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Bioinformatics Programming Using Python.pdf

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    Table of Contents
    Preface
    Introduction
    About This Book
    About Bioinformatics
    About the Reader
    Python
    Some Context
    The Python Language
    Installing Python
    Running Python
    Notes
    Reading and Reference Recommendations
    Example Code
    Unfortunate and Unavoidable Vocabulary Overlap
    Comments
    Conventions Used in This Book
    Weâ•Žd Like to Hear from You
    Using Code Examples
    Safari® Books Online
    Acknowledgments
    Chapter€1.€Primitives
    Simple Values
    Booleans
    Integers
    Floats
    Strings
    Expressions
    Numeric Operators
    Logical Operations
    String Operations
    String operators
    Subscription
    Slicing
    Calls
    Function calls
    Method calls
    Compound Expressions
    Tips, Traps, and Tracebacks
    Tips
    Statements and expressions
    Running Python interactively
    Traps
    Tracebacks
    Chapter€2.€Names, Functions, and Modules
    Assigning Names
    Defining Functions
    Function Parameters
    Comments and Documentation
    Assertions
    Default Parameter Values
    Using Modules
    Importing
    Module namespaces
    The random module
    Python Files
    Tips, Traps, and Tracebacks
    Tips
    Names
    Function definitions
    Executing code
    Using IDLE
    Managing Python files
    Traps
    Tracebacks
    Chapter€3.€Collections
    Sets
    Sequences
    Strings, Bytes, and Bytearrays
    Creating
    Testing
    Searching
    Replacing
    Changing case
    Reformatting
    The format method and function
    Ranges
    Tuples
    Tuple syntax
    Tuple packing and unpacking
    Lists
    Statements that modify lists
    List modification methods
    Sequence-oriented string methods
    Mappings
    Dictionaries
    Dictionary example: RNA codon translation table
    Dictionary operations
    Dictionary methods
    Streams
    Files
    Creating file objects
    File methods
    Example
    Generators
    Collection-Related Expression Features
    Comprehensions
    List comprehensions
    Set and dictionary comprehensions
    Generator expressions
    Conditional comprehensions
    Nested comprehensions
    Functional Parameters
    The parameter â•œkeyâ•š
    Function objects
    Anonymous functions
    Tips, Traps, and Tracebacks
    Tips
    Language features
    Developing and testing code
    Traps
    Tracebacks
    Chapter€4.€Control Statements
    Conditionals
    Loops
    Simple Loop Examples
    Initialization of Loop Values
    Looping Forever
    Loops with Guard Conditions
    Iterations
    Iteration Statements
    Kinds of Iterations
    Do
    Collect
    Combine
    Search
    Filter
    Nested iterations
    Recursive iterations
    Exception Handlers
    Python Errors
    Tracebacks
    Runtime errors
    Exception Handling Statements
    Optional features of exception handling statements
    Exception handling and generator objects
    Raising Exceptions
    The raise statement
    Raising an exception to end a loop
    Extended Examples
    Extracting Information from an HTML File
    The Grand Unified Bioinformatics File Parser
    Reading the sequences in a FASTA file
    Generalized parsing
    Parsing GenBank Files
    Translating RNA Sequences
    Step 1
    Step 2
    Step 3
    Step 4
    Step 5
    Constructing a Table from a Text File
    Step 1
    Step 2
    Step 3
    Step 4
    Step 5
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€5.€Classes
    Defining Classes
    Instance Attributes
    Access methods
    Predicate methods
    Initialization methods
    String methods
    Modification methods
    Action methods
    Support methods
    Summary
    Class Attributes
    Class fields
    Class methods
    Classes as objects
    Class and Method Relationships
    Decomposition
    Class decomposition
    Method decomposition
    Singleton classes
    Inheritance
    Defining subclasses
    Factoring out common code
    Generalization
    Subclass methods
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€6.€Utilities
    System Environment
    Dates and Times: datetime
    Classes
    Instance creation
    Operations
    Methods
    System Information
    The Python runtime environment: sys
    The system clock: time
    Command-Line Utilities
    Reading multiple files: fileinput
    Command-line options: optparse
