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A comprehensive guide to the text editing, formatting, and document preparation tools with the UNIX operating system, from the author of the widely-used The UNIX Operating system. The first chapter acts as a guide to the material in the succeeding 11 chapters. Goes on to cover the UNIX system's most popular text editor: vi; how vi can be retrofitted as a rudimentary word processor for simple jobs; the standard formatters nroff and troff; and the two most popular macro packages, -ms and -mm. Also discusses eqn (the first preprocessor), an aid for typesetting mathematics; The tbl preprocessor, for typesetting tables; refer, an aid for typesetting and managing references. The UNIX system's latest preprocessor, pic, an aid for typesetting line drawings, is also explored, as well as various standard UNIX utility programs that aid document preparation.
GNU Emacs is the most popular and widespread of the Emacs family of editors. It is also the most powerful and flexible. Unlike all other text editors, GNU Emacs is a complete working environment -- you can stay within Emacs all day without leaving. The GNU Emacs Pocket Reference is a companion volume to O'Reilly's Learning GNU Emacs, which tells you how to get started with the GNU Emacs editor and, as you become more proficient, it will help you learn how to use Emacs more effectively.This small book, covering Emacs version 20, is a handy reference guide to the basic elements of this powerful editor, presenting the Emacs commands in an easy-to-use tabular format.
-Teaches the reader how to use Unix, which is the key to basic computing and allows the most flexibility for bioinformatics applications -Written specifically with the needs of molecular biologists in mind -Easy to follow, written for beginners with no computational knowledge -Includes examples from biological data analysis -Can be use either for self-teaching or in courses
If you need to parse or process text data in Linux or Unix, this useful book explains how to use flex and bison to solve your problems quickly. flex & bison is the long-awaited sequel to the classic O'Reilly book, lex & yacc. In the nearly two decades since the original book was published, the flex and bison utilities have proven to be more reliable and more powerful than the original Unix tools. flex & bison covers the same core functionality vital to Linux and Unix program development, along with several important new topics. You'll find revised tutorials for novices and references for advanced users, as well as an explanation of each utility's basic usage and simple, standalone applications you can create with them. With flex & bison, you'll discover the wide range of uses these flexible tools offer. Address syntax crunching that regular expressions tools can't handle Build compilers and interpreters, and handle a wide range of text processing functions Interpret code, configuration files, or any other structured format Learn key programming techniques, including abstract syntax trees and symbol tables Implement a full SQL grammar-with complete sample code Use new features such as pure (reentrant) lexers and parsers, powerful GLR parsers, and interfaces to C++
Shell scripting skills never go out of style. It's the shell that unlocks the real potential of Unix. Shell scripting is essential for Unix users and system administrators-a way to quickly harness and customize the full power of any Unix system. With shell scripts, you can combine the fundamental Unix text and file processing commands to crunch data and automate repetitive tasks. But beneath this simple promise lies a treacherous ocean of variations in Unix commands and standards. Classic Shell Scripting is written to help you reliably navigate these tricky waters.Writing shell scripts requires more than just a knowledge of the shell language, it also requires familiarity with the individual Unix programs: why each one is there, how to use them by themselves, and in combination with the other programs. The authors are intimately familiar with the tips and tricks that can be used to create excellent scripts, as well as the traps that can make your best effort a bad shell script. With Classic Shell Scripting you'll avoid hours of wasted effort. You'll learn not only write useful shell scripts, but how to do it properly and portably.The ability to program and customize the shell quickly, reliably, and portably to get the best out of any individual system is an important skill for anyone operating and maintaining Unix or Linux systems. Classic Shell Scripting gives you everything you need to master these essential skills.
There's nothing that hard-core Unix and Linux users are more fanatical about than their text editor. Editors are the subject of adoration and worship, or of scorn and ridicule, depending upon whether the topic of discussion is your editor or someone else's. vi has been the standard editor for close to 30 years. Popular on Unix and Linux, it has a growing following on Windows systems, too. Most experienced system administrators cite vi as their tool of choice. And since 1986, this book has been the guide for vi. However, Unix systems are not what they were 30 years ago, and neither is this book. While retaining all the valuable features of previous editions, the 7th edition of Learning the vi and vim Editors has been expanded to include detailed information on vim, the leading vi clone. vim is the default version of vi on most Linux systems and on Mac OS X, and is available for many other operating systems too. With this guide, you learn text editing basics and advanced tools for both editors, such as multi-window editing, how to write both interactive macros and scripts to extend the editor, and power tools for programmers -- all in the easy-to-follow style that has made this book a classic. Learning the vi and vim Editors includes: A complete introduction to text editing with vi: How to move around vi in a hurry Beyond the basics, such as using buffers vi's global search and replacement Advanced editing, including customizing vi and executing Unix commands How to make full use of vim: Extended text objects and more powerful regular expressions Multi-window editing and powerful vim scripts How to make full use of the GUI version of vim, called gvim vim's enhancements for programmers, such as syntax highlighting, folding and extended tags Coverage of three other popular vi clones -- nvi, elvis, and vile -- is also included. You'll find several valuable appendixes, including an alphabetical quick reference to both vi and ex mode commands for regular vi and for vim, plus an updated appendix on vi and the Internet. Learning either vi or vim is required knowledge if you use Linux or Unix, and in either case, reading this book is essential. After reading this book, the choice of editor will be obvious for you too.
In Sed & Awk, Dale Dougherty and Arnold Robbins describe two text manipulation programs that are mainstays of the UNIX programmer's toolbox. This new edition covers the Sed and Awk systems as they are now mandated by the POSIX standard.
This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.
Awk was developed in 1977 at Bell Labs, and it's still a remarkably useful tool for solving a wide variety of problems quickly and efficiently. In this update of the classic Awk book, the creators of the language show you what Awk can do and teach you how to use it effectively. Here's what programmers today are saying: "I love Awk." "Awk is amazing." "It is just so damn good." "Awk is just right." "Awk is awesome." "Awk has always been a language that I loved." It's easy: "Simple, fast and lightweight." "Absolutely efficient to learn because there isn't much to learn." "3-4 hours to learn the language from start to finish." "I can teach it to new engineers in less than 2 hours." It's productive: "Whenever I need to do a complex analysis of a semi-structured text file in less than a minute, Awk is my tool." "Learning Awk was the best bang for buck investment of time in my entire career." "Designed to chew through lines of text files with ease, with great defaults that minimize the amount of code you actually have to write to do anything." It's always available: "AWK runs everywhere." "A reliable Swiss Army knife that is always there when you need it." "Many systems lack Perl or Python, but include Awk." Register your book for convenient access to downloads, updates, and/or corrections as they become available. See inside book for details.