Mastering Python for Bioinformatics

Chapter 14. Finding Open Reading Frames

The ORF challenge is the last Rosalind problem I’ll tackle in this book. The goal is to find all the possible open reading frames (ORFs) in a sequence of DNA. An ORF is a region of nucleotides between the start codon and the stop codon. The solution will consider both the forward and reverse complement as well as frameshifts. Although there are existing tools such as TransDecoder to find coding regions, writing a bespoke solution brings together many skills from previous chapters, including reading a FASTA file, creating the reverse complement of a sequence, using string slices, finding k-mers, using multiple for loops/iterations, translating DNA, and using regular expressions.

You will learn:

• How to truncate a sequence to a length evenly divisible by a codon size

• How to use the str.find() and str.partition() functions

• How to document a regular expression using code formatting, comments, and Python’s implicit string concatenation

Getting Started

The code, tests, and solutions for this challenge are located in the 14_orf directory. Start by copying the first solution to the program orf.py:

$ cd 14_orf/
$ cp solution1_iterate_set.py orf.py

If you request the usage, you’ll see the program takes a single positional argument of a FASTA-formatted file of sequences:

$ ./orf.py -h
usage: orf.py [-h] FILE

Open Reading Frames

positional arguments:
  FILE        Input FASTA file

optional arguments:
  -h, --help  show this help message and exit

The first ...