    Command-line commands: subprocess
    Communications
    Sending email: smtplib
    Logging: logging
    The Filesystem
    Operating System Interface: os
    Environment access
    Managing files and directories
    Directories
    Files
    Directory contents
    Temporary files: tempfile
    Manipulating Paths: os.path
    Path components
    Path manipulations
    Path information
    Filename Expansion: fnmatch and glob
    fnmatch
    glob
    Shell Utilities: shutil
    Comparing Files and Directories
    File and directory comparison: filecmp
    Showing the differences between two files: difflib
    Working with Text
    Formatting Blocks of Text: textwrap
    String Utilities: string
    Comma- and Tab-Separated Formats: csv
    String-Based Reading and Writing: io
    Persistent Storage
    Persistent Text: dbm
    Persistent Objects: pickle
    Keyed Persistent Object Storage: shelve
    Debugging Tools
    The Python debugger: pdb
    The IDLE debugger
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€7.€Pattern Matching
    Fundamental Syntax
    Fixed-Length Matching
    Literal matches
    Character sets
    Character classes
    Boundaries
    Variable-Length Matching
    Repetition
    Greedy Versus Nongreedy Matching
    Grouping and Disjunction
    The Actions of the re Module
    Functions
    Flags
    Methods
    Results of re Functions and Methods
    Match Object Fields
    Match Object Methods
    Putting It All Together: Examples
    Some Quick Examples
    Using regular expressions to ignore case
    Listing files in a directory, excluding some
    Finding open reading frames
    Extracting Descriptions from Sequence Files
    Extracting Entries From Sequence Files
    Using regular expressions to extract entries
    Keeping track of the position between calls
    Buffering input
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€8.€Structured Text
    HTML
    Simple HTML Processing
    Searching HTML text
    More elaborate HTML pattern matching
    Turning HTML into plain text
    Structured HTML Processing
    Problems with HTML pattern matching
    Structured HTML parsing: html.parser
    XML
    The Nature of XML
    An XML File for a Complete Genome
    The ElementTree Module
    Getting started with ElementTree
    Navigating around an ElementTree
    Event-Based Processing
    Function calls, exceptions, and the call stack
    Callbacks: Reversed function calls
    Programming for an event-based processor
    expat
    Obtaining a single piece of information
    Extracting a few pieces of data
    Getting the content of all tags with a specified name
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€9.€Web Programming
    Manipulating URLs: urllib.parse
    Disassembling URLs
    Assembling URLs
    Opening Web Pages: webbrowser
    Module Functions
    Constructing and Submitting Queries
    Constructing and Viewing an HTML Page
    Web Clients
    Making the URLs in a Response Absolute
    Constructing an HTML Page of Extracted Links
    Downloading a Web Pageâ•Žs Linked Files
    Web Servers
    Sockets and Servers
    Server fundamentals
    Running a server: The http.server module
    CGI
    Serving CGI requests
    Setting up CGI
    CGI script arguments and responses
    Simple Web Applications
    Using CGI scripts
    HTML forms with CGI scripts
    Tips, Traps, and Tracebacks
    Tips
    Web pages
    Debugging CGI scripts
    HTTP servers
    Traps
    Tracebacks
    Chapter€10.€Relational Databases
    Representation in Relational Databases
    Database Tables
    Avoiding duplication of values
    Representation of relationships
    Database definition
    A Restriction Enzyme Database
    The data
    Reading the data
    A schema for the Rebase database
    Using Relational Data
    SQL Basics
    Using the sqlite3 module
    Connecting to the database
    Creating the database
    Loading data into tables
    SQL Queries
    Simple database queries
    Qualified database queries
    Relationship queries
    Querying the Database from a Web Page
    HTML frames
    An HTML page of query forms
    Tips, Traps, and Tracebacks
    Tips
    Traps
    Tracebacks
    Chapter€11.€Structured Graphics
    Introduction to Graphics Programming
    Concepts
    Coordinate system
    Components
    Properties
    GUI Toolkits
    GUI toolkits for Python
    Using a GUI toolkit
    Structured Graphics with tkinter
    tkinter Fundamentals
    The basic steps
    Common widget options
