Python bindings Examples

Python bindings examples

All runnable Python examples are in ./examples/python. For completeness, this folder includes duplicated FASTA input data in:

• ./examples/python/data/cgr

Setup

Install bindings:

pip install pykmertools

Or via Bioconda:

conda install -c bioconda kmertools

Run each script from the repository root.

1. Utility conversion helpers

Script: utils_roundtrip.py

python kmertools.wiki/examples/python/utils_roundtrip.py

Shows:

• ACGT string -> (forward, reverse) numeric tuple
• numeric -> ACGT roundtrip

2. K-mer iterator API

Script: kmer_generator.py

python kmertools.wiki/examples/python/kmer_generator.py

Shows:

• iterating (forward, reverse) integer k-mers
• converting iterator output back to strings
• using kmer_pos_maps()

3. Minimiser iterator API

Script: minimiser_generator.py

python kmertools.wiki/examples/python/minimiser_generator.py

Shows:

• iterating (minimiser, start, end)
• mapping minimisers to sequence spans via seq[start:end]
• converting minimiser ints to strings with to_acgt

4. Oligonucleotide vectors

Script: oligo_vectors.py

python kmertools.wiki/examples/python/oligo_vectors.py

Shows:

• vectorise_one and vectorise_batch
• mins=True headers and top features
• raw forward-space vectors with mins=False

5. CGR vectors

Script: cgr_vectors.py

python kmertools.wiki/examples/python/cgr_vectors.py

Shows:

• sequence-to-CGR point conversion
• batch CGR conversion
• invalid-base error handling

6. Plot CGR using Python API from FASTA input

Script: cgr_api_plots.py

python kmertools.wiki/examples/python/cgr_api_plots.py

Inputs:

• ./examples/python/data/cgr/NC_001802.1.fasta

Outputs:

• cgr_scatter_from_api.png
• cgr_density_from_api.png

Simple plot conventions used:

• x-axis and y-axis are always labeled.
• colorbar is labeled for density plot.