Question

This question is actually for DNA codon analysis, to put it in a simple way, let’s say I have a file like this:
atgaaaccaaag…
and I want to count the number of ‘aaa’ triplet present in this file. Importantly, the triplets start from the very beginning (which means atg,aaa,cca,aag,…) So the result should be 1 instead of 2 ‘aaa’ in this example.
Is there any Python or Shellscript methods to do this? Thanks!

Answer 1

first readin the file

with open("some.txt") as f:
    file_data = f.read()

then split it into 3’s

codons = [file_data[i:i+3] for i in range(0,len(file_data),3)]

then count em

print codons.count('aaa')

like so

>>> my_codons = 'atgaaaccaaag'
>>> codons = [my_codons[i:i+3] for i in range(0,len(my_codons),3)]
>>> codons
['atg', 'aaa', 'cca', 'aag']
>>> codons.count('aaa')
1