Python for Bioinformatics

Cover
Half Title
Chapman & Hall/crc
Published Titles
Title
Copyright
Contents
List Of Figures
List Of Tables
Preface To The First Edition
Preface To The Second Edition
Acknowledgments
Section I Programming
Chapter 1  Introduction
	1.1 Who Should Read This Book
		1.1.1 What The Reader Should Already Know
	1.2 Using This Book
		1.2.1 Typographical Conventions
		1.2.2 Python Versions
		1.2.3 Code Style
		1.2.4 Get The Most From This Book Without Reading It All
		1.2.5 Online Resources Related To This Book
	1.3 Why Learn To Program
	1.4 Basic Programming Concepts
		1.4.1 What Is A Program
	1.5 Why Python
		1.5.1 Main Features Of Python
		1.5.2 Comparing Python With Other Languages
		1.5.3 How Is It Used
		1.5.4 Who Uses Python
		1.5.5 Flavors Of Python
		1.5.6 Special Python Distributions
	1.6 Additional Resources
Chapter 2   First Steps With Python
	2.1 Installing Python
		2.1.1 Learn Python By Using It
		2.1.2 Install Python Locally
		2.1.3 Using Python Online
		2.1.4 Testing Python
		2.1.5 First Use
	2.2 Interactive Mode
		2.2.1 Baby Steps
		2.2.2 Basic Input And Output
		2.2.3 More On The Interactive Mode
		2.2.4 Mathematical Operations
		2.2.5 Exit From The Python Shell
	2.3 Batch Mode
		2.3.1 Comments
		2.3.2 Indentation
	2.4 Choosing An Editor
		2.4.1 Sublime Text
		2.4.2 Atom
		2.4.3 Pycharm
		2.4.4 Spyder Ide
		2.4.5 Final Words About Editors
	2.5 Other Tools
	2.6 Additional Resources
	2.7 Self-evaluation
Chapter 3   Basic Programming: Data Types
	3.1 Strings
		3.1.1 Strings Are Sequences Of Unicode Characters
		3.1.2 String Manipulation
		3.1.3 Methods Associated With Strings
	3.2 Lists
		3.2.1 Accessing List Elements
		3.2.2 List With Multiple Repeated Items
		3.2.3 List Comprehension
		3.2.4 Modifying Lists
		3.2.5 Copying A List
	3.3 Tuples
		3.3.1 Tuples Are Immutable Lists
	3.4 Common Properties Of The Sequences
	3.5 Dictionaries
		3.5.1 Mapping: Calling Each Value By A Name
		3.5.2 Operating With Dictionaries
	3.6 Sets
		3.6.1 Unordered Collection Of Objects
		3.6.2 Set Operations
		3.6.3 Shared Operations With Other Data Types
		3.6.4 Immutable Set: Frozenset
	3.7 Naming Objects
	3.8 Assigning A Value To A Variable Versus Binding A Name  To An Object
	3.9 Additional Resources
	3.10 Self-evaluation
Chapter 4   Programming: Flow Control
	4.1 If-else
		4.1.1 Pass Statement
	4.2 For Loop
	4.3 While Loop
	4.4 Break: Breaking The Loop
	4.5 Wrapping It Up
		4.5.1 Estimate The Net Charge Of A Protein
		4.5.2 Search For A Low-degeneration Zone
	4.6 Additional Resources
	4.7 Self-evaluation
Chapter 5   Handling Files
	5.1 Reading Files
		5.1.1 Example Of File Handling
	5.2 Writing Files
		5.2.1 File Reading And Writing Examples
	5.3 Csv Files
	5.4 Pickle: Storing And Retrieving The Contents Of Vari-  Ables
	5.5 Json Files
	5.6 File Handling: Os, Os.path, Shutil, And Path.py Module
		5.6.1 Path.py Module
		5.6.2 Consolidate Multiple Dna Sequences Into One Fasta File
	5.7 Additional Resources
	5.8 Self-evaluation
Chapter 6   Code Modularizing
	6.1 Introduction To Code Modularizing
