INT. J.

BIOAUTOMATION, 2014, 18(2), 153-154 NEW BOOKS

ALLEGRA VIA, KRISTIAN ROTHER, ANNA TRAMONTANO

MANAGING YOUR BIOLOGICAL DATA
WITH PYTHON

Managing Your Biological Data with Python

requires no prior programming experience and it
provides biologists and other life scientists with the
capability to work with biological data on their own
using the powerful Python language. The book
teaches programming techniques as well as ways to
manage the data. It shows how to read data from
files in different formats, analyze and manipulate
the data, and write the results to a file or computer
screen.

The first part of the text is an introduction to the

Python language. The second part presents the basic
elements of the language. The third part explains
how to create bigger programs using techniques to
write well-organized, efficient, and error-free code.
The fourth part is focused on data visualization.
The fifth part covers the Biopython programming
library for reading and writing several biological file
formats, querying the NCBI online databases, and
retrieving biological records from the web. The last
CRC Press
part is a cookbook of 20 specific programming
ISBN 978-1-4398-8093-7
“recipes”, ranging from secondary structure
Hard cover
560 pages prediction and multiple sequence alignment
August 2014 analyses to superimposing protein three-
dimensional structures.

There are numerous appendices to help the readers

in their tasks and helps them easily analyze data and
ultimately make better discoveries. Every piece of
code presented in the book is aimed at solving real
biological problems.

Table of Contents
Preface ................................................................................................................................................. xix
Part 1 Getting Started............................................................................................................................1
Chapter 1 The Python Shell ....................................................................................................................5
Chapter 2 Your first Python Program ...................................................................................................23
Part 2 Data Management.....................................................................................................................43
Chapter 3 Analyzing a Data Column ....................................................................................................45
Chapter 4 Parsing Data Records ...........................................................................................................59
Chapter 5 Searching Data .....................................................................................................................77
Chapter 6 Filtering Data .......................................................................................................................93

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 INT. J. BIOAUTOMATION, 2014, 18(2), 153-154 NEW BOOKS

Chapter 7 Managing Tabular Data......................................................................................................111

Chapter 8 Sorting Data .......................................................................................................................129
Chapter 9 Pattern Matching and Text Mining ...................................................................................143
Part 3 Modular Programming ..........................................................................................................163
Chapter 10 Divide a Program Into Functions .....................................................................................167
Chapter 11 Managing Complexity with Classes ...........................................................................189
Chapter 12 Debugging ........................................................................................................................205
Chapter 13 Using External Modules: The Python Interface to R .......................................................225
Chapter 14 Building Program Pipelines .............................................................................................245
Chapter 15 Writing Good Programs ...................................................................................................263
Part 4 Data Visualization...................................................................................................................285
Chapter 16 Creating Scientific Diagrams ...........................................................................................287
Chapter 17 Creating Molecule Images with PyMOL ........................................................................301
Chapter 18 Manipulating Images........................................................................................................323
Part 5 Biopyhton.................................................................................................................................341
Chapter 19 Working with Sequence Data...........................................................................................347
Chapter 20 Retrieving Data from Web Resources..............................................................................363
Chapter 21 Working with 3D Structure Data .....................................................................................375
Part 6 Cookbok...................................................................................................................................535
Recipe 1: The PyCogent Library .........................................................................................................395
Recipe 2: Reversing and Randomizing a Sequence.............................................................................399
Recipe 3: Creating a Random Sequence with Probabilities.................................................................403
Recipe 4: Parsing Multiple Sequence Alignments Using Biopython ..................................................405
Recipe 5: Calculating a Consensus Sequence from a Multiple Sequence Alignment .........................409
Recipe 6: Calculating the Distance between Phylogenetic Tree Nodes ..............................................413
Recipe 7: Codon Frequencies in a Nucleotide Sequence ....................................................................417
Recipe 8: Parsing RNA 2D Structures in the Vienna Format..............................................................421
Recipe 9: Parsing BLAST XML Output..............................................................................................425
Recipe 10: Parsing SBML Files ..........................................................................................................427
Recipe 11: Running BLAST................................................................................................................431
Recipe 12: Accessing, Downloading, and Reading Web Pages in Python..........................................437
Recipe 13: Parsing HTML Files ..........................................................................................................441
Recipe 14: Split a PDB File into PDB Chain Files..............................................................................445
Recipe 15: Find the Two Closest Cα Atoms in a PDB Structure ........................................................447
Recipe 16: Extract the Interface between Two PDB Chains ...............................................................451
Recipe 17: Building Homology Models Using Modeller ...................................................................455
Recipe 18: RNA 3D Homology Modeling with ModeRNA ..............................................................459
Recipe 19: Calculating RNA Base Pairs from a 3D Structure.............................................................463
Recipe 20: A Real Case of Structural Superimposition: The Serine Protease Catalytic Triad............467
APPENDIX A: COMMAND OVERVIEW........................................................................................471
APPENDIX B: PYTHON RESOURCES ...........................................................................................495
APPENDIX C: RECORD SAMPLES ................................................................................................499
APPENDIX D: HANDLING DIRECTORIES AND PROGRAMS WITH UNIX ............................507
INDEX .................................................................................................................................................525

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