    Canvas drawing methods
    Writing the contents of a canvas to a PostScript file
    Examples
    An abstract class for tkinter graphics
    Dot plots
    Histograms
    Structured Graphics with SVG
    SVG File Contents
    SVG tags
    SVG styles
    Examples
    Histograms of codon use
    Sequencing trace file curves using SVG
    Tips, Traps, and Tracebacks
    Tips
    Traps
    SVG traps
    Tracebacks
    Appendix€A.€Python Language Summary
    Language Components
    Special Syntactic Elements
    Keywords
    Special Names
    Operators
    Anonymous Functions
    Types and Expressions
    Statements
    Notes
    Appendix€B.€Collection Type Summary
    Types and General Operations
    Common Operations
    Creating Collections
    Specific Collection Types
    Sets
    Sequences
    Strings
    Lists
    Mappings
    Streams
    File objects
    Generators
    Iteration Templates
    Basic Iteration Templates
    Filtering Templates
    Other Kinds of Templates
    Index
    www.1024ebook.com
    Bioinformatics Programming Using Python www.1024ebook.com
    www.1024ebook.com
    Bioinformatics Programming Using Python Mitchell L Model Beijing • Cambridge • Farnham • Köln • Sebastopol • Taipei • Tokyo www.1024ebook.com
    Bioinformatics Programming Using Python by Mitchell L Model Copyright © 2010 Mitchell L Model. All rights reserved. Printed in the United States of America. Published by O’Reilly Media, Inc., 1005 Gravenstein Highway North, Sebastopol, CA 95472. O’Reilly books may be purchased for educational, business, or sales promotional use. Online editions are also available for most titles (http://my.safaribooksonline.com). For more information, contact our corporate/institutional sales department: 800-998-9938 or corporate@oreilly.com. Editor: Mike Loukides Production Editor: Sarah Schneider Copyeditor: Rachel Head Proofreader: Sada Preisch Printing History: December 2009: First Edition. Indexer: Lucie Haskins Cover Designer: Karen Montgomery Interior Designer: David Futato Illustrator: Robert Romano O’Reilly and the O’Reilly logo are registered trademarks of O’Reilly Media, Inc. Bioinformatics Pro- gramming Using Python, the image of a brown rat, and related trade dress are trademarks of O’Reilly Media, Inc. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and O’Reilly Media, Inc. was aware of a trademark claim, the designations have been printed in caps or initial caps. While every precaution has been taken in the preparation of this book, the publisher and author assume no responsibility for errors or omissions, or for damages resulting from the use of the information con- tained herein. TM This book uses RepKover, a durable and flexible lay-flat binding. ISBN: 978-0-596-15450-9 [M] 1259959883 www.1024ebook.com
    Table of Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi Expressions Simple Values Booleans Integers Floats Strings 1. Primitives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1 2 2 3 4 5 5 7 9 12 16 18 18 20 20 Numeric Operators Logical Operations String Operations Calls Compound Expressions Tips Traps Tracebacks Tips, Traps, and Tracebacks Assigning Names Defining Functions Function Parameters Comments and Documentation Assertions Default Parameter Values 2. Names, Functions, and Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 23 24 27 28 30 32 34 34 38 40 40 Tips, Traps, and Tracebacks Importing Python Files Using Modules Tips www.1024ebook.com v
    Traps Tracebacks 45 46 Mappings Dictionaries Sets Sequences Strings, Bytes, and Bytearrays Ranges Tuples Lists 3. Collections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 48 51 53 60 61 62 66 67 72 73 78 79 79 89 94 94 96 97 Comprehensions Functional Parameters Streams Files Generators Collection-Related Expression Features Tips Traps Tracebacks Tips, Traps, and Tracebacks Iterations Conditionals Loops Iteration Statements Kinds of Iterations Simple Loop Examples Initialization of Loop Values Looping Forever Loops with Guard Conditions 4. Control Statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 101 104 105 106 107 109 111 111 113 134 136 138 141 143 143 146 148 151 155 Extracting Information from an HTML File The Grand Unified Bioinformatics File Parser Parsing GenBank Files Translating RNA Sequences Constructing a Table from a Text File Python Errors Exception Handling Statements Raising Exceptions Exception Handlers Extended Examples vi | Table of Contents www.1024ebook.com
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