	6.2 Functions
		6.2.1 Standard Way To Make Python Code Modular
		6.2.2 Function Parameter Options
		6.2.3 Generators
	6.3 Modules And Packages
		6.3.1 Using Modules
		6.3.2 Packages
		6.3.3 Installing Third-party Modules
		6.3.4 Virtualenv: Isolated Python Environments
		6.3.5 Conda: Anaconda Virtual Environment
		6.3.6 Creating Modules
		6.3.7 Testing Modules
	6.4 Additional Resources
	6.5 Self-evaluation
Chapter 7   Error Handling
	7.1 Introduction To Error Handling
		7.1.1 Try And Except
		7.1.2 Exception Types
		7.1.3 Triggering Exceptions
	7.2 Creating Customized Exceptions
	7.3 Additional Resources
	7.4 Self-evaluation
Chapter 8   Introduction To Object Orienting Programming (oop
	8.1 Object Paradigm And Python
	8.2 Exploring The Jargon
	8.3 Creating Classes
	8.4 Inheritance
	8.5 Special Methods
		8.5.1 Create A New Data Type Using A Built-in Data Type
	8.6 Making Our Code Private
	8.7 Additional Resources
	8.8 Self-evaluation
Chapter 9   Introduction To Biopython
	9.1 What Is Biopython
		9.1.1 Project Organization
	9.2 Installing Biopython
	9.3 Biopython Components
		9.3.1 Alphabet
		9.3.2 Seq
		9.3.3 Mutableseq
		9.3.4 Seqrecord
		9.3.5 Align
		9.3.6 Alignio
		9.3.7 Clustalw
		9.3.8 Seqio
		9.3.9 Alignio
		9.3.10 Blast
		9.3.11 Biological Related Data
		9.3.12 Entrez
		9.3.13 Pdb
		9.3.14 Prosite
		9.3.15 Restriction
		9.3.16 Sequtils
		9.3.17 Sequencing
		9.3.18 Swissprot
	9.4 Conclusion
	9.5 Additional Resources
	9.6 Self-evaluation
Section Ii Advanced Topics
Chapter 10   Web Applications
	10.1 Introduction To Python On The Web
	10.2 Cgi In Python
		10.2.1 Configuring A Web Server For Cgi
		10.2.2 Testing The Server With Our Script
		10.2.3 Web Program To Calculate The Net Charge Of A Protein  (cgi Version
	10.3 Wsgi
		10.3.1 Bottle: A Python Web Framework For Wsgi
		10.3.2 Installing Bottle
		10.3.3 Minimal Bottle Application
		10.3.4 Bottle Components
		10.3.5 Web Program To Calculate The Net Charge Of A Protein  (bottle Version
		10.3.6 Installing A Wsgi Program In Apache
	10.4 Alternative Options For Making Python-based Dynamic  Web Sites
	10.5 Some Words About Script Security
	10.6 Where To Host Python Programs
	10.7 Additional Resources
	10.8 Self-evaluation
Chapter 11   Xml
	11.1 Introduction To Xml
	11.2 Structure Of An Xml Document
	11.3 Methods To Access Data Inside An Xml Document
		11.3.1 Sax: Celementtree Iterparse
	11.4 Summary
	11.5 Additional Resources
	11.6 Self-evaluation
Chapter 12   Python And Databases
	12.1 Introduction To Databases
		12.1.1 Database Management: Rdbms
		12.1.2 Components Of A Relational Database
		12.1.3 Database Data Types
	12.2 Connecting To A Database
	12.3 Creating A Mysql Database
		12.3.1 Creating Tables
		12.3.2 Loading A Table
	12.4 Planning Ahead
		12.4.1 Pythonu: Sample Database
	12.5 Select: Querying A Database
		12.5.1 Building A Query
		12.5.2 Updating A Database
		12.5.3 Deleting A Record From A Database
	12.6 Accessing A Database From Python
		12.6.1 Pymysql Module
		12.6.2 Establishing The Connection
