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  optional arguments: -h, --help show this help message ...