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Mastering Python for Bioinformatics
book

Mastering Python for Bioinformatics

by Ken Youens-Clark
May 2021
Intermediate to advanced content levelIntermediate to advanced
454 pages
10h 42m
English
O'Reilly Media, Inc.
Content preview from Mastering Python for Bioinformatics

Chapter 12. Inferring mRNA from Protein: Products and Reductions of Lists

As described in the Rosalind mRNA challenge, the goal of this program is to find the number of mRNA strings that could produce a given protein sequence. You’ll see that this number can become exceedingly large, so the final answer will be the remainder after dividing by a given value. I hope to show that I can turn the tables on regular expressions by trying to generate all the strings that could be matched by a particular pattern. I’ll also show how to create the products of numbers and lists as well as how to reduce any list of values to a single value, and along the way I’ll talk about some memory issues that can cause problems.

You will learn:

  • How to use the functools.reduce() function to create a mathematical product() function for multiplying numbers

  • How to use Python’s modulo (%) operator

  • About buffer overflow problems

  • What monoids are

  • How to reverse a dictionary by flipping the keys and values

Getting Started

You should work in the 12_mrna directory of the repository. Begin by copying the first solution to the program mrna.py:

$ cd 12_mrna/
$ cp solution1_dict.py mrna.py

As usual, inspect the usage first:

$ ./mrna.py -h
usage: mrna.py [-h] [-m int] protein

Inferring mRNA from Protein

positional arguments:
  protein               Input protein or file 1 optional arguments: -h, --help show this help message ...
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Publisher Resources

ISBN: 9781098100872Errata PageSupplemental Content