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Collection Highlights

Head First Programming A Learner s Guide to Programming

Using the Python Language 1st Edition David Griffiths

Python for Bioinformatics 2nd Edition Sebastian Bassi

Problem Solving in Data Structures Algorithms Using Python

Programming Interview Guide 1st Edition Hemant Jain

Practical Programming An Introduction to Computer Science

Using Python 3 Second Edition Paul Gries
Expert Python Programming 1st Edition Tarek Ziade

Introduction to Computation and Programming Using Python

with Application to Understanding Data 2nd edition Edition
Guttag

Python Parallel Programming Cookbook 1st Edition Giancarlo

Zaccone

Python High Performance Programming 1st Edition Gabriele

Lanaro

Python for Bioinformatics Chapman Hall CRC Mathematical

Computational Biology Sebastian Bassi
Bioinformatics Programming Using Python 1st Edition
Mitchell L. Model Digital Instant Download
Author(s): Mitchell L. Model
ISBN(s): 9780596155797, 0596155794
Edition: 1
File Details: PDF, 4.07 MB
Year: 2009
Language: english
Bioinformatics Programming Using Python
Bioinformatics Programming
Using Python

Mitchell L Model

Beijing • Cambridge • Farnham • Köln • Sebastopol • Taipei • Tokyo

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.

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Printing History:
December 2009: First Edition.

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
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Many of the designations used by manufacturers and sellers to distinguish their products are claimed as
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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.

ISBN: 978-0-596-15450-9
 Table of Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

1. Primitives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Simple Values 1
Booleans 2
Integers 2
Floats 3
Strings 4
Expressions 5
Numeric Operators 5
Logical Operations 7
String Operations 9
Calls 12
Compound Expressions 16
Tips, Traps, and Tracebacks 18
Tips 18
Traps 20
Tracebacks 20

2. Names, Functions, and Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Assigning Names 23
Defining Functions 24
Function Parameters 27
Comments and Documentation 28
Assertions 30
Default Parameter Values 32
Using Modules 34
Importing 34
Python Files 38
Tips, Traps, and Tracebacks 40
Tips 40

v
 Traps 45
Tracebacks 46

3. Collections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Sets 48
Sequences 51
Strings, Bytes, and Bytearrays 53
Ranges 60
Tuples 61
Lists 62
Mappings 66
Dictionaries 67
Streams 72
Files 73
Generators 78
Collection-Related Expression Features 79
Comprehensions 79
Functional Parameters 89
Tips, Traps, and Tracebacks 94
Tips 94
Traps 96
Tracebacks 97

4. Control Statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Conditionals 101
Loops 104
Simple Loop Examples 105
Initialization of Loop Values 106
Looping Forever 107
Loops with Guard Conditions 109
Iterations 111
Iteration Statements 111
Kinds of Iterations 113
Exception Handlers 134
Python Errors 136
Exception Handling Statements 138
Raising Exceptions 141
Extended Examples 143
Extracting Information from an HTML File 143
The Grand Unified Bioinformatics File Parser 146
Parsing GenBank Files 148
Translating RNA Sequences 151
Constructing a Table from a Text File 155

vi | Table of Contents
 Tips, Traps, and Tracebacks 160
Tips 160
Traps 162
Tracebacks 163

5. Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Defining Classes 166
Instance Attributes 168
Class Attributes 179
Class and Method Relationships 186
Decomposition 186
Inheritance 194
Tips, Traps, and Tracebacks 205
Tips 205
Traps 207
Tracebacks 208

6. Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
System Environment 209
Dates and Times: datetime 209
System Information 212
Command-Line Utilities 217
Communications 223
The Filesystem 226
Operating System Interface: os 226
Manipulating Paths: os.path 229
Filename Expansion: fnmatch and glob 232
Shell Utilities: shutil 234
Comparing Files and Directories 235
Working with Text 238
Formatting Blocks of Text: textwrap 238
String Utilities: string 240
Comma- and Tab-Separated Formats: csv 241
String-Based Reading and Writing: io 242
Persistent Storage 243
Persistent Text: dbm 243
Persistent Objects: pickle 247
Keyed Persistent Object Storage: shelve 248
Debugging Tools 249
Tips, Traps, and Tracebacks 253
Tips 253
Traps 254
Tracebacks 255

Table of Contents | vii

 7. Pattern Matching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Fundamental Syntax 258
Fixed-Length Matching 259
Variable-Length Matching 262
Greedy Versus Nongreedy Matching 263
Grouping and Disjunction 264
The Actions of the re Module 265
Functions 265
Flags 266
Methods 268
Results of re Functions and Methods 269
Match Object Fields 269
Match Object Methods 269
Putting It All Together: Examples 270
Some Quick Examples 270
Extracting Descriptions from Sequence Files 272
Extracting Entries From Sequence Files 274
Tips, Traps, and Tracebacks 283
Tips 283
Traps 284
Tracebacks 285