		12.6.3 Executing The Query From Python
	12.7 Sqlite
	12.8 Nosql Databases: Mongodb
		12.8.1 Using Mongodb With Pymongo
	12.9 Additional Resources
	12.10 Self-evaluation
Chapter 13   Regular Expressions
	13.1 Introduction To Regular Expressions (regex
		13.1.1 Regex Syntax
	13.2 The Re Module
		13.2.1 Compiling A Pattern
		13.2.2 Regex Examples
		13.2.3 Pattern Replace
	13.3 Regex In Bioinformatics
		13.3.1 Cleaning Up A Sequence
	13.4 Additional Resources
	13.5 Self-evaluation
Chapter 14   Graphics In Python
	14.1 Introduction To Bokeh
	14.2 Installing Bokeh
	14.3 Using Bokeh
		14.3.1 A Simple X-y Plot
		14.3.2 Two Data Series Plot
		14.3.3 A Scatter Plot
		14.3.4 A Heatmap
		14.3.5 A Chord Diagram
Section Iii Python Recipes With Commentedsource Code3
Chapter 15 Sequence Manipulation In Batch
	15.1 Problem Description
	15.2 Problem One: Create A Fasta File With Random Se-  Quences
		15.2.1 Commented Source Code
	15.3 Problem Two: Filter Not Empty Sequences From A  Fasta File
		15.3.1 Commented Source Code
	15.4 Problem Three: Modify Every Record Of A Fasta File
		15.4.1 Commented Source Code
Chapter 16   Web Application For Filtering Vector Contamination
	16.1 Problem Description
		16.1.1 Commented Source Code
	16.2 Additional Resources
Chapter 17   Searching For Pcr Primers Using Primer3
	17.1 Problem Description
	17.2 Primer Design Flanking A Variable Length Region
		17.2.1 Commented Source Code
	17.3 Primer Design Flanking A Variable Length Region,  With Biopython
	17.4 Additional Resources
Chapter 18   Calculating Melting Temperature From A Set Of Primers
	18.1 Problem Description
		18.1.1 Commented Source Code
	18.2 Additional Resources
Chapter 19   Filtering Out Specific Fields From A Genbank File
	19.1 Extracting Selected Protein Sequences
		19.1.1 Commented Source Code
	19.2 Extracting The Upstream Region Of Selected Pro-  Teins
		19.2.1 Commented Source Code
	19.3 Additional Resources
Chapter 20   Inferring Splicing Sites
	20.1 Problem Description
		20.1.1 Infer Splicing Sites With Commented Source Code
		20.1.2 Sample Run Of Estimate Intron Program
Chapter 21   Web Server For Multiple Alignment
	21.1 Problem Description
		21.1.1 Web Interface: Front-end. Html Code
		21.1.2 Web Interface: Server-side Script. Commented Source Code
	21.2 Additional Resources
Chapter 22   Drawing Marker Positions Using Data Stored In A Database
	22.1 Problem Description
		22.1.1 Preliminary Work On The Data
		22.1.2 Mongodb Version With Commented Source Code
Section Iv Appendices
Appendix A  Collaborative Development: Version Control With Github
	A.1 Introduction To Version Control
	A.2 Version Your Code
	A.3 Share Your Code
	A.4 Contribute To Other Projects
	A.5 Conclusion
	A.6 Methods
	A.7 Additional Resources
Appendix B   Install A Bottle App In Pythonanywhere
	B.1 Pythonanywhere
		B.1.1 What Is Pythonanywhere
		B.1.2 Installing A Web App In Pythonanywhere
Appendix C   Scientific Python Cheat Sheet
	C.1 Pure Python
	C.2 Virtualenv
	C.3 Conda
	C.4 Ipython
	C.5 Numpy
	C.6 Matplotlib
	C.7 Scipy
	C.8 Pandas
Index