Bioinformatics Programming Using Python

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Bioinformatics Programming Using Python

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  • 製本 Paperback:紙装版/ペーパーバック版/ページ数 492 p.
  • 言語 ENG,ENG
  • 商品コード 9780596154509
  • DDC分類 572

Full Description


Through many examples and exercises, this book helps simplify bioinformatics programming using Python. It's an ideal guide for biologists who want to learn either basic scripting or substantial programming for various computational tasks, and for programmers who want to learn bioinformatics programming. "Bioinformatics Programming Using Python" can be used as a reference, for self-instruction, or as a companion book to help you through undergraduate courses in computer science, biology, and other life sciences. With the level of detail this book provides, it's also perfect for Professional Master's graduate courses in Bioinformatics.

Table of Contents

Preface                                            xi
Primitives 1 (20)
Simple Values 1 (4)
Booleans 2 (1)
Integers 2 (1)
Floats 3 (1)
Strings 4 (1)
Expressions 5 (13)
Numeric Operators 5 (2)
Logical Operations 7 (2)
String Operations 9 (3)
Calls 12 (4)
Compound Expressions 16 (2)
Tips, Traps, and Tracebacks 18 (3)
Tips 18 (2)
Traps 20 (1)
Tracebacks 20 (1)
Names, Functions, and Modules 21 (26)
Assigning Names 23 (1)
Defining Functions 24 (10)
Function Parameters 27 (1)
Comments and Documentation 28 (2)
Assertions 30 (2)
Default Parameter Values 32 (2)
Using Modules 34 (6)
Importing 34 (4)
Python Files 38 (2)
Tips, Traps, and Tracebacks 40 (5)
Tips 40 (5)
Traps 45 (1)
Tracebacks 46 (1)
Collections 47 (52)
Sets 48 (3)
Sequences 51 (15)
Strings, Bytes, and Bytearrays 53 (7)
Ranges 60 (1)
Tuples 61 (1)
Lists 62 (4)
Mappings 66 (6)
Dictionaries 67 (5)
Streams 72 (7)
Files 73 (5)
Generators 78 (1)
Collection-Related Expression Features 79 (15)
Comprehensions 79 (10)
Functional Parameters 89 (5)
Tips, Traps, and Tracebacks 94 (5)
Tips 94 (2)
Traps 96 (1)
Tracebacks 97 (2)
Control Statements 99 (66)
Conditionals 101(3)
Loops 104(7)
Simple Loop Examples 105(1)
Initialization of Loop Values 106(1)
Looping Forever 107(2)
Loops with Guard Conditions 109(2)
Iterations 111(23)
Iteration Statements 111(2)
Kinds of Iterations 113(21)
Exception Handlers 134(9)
Python Errors 136(2)
Exception Handling Statements 138(3)
Raising Exceptions 141(2)
Extended Examples 143(17)
Extracting Information from an HTML File 143(3)
The Grand Unified Bioinformatics File 146(2)
Parser
Parsing GenBank Files 148(3)
Translating RNA Sequences 151(4)
Constructing a Table from a Text File 155(5)
Tips, Traps, and Tracebacks 160(5)
Tips 160(2)
Traps 162(1)
Tracebacks 163(2)
Classes 165(44)
Defining Classes 166(20)
Instance Attributes 168(11)
Class Attributes 179(7)
Class and Method Relationships 186(19)
Decomposition 186(8)
Inheritance 194(11)
Tips, Traps, and Tracebacks 205(4)
Tips 205(2)
Traps 207(1)
Tracebacks 208(1)
Utilities 209(48)
System Environment 209(17)
Dates and Times: datetime 209(3)
System Information 212(5)
Command-Line Utilities 217(6)
Communications 223(3)
The Filesystem 226(12)
Operating System Interface: os 226(3)
Manipulating Paths: os.path 229(3)
Filename Expansion: fnmatch and glob 232(2)
Shell Utilities: shutil 234(1)
Comparing Files and Directories 235(3)
Working with Text 238(5)
Formatting Blocks of Text: textwrap 238(2)
String Utilities: string 240(1)
Comma- and Tab-Separated Formats: csv 241(1)
String-Based Reading and Writing: io 242(1)
Persistent Storage 243(10)
Persistent Text: dbm 243(4)
Persistent Objects: pickle 247(1)
Keyed Persistent Object Storage: shelve 248(1)
Debugging Tools 249(4)
Tips, Traps, and Tracebacks 253(4)
Tips 253(1)
Traps 254(1)
Tracebacks 255(2)
Pattern Matching 257(30)
Fundamental Syntax 258(7)
Fixed-Length Matching 259(3)
Variable-Length Matching 262(1)
Greedy Versus Nongreedy Matching 263(1)
Grouping and Disjunction 264(1)
The Actions of the re Module 265(4)
Functions 265(1)
Flags 266(2)
Methods 268(1)
Results of re Functions and Methods 269(1)
Match Object Fields 269(1)
Match Object Methods 269(1)
Putting It All Together: Examples 270(13)
Some Quick Examples 270(2)
Extracting Descriptions from Sequence 272(2)
Files
Extracting Entries From Sequence Files 274(9)
Tips, Traps, and Tracebacks 283(4)
Tips 283(1)
Traps 284(1)
Tracebacks 285(2)
Structured Text 287(38)
HTML 287(13)
Simple HTML Processing 289(8)
Structured HTML Processing 297(3)
XML 300(22)
The Nature of XML 300(2)
An XML File for a Complete Genome 302(1)
The ElementTree Module 303(7)
Event-Based Processing 310(7)
expat 317(5)
Tips, Traps, and Tracebacks 322(3)
Tips 322(1)
Traps 323(1)
Tracebacks 323(2)
Web Programming 325(34)
Manipulating URLs: urllib.parse 325(3)
Disassembling URLs 326(1)
Assembling URLs 327(1)
Opening Web Pages: webbrowser 328(3)
Module Functions 328(1)
Constructing and Submitting Queries 329(1)
Constructing and Viewing an HTML Page 330(1)
Web Clients 331(6)
Making the URLs in a Response Absolute 332(1)
Constructing an HTML Page of Extracted 333(1)
Links
Downloading a Web Page's Linked Files 334(3)
Web Servers 337(17)
Sockets and Servers 337(6)
CGI 343(5)
Simple Web Applications 348(6)
Tips, Traps, and Tracebacks 354(5)
Tips 355(2)
Traps 357(1)
Tracebacks 358(1)
Relational Databases 359(40)
Representation in Relational Databases 360(10)
Database Tables 360(5)
A Restriction Enzyme Database 365(5)
Using Relational Data 370(25)
SQL Basics 371(9)
SQL Queries 380(12)
Querying the Database from a Web Page 392(3)
Tips, Traps, and Tracebacks 395(4)
Tips 395(3)
Traps 398(1)
Tracebacks 398(1)
Structured Graphics 399(50)
Introduction to Graphics Programming 399(7)
Concepts 400(4)
GUI Toolkits 404(2)
Structured Graphics with tkinter 406(25)
Tkinter Fundamentals 406(5)
Examples 411(20)
Structured Graphics with SVG 431(13)
SVG File Contents 432(4)
Examples 436(8)
Tips, Traps, and Tracebacks 444(5)
Tips 444(1)
Traps 445(2)
Tracebacks 447(2)
Python Language Summary 449(10)
Collection Type Summary 459(14)
Index 473