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Mastering Python for Bioinformatics-
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Mastering Python for Bioinformatics_
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Mastering Python
for Bioinformatics
How to Write Flexible, Documented,
Tested Python Code for Research Computing
Ken Youens-Clark
Ken Youens-Clark
Mastering Python for
Bioinformatics
How to Write Flexible, Documented, Tested
Python Code for Research Computing
Boston Farnham Sebastopol
Tokyo
Beijing Boston Farnham Sebastopol
Tokyo
Beijing
978-1-098-10088-9
[LSI]
Mastering Python for Bioinformatics
by Ken Youens-Clark
Copyright © 2021 Charles Kenneth Youens-Clark. 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://oreilly.com). For more information, contact our corporate/institutional
sales department: 800-998-9938 or corporate@oreilly.com.
Acquisitions Editor: Michelle Smith
Development Editor: Corbin Collins
Production Editor: Caitlin Ghegan
Copyeditor: Sonia Saruba
Proofreader: Rachel Head
Indexer: Sue Klefstad
Interior Designer: David Futato
Cover Designer: Karen Montgomery
Illustrator: Kate Dullea
May 2021: First Edition
Revision History for the First Edition
2021-05-04: First Release
See http://oreilly.com/catalog/errata.csp?isbn=9781098100889 for release details.
The O’Reilly logo is a registered trademark of O’Reilly Media, Inc. Mastering Python for Bioinformatics,
the cover image, and related trade dress are trademarks of O’Reilly Media, Inc.
The views expressed in this work are those of the author, and do not represent the publisher’s views.
While the publisher and the author have used good faith efforts to ensure that the information and
instructions contained in this work are accurate, the publisher and the author disclaim all responsibility
for errors or omissions, including without limitation responsibility for damages resulting from the use of
or reliance on this work. Use of the information and instructions contained in this work is at your own
risk. If any code samples or other technology this work contains or describes is subject to open source
licenses or the intellectual property rights of others, it is your responsibility to ensure that your use
thereof complies with such licenses and/or rights.
Table of Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Part I. The Rosalind.info Challenges
1.
Tetranucleotide Frequency: Counting Things. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Getting Started 4
Creating the Program Using new.py 5
Using argparse 7
Tools for Finding Errors in the Code 10
Introducing Named Tuples 12
Adding Types to Named Tuples 15
Representing the Arguments with a NamedTuple 16
Reading Input from the Command Line or a File 18
Testing Your Program 20
Running the Program to Test the Output 23
Solution 1: Iterating and Counting the Characters in a String 25
Counting the Nucleotides 26
Writing and Verifying a Solution 28
Additional Solutions 30
Solution 2: Creating a count() Function and Adding a Unit Test 30
Solution 3: Using str.count() 34
Solution 4: Using a Dictionary to Count All the Characters 35
Solution 5: Counting Only the Desired Bases 38
Solution 6: Using collections.defaultdict() 39
Solution 7: Using collections.Counter() 41
Going Further 42
Review 42
iii
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