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

4.36/5 (22 hinnangut Goodreads-ist)
(University of California, Davis), (University of California, Davis)
  • Formaat: Paperback / softback, 428 pages, kõrgus x laius x paksus: 244x170x22 mm, kaal: 700 g, 5 Halftones, unspecified
  • Ilmumisaeg: 19-Jul-2012
  • Kirjastus: Cambridge University Press
  • ISBN-10: 0521169828
  • ISBN-13: 9780521169820
Teised raamatud teemal:
UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits)Suurem pilt
  • Formaat: Paperback / softback, 428 pages, kõrgus x laius x paksus: 244x170x22 mm, kaal: 700 g, 5 Halftones, unspecified
  • Ilmumisaeg: 19-Jul-2012
  • Kirjastus: Cambridge University Press
  • ISBN-10: 0521169828
  • ISBN-13: 9780521169820
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9780521169820.html
Märksõnad:
"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 programmingknowledge, 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"--

Arvustused

'UNIX and Perl to the Rescue! is a book I highly recommend for all those students, post-docs, and academics who are scared of programming but can benefit immensely from the power of Unix and scripting languages. It's time to come out of your shell.' Dr M. D. Sharma, Genetics Society News 'My chief regret about this book is that it wasn't available last year, when I was working with a group of life-science researchers. I could have persuaded them all to purchase a copy, thereby saving myself a great deal of the time I spent assisting with their data analysis tasks!' G. K. Jenkins, Computing Reviews 'Bradnam and Korf provide an intuitive and enjoyable volume that shows how to make the terminal window useful to scientists looking to build automation into data queries using UNIX and Perl scripting. With a thorough treatment of more than just the basics, this book fills a missing niche in the Perl and UNIX world with a focus on data processing. The authors have crafted a brilliant treatment of pattern searching with regular expressions to help the reader unleash some of the most powerful parts of the Perl programming language. For scientists looking to parse data files and extract the essential pieces this is a thorough and well explained [ work] complete with sprinkles of humor and biologically motivated examples.' Jason Stajich, University of California, Riverside 'With their book on UNIX and Perl, scientists Bradnam and Korf have come to the aid of laboratory or field researchers floundering helplessly under overwhelming gigabytes of unstructured raw data. With a characteristic charming and chipper cheerfulness, the book quickly guides the readers through finding/installing a UNIX system of any variety Highly recommended.' F. E. J. Linton, Choice

Muu info

An accessible guide to learning the key features of Unix and Perl, written with the non-programmer in mind.
Part 1 Introduction and background page
1(8)
1.1 Introduction
3(3)
1.2 How to use this book
6(3)
Part 2 Installing Unix and Perl
9(8)
2.1 What do I need in order to learn Unix and Perl?
11(2)
2.2 Installing Linux on a PC
13(2)
2.3 Installing a code editor
15(2)
Part 3 Essential Unix
17(88)
3.1 Introduction to Unix
19(1)
3.2 The Unix terminal
20(2)
3.3 The Unix command prompt
22(2)
3.4 Your first Unix command
24(2)
3.5 The hierarchy of a Unix filesystem
26(2)
3.6 Finding out where you are in the filesystem
28(1)
3.7 How to navigate a Unix filesystem
29(3)
3.8 Absolute and relative paths
32(2)
3.9 Working with your home directory
34(2)
3.10 The Unix shell
36(2)
3.11 Environment variables
38(2)
3.12 Introduction to command-line options
40(4)
3.13 Man pages
44(3)
3.14 Working with directories
47(3)
3.15 The importance of saving keystrokes
50(5)
3.16 Moving and renaming files
55(4)
3.17 Moving and renaming directories
59(2)
3.18 How to remove files
61(2)
3.19 How to copy files and directories
63(5)
3.20 Working with text files
68(3)
3.21 Introduction to aliases
71(5)
3.22 Editing text files
76(4)
3.23 Automating Unix commands
80(3)
3.24 How to hide files and find hidden files
83(3)
3.25 Creating a configuration file
86(5)
3.26 Programming with Unix
91(2)
3.27 Unix file permissions
93(3)
3.28 How to specify which directories contain programs
96(4)
3.29 Creating useful shell scripts
100(3)
3.30 Unix summary
103(2)
Part 4 Essential Perl
105(152)
4.1 Hello world
107(3)
4.2 Scalar variables
110(4)
4.3 Use warnings
114(3)
4.4 Maths and functions
117(6)
4.5 Perl vs. perl
123(2)
4.6 Conditional statements
125(7)
4.7 Use strict
132(6)
4.8 Stopping programs
138(3)
4.9 Working with strings
141(6)
4.10 Dealing with special characters
147(2)
4.11 Matching operators
149(7)
4.12 The transliteration operator
156(4)
4.13 List context
160(3)
4.14 Introduction to Arrays
163(6)
4.15 Array manipulation
169(7)
4.16 The @ARGV array
176(4)
4.17 Defined and undefined variables
180(3)
4.18 Sorting
183(4)
4.19 Introduction to loops
187(5)
4.20 More loops
192(5)
4.21 Loop control
197(5)
4.22 Data input and output
202(5)
4.23 Reading and writing files
207(7)
4.24 Introduction to hashes
214(6)
4.25 Working with hashes
220(5)
4.26 Introduction to regular expressions
225(2)
4.27 Regular expression metacharacters
227(8)
4.28 Working with regular expressions
235(6)
4.29 Interacting with other programs
241(5)
4.30 Using functions and subroutines
246(5)
4.31 Returning data from a subroutine
251(4)
4.32 Part 4 summary
255(2)
Part 5 Advanced Unix
257(36)
5.1 Introduction to advanced Unix
259(4)
5.2 Introduction to process control
263(6)
5.3 The grep command
269(5)
5.4 Viewing and controlling program output
274(2)
5.5 Redirecting input and output
276(6)
5.6 Standard error
282(3)
5.7 Connecting commands with pipelines
285(4)
5.8 Advanced text manipulation
289(4)
Part 6 Advanced Perl
293(50)
6.1 Regular expressions revisited
295(5)
6.2 Function libraries
300(6)
6.3 References and two-dimensional arrays
306(8)
6.4 Records and other hash references
314(5)
6.5 Using references with subroutines
319(2)
6.6 Complex data structures
321(7)
6.7 Adding command-line options
328(5)
6.8 OOP basics
333(7)
6.9 CPAN
340(3)
Part 7 Programming topics
343(50)
7.1 Debugging strategies
345(6)
7.2 Common error messages
351(4)
7.3 Code beautification
355(6)
7.4 Abstraction
361(7)
7.5 Data management
368(9)
7.6 Documentation
377(5)
7.7 Revision control
382(3)
7.8 Working with other people's data
385(4)
7.9 Getting help
389(4)
Appendix 393(17)
Index 410
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. Ian Korf is an Associate Professor in Molecular and Cellular Biology at the University of California, Davis. His research seeks to understand structure and function in genomic DNA. He has developed new tools for gene prediction, co-authored the only book devoted to BLAST and helped in the development of BioPerl.