scikit-bio

name	scikit-bio
description	Count k-mers (subsequences of length k) in DNA sequences. Use when counting DNA k-mers, analyzing sequence composition, or computing k-mer frequency distributions.

scikit-bio: DNA K-mer Counting

Overview

Given a DNA sequence, count occurrences of all k-mers (subsequences of length k). Output k-mers with count > 0, sorted alphabetically.

K-mer Counting

from skbio import DNA

# Read DNA sequence from file
with open("/root/input.txt") as f:
    seq_str = f.read().strip()

# Create DNA sequence object
dna = DNA(seq_str)

# Count k-mers (k=3 for 3-mers)
kmers = dna.kmer_frequencies(k=3)

# Sort by k-mer alphabetically
for kmer in sorted(kmers.keys()):
    count = kmers[kmer]
    print(f"{kmer}: {count}")

K-mer Frequencies

# Get all k-mers of length k
kmers = dna.kmer_frequencies(k=3)

# Returns dict: {'AAA': 3, 'AAC': 1, ...}
# Each k-mer appears count times in sequence

# For overlapping k-mers (sliding window)
# Default behavior: overlapping counts

# Non-overlapping k-mers
# Not directly supported; use step parameter if available

Output Format

For each k-mer with count > 0:

AXXXXXXXXXX: count

Sorted alphabetically by k-mer name.

with open("/root/output.txt", "w") as f:
    for kmer in sorted(kmers.keys()):
        f.write(f"{kmer}: {kmers[kmer]}\n")

Key Reference

• DNA(sequence_string) — Create DNA sequence object
• dna.kmer_frequencies(k=N) — Count all k-mers of length N
• sorted(dict.keys()) — Get k-mers in alphabetical order
• Only k-mers with count > 0 are returned in the dict