working with regular expressions
4.29 Interacting with other programs
4.30 Using functions and subroutines
4.31 Returning data from a subroutine
4.32 Part 4 summary
Advanced Unix
5.1 Introduction to advanced Unix
5.2 Introduction to process control
5.3 The grep command
5.4 Viewing and controlling program output
5.5 Redirecting input and output
5.6 Standard error
5.7 Connecting commands with pipelines
5.8 Advanced text manipulation
Advanced Perl
6.1 Regular expressions revisited
6.2 Function libraries
6.3 References and two-dimensional arrays
6.4 Records and other hash references
6.5 Using references with subroutines
6.6 Complex data structures
6.7 Adding command-line options
6.8 OOP basics
6.9 CPAN
Programming topics
7.1 Debugging strategies
7.2 Common error messages
7.3 Code beautification
7.4 Abstraction
7.5 Data management
7.6 Documentation
7.7 Revision control
7.8 Working with other people’s data
7.9 Getting help
Appendix
Solutions to problems
Unix solutions
Perl solutions
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Tags: Keith Bradnam, Ian Korf, Rescue, Sciences