admixture 0.0.2

Python wrapper around OpenADMIXTURE.jl

admixture

A Python wrapper around OpenADMIXTURE.jl from the OpenMendel project.

This package is not the original OpenADMIXTURE implementation and does not reimplement the algorithm. It validates inputs, launches Julia, runs OpenADMIXTURE.jl, and parses the resulting files into Python objects.

OpenADMIXTURE.jl is a separate upstream Julia package for maximum-likelihood ancestry estimation on binary PLINK 1 BED datasets. Users install OpenADMIXTURE.jl separately in their Julia environment; this Python package does not vendor or relicense OpenADMIXTURE.jl.

Why this package exists

Many genomics workflows are Python-based, while OpenADMIXTURE.jl provides the core ancestry-inference implementation in Julia. This package provides a small Python layer for:

• validating a PLINK .bed/.bim/.fam prefix;
• building a cross-platform Julia subprocess command without shell=True;
• capturing stdout/stderr and surfacing helpful errors;
• parsing .Q ancestry proportions and .P allele frequencies into pandas.DataFrame objects.

Installation from PyPI

pip install admixture
admixture setup

The wheel includes a Julia project under the Python package at admixture/julia-env. admixture setup runs Pkg.instantiate() for that packaged project.

Installation for development

This repository uses conda and Poetry together. Conda provides the base Python environment and common compiled packages; Poetry installs the project. juliaup is included in the conda environment. Use it to install/select a Julia runtime inside makim setup.install.

conda env create -f conda/dev-linux.yaml
conda activate admixture
poetry config virtualenvs.create false
makim setup.install

Use the environment file for your operating system:

• Linux: conda/dev-linux.yaml
• macOS: conda/dev-macos.yaml
• Windows: conda/dev-win.yaml

makim setup.install runs poetry install --with dev and then instantiates the packaged Julia project.

For a pip-style editable install inside the activated conda environment:

pip install -e ".[dev]"

Documentation

Documentation lives in docs/ and uses Quarto. The conda environment includes the Quarto CLI.

Render the site with Makim:

makim docs.build

Preview while editing with:

makim docs.preview

Direct Quarto commands also work when your temp/cache directories are writable:

quarto render docs
quarto preview docs

Generated documentation output is written to docs/_site/ and is ignored by Git.

Julia and OpenADMIXTURE.jl setup

Julia is an external runtime, not a Python dependency. The development conda environments include juliaup, a cross-platform Julia installer and version manager from conda-forge:

juliaup add release
juliaup default release
julia --version

The conda environment files in this repository include juliaup instead of the old julia conda package because juliaup is available on Linux, macOS, and Windows. If you are not using the provided conda environment files, install it with conda install -c conda-forge juliaup first.

For non-conda installs, the official Julia installer from https://julialang.org/downloads/ is also supported as long as julia is on PATH.

The Python package ships a Julia project with Project.toml and Manifest.toml. Instantiate it with:

admixture setup

From Poetry, run poetry run admixture setup.

Or bootstrap from Python:

import admixture

project_dir = admixture.setup()

admixture.setup() and admixture setup never modify the global Julia environment. OpenAdmixtureRunner() always uses the packaged Julia project. OpenAdmixtureRunner(install_if_missing=True) is also available for explicit opt-in instantiation during a run.

Basic usage

from admixture import OpenAdmixtureRunner

runner = OpenAdmixtureRunner(
    julia="julia",
    install_if_missing=False,
)

result = runner.run(
    bfile="data/example",
    k=3,
    out_prefix="results/example_k3",
    seed=42,
    threads=4,
)

print(result.q)          # ancestry proportions, individuals x K
print(result.p)          # allele frequencies, if produced
print(result.metadata)   # paths and runtime metadata

Convenience function:

from admixture import run_openadmixture

result = run_openadmixture(
    bfile="data/example",
    k=3,
    out_prefix="results/example_k3",
    seed=42,
    threads=4,
)

Input format

Pass a binary PLINK prefix. For these files:

data/example.bed
data/example.bim
data/example.fam

use:

bfile="data/example"

Passing data/example.bed is normalized to the same prefix when safe.

