Counting DNA Nucleotides

This is the very first problem on the website in the “Bioinformatics Stronghold” category. As expected we are starting fairly light.


We receive a DNA string consisting of the letters A, C, G and T and are asked to count the occurrence of each letter.

The sample dataset looks as follows:


with the solution for it being 20 12 17 21.


Since the dataset comes in the form of a file we first need to read it

data = open("rosalind_dna.txt").read()

then remove any extraneous whitespace

data = data.strip()

and finally we can use a defaultdict as a simple structure to store character counts.

from collections import defaultdict

counts = defaultdict(int)
for ch in data:
  counts[ch] += 1

print(f"{counts['A']} {counts['C']} {counts['G']} {counts['T']}")

The defaultdict uses an int as a default type for missing keys and since the default for int is 0 we can += on it.

Protip: Instead of using a defaultdict here, Python also comes with a special Counter collection that is made for, well, counting things.

The code could be simplified to:

from collections import Counter

data = open("rosalind_dna.txt").read()
data = data.strip()
cnt = Counter(data)
print(" ".join([str(c[k]) for k in sorted(c.keys())]))