Python bindings

Python bindings (pykmertools)

Overview

kmertools exposes Python bindings through the module pykmertools. The public API is exported from kmertools/conda/src/lib.rs and includes:

• OligoComputer
• CgrComputer
• KmerGenerator
• MinimiserGenerator
• utils (to_numeric, to_acgt)

These bindings are available when you install from:

• pip install pykmertools
• conda install -c bioconda kmertools

Quick start

import pykmertools as kt
from pykmertools import utils as ktutils

print(kt.__doc__)
print(ktutils.to_numeric("ACGTT"))  # (111, 27)
print(ktutils.to_acgt(111, 5))      # ACGTT

API guide

• Detailed API reference: Python bindings reference
• Runnable examples: Python bindings examples
• API-based plotting examples (CGR): Python bindings examples

Notes

• DNA alphabet handling is mostly A/C/G/T/U (case-insensitive).
• CgrComputer is strict and raises ValueError on invalid bases.
• KmerGenerator, MinimiserGenerator, and OligoComputer skip windows crossing ambiguous bases.
• utils.to_numeric(kmer) currently enforces len(kmer) <= 32.