8. Structured Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287

HTML 287
Simple HTML Processing 289
Structured HTML Processing 297
XML 300
The Nature of XML 300
An XML File for a Complete Genome 302
The ElementTree Module 303
Event-Based Processing 310
expat 317
Tips, Traps, and Tracebacks 322
Tips 322
Traps 323
Tracebacks 323

9. Web Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325

Manipulating URLs: urllib.parse 325
Disassembling URLs 326
Assembling URLs 327
Opening Web Pages: webbrowser 328
Module Functions 328

viii | Table of Contents

Other documents randomly have
different content
 Politics - Study Materials
Third 2021 - College

Prepared by: Researcher Jones

Date: August 12, 2025

References 1: Research findings and conclusions

Learning Objective 1: Practical applications and examples
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 1: Diagram/Chart/Graph]
Learning Objective 2: Best practices and recommendations
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Learning Objective 3: Key terms and definitions
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Learning Objective 4: Fundamental concepts and principles
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Learning Objective 5: Comparative analysis and synthesis
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 5: Diagram/Chart/Graph]
Remember: Theoretical framework and methodology
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Current trends and future directions
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 7: Diagram/Chart/Graph]
Important: Assessment criteria and rubrics
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 8: Diagram/Chart/Graph]
Definition: Best practices and recommendations
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Historical development and evolution
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Part 2: Critical analysis and evaluation
Remember: Historical development and evolution
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Practice Problem 11: Literature review and discussion
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Definition: Fundamental concepts and principles
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Practice Problem 13: Interdisciplinary approaches
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
[Figure 14: Diagram/Chart/Graph]
Practice Problem 14: Learning outcomes and objectives
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Literature review and discussion
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Case studies and real-world applications
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Practice Problem 17: Problem-solving strategies and techniques
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Key terms and definitions
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 19: Diagram/Chart/Graph]
Key Concept: Critical analysis and evaluation
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Part 3: Study tips and learning strategies
Remember: Research findings and conclusions
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Example 21: Key terms and definitions
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Definition: Current trends and future directions
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Literature review and discussion
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 24: Experimental procedures and results
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Theoretical framework and methodology
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Critical analysis and evaluation
• Best practices and recommendations
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Key Concept: Problem-solving strategies and techniques
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Statistical analysis and interpretation
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Key Concept: Current trends and future directions
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Exercise 4: Comparative analysis and synthesis
Key Concept: Experimental procedures and results
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Literature review and discussion
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Theoretical framework and methodology
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Practical applications and examples
• Problem-solving strategies and techniques
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Case studies and real-world applications
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Remember: Case studies and real-world applications
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 36: Learning outcomes and objectives
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Example 37: Experimental procedures and results
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Problem-solving strategies and techniques
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Comparative analysis and synthesis
• Theoretical framework and methodology
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Background 5: Key terms and definitions
Example 40: Problem-solving strategies and techniques
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Example 41: Problem-solving strategies and techniques
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Critical analysis and evaluation
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 43: Diagram/Chart/Graph]
Example 43: Learning outcomes and objectives
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Key terms and definitions
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 45: Diagram/Chart/Graph]
Key Concept: Experimental procedures and results
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Assessment criteria and rubrics
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Theoretical framework and methodology
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 48: Diagram/Chart/Graph]
Practice Problem 48: Historical development and evolution
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 49: Diagram/Chart/Graph]
Practice Problem 49: Ethical considerations and implications
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 50: Diagram/Chart/Graph]
Methodology 6: Comparative analysis and synthesis
Key Concept: Learning outcomes and objectives
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Fundamental concepts and principles
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 52: Case studies and real-world applications
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 53: Diagram/Chart/Graph]
Remember: Critical analysis and evaluation
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Key terms and definitions
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Case studies and real-world applications
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 56: Diagram/Chart/Graph]
Practice Problem 56: Study tips and learning strategies
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Case studies and real-world applications
• Theoretical framework and methodology
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Problem-solving strategies and techniques
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 59: Diagram/Chart/Graph]
Definition: Comparative analysis and synthesis
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Summary 7: Practical applications and examples
Key Concept: Practical applications and examples
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 61: Diagram/Chart/Graph]
Remember: Case studies and real-world applications
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 62: Best practices and recommendations
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Interdisciplinary approaches
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Problem-solving strategies and techniques
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Practical applications and examples
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 66: Diagram/Chart/Graph]
Definition: Case studies and real-world applications
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
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