Output

The wrapper writes and discovers common ADMIXTURE-style outputs:

<out_prefix>.Q
<out_prefix>.P
<out_prefix>.log

The returned OpenAdmixtureResult contains:

• result.q: ancestry proportions as a pandas.DataFrame;
• result.p: allele-frequency matrix as a pandas.DataFrame, or None;
• result.q_path, result.p_path, result.log_path;
• result.stdout and result.stderr from Julia;
• result.metadata with runtime and input-file metadata.

Platform support

The wrapper is designed for Linux, macOS, and Windows. It uses pathlib, shutil.which, and subprocess.run(..., shell=False) so paths with spaces are passed safely as single arguments.

Windows notes

PowerShell example:

conda env create -f conda/dev-win.yaml
conda activate admixture
juliaup add release
juliaup default release
julia --version
poetry config virtualenvs.create false
poetry install --with dev

If Julia is not on PATH, pass the executable explicitly:

runner = OpenAdmixtureRunner(
    julia=r"C:\Users\you\AppData\Local\Programs\Julia-1.11.0\bin\julia.exe"
)

The Windows conda environment does not include the Google Cloud CLI. To run manual malariagen-data experiments against Google Cloud Storage on Windows, install Google Cloud CLI with the official Windows installer, open a new terminal, and then authenticate:

(New-Object Net.WebClient).DownloadFile(
  "https://dl.google.com/dl/cloudsdk/channels/rapid/GoogleCloudSDKInstaller.exe",
  "$env:Temp\GoogleCloudSDKInstaller.exe"
)
& "$env:Temp\GoogleCloudSDKInstaller.exe"
gcloud auth application-default login

Paths with spaces are passed as separate subprocess arguments, not through a shell command string.

Troubleshooting

Julia not found

Install Julia from https://julialang.org/downloads/ or pass the executable path to OpenAdmixtureRunner(julia=...).

OpenADMIXTURE.jl not installed

Run admixture setup to instantiate the packaged Julia project.

Missing PLINK files

Ensure the .bed, .bim, and .fam files all exist and are non-empty. Pass the shared prefix, not a directory.

Output files not found

Check result.stdout/result.stderr or the raised exception. Remove stale outputs if multiple candidate .Q files match the same output prefix.

OpenADMIXTURE runtime tests

Runtime tests require all of:

• Julia on PATH;
• OpenADMIXTURE.jl installed;

These tests fail if Julia or OpenADMIXTURE.jl is unavailable. The default runtime test uses a tiny local PLINK data set and does not read from Google Cloud Storage.

The malariagen-data compatibility test is development-only, skips on Python 3.13+, and imports malariagen_data inside the test only, so the package does not gain a production dependency on malariagen-data.

For manual experiments against real MalariaGEN data on Google Cloud Storage, you need access to the relevant bucket and Google Cloud Application Default Credentials. Authenticate locally with:

makim gcloud.auth

For non-interactive local runs with a service-account JSON key:

export GOOGLE_APPLICATION_CREDENTIALS=/path/to/service-account.json

For custom GitHub Actions workflows that need real MalariaGEN-GCS access, set the GOOGLE_CREDENTIALS repository secret to a service-account JSON key with access to MalariaGEN data on Google Cloud Storage. A Google API key is not sufficient because malariagen-data uses Google Cloud Application Default Credentials for GCS. This is not required by the default CI test suite.

Run tests with:

makim tests.unit

Citation and attribution

If this wrapper helps your work, cite the upstream OpenADMIXTURE.jl project and paper:

• OpenADMIXTURE.jl: https://github.com/OpenMendel/OpenADMIXTURE.jl
• OpenMendel: https://openmendel.github.io/
• OpenADMIXTURE paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC9943729/

Roadmap

Version 0 focuses on one task: run OpenADMIXTURE.jl on an existing binary PLINK prefix and parse the result. Future work may add multi-K runs, multiple seeds, plotting helpers, and tighter integration with other genomics tools.