pepkio-hwe-equilibrium-studio 0.1.0

Python client for Hardy-Weinberg equilibrium testing and simulation via the Pepkio API

Pepkio HWE Equilibrium Studio

Call the Pepkio hwe-equilibrium-studio REST API from Python to test multiallelic Hardy-Weinberg equilibrium and run Wright-Fisher allele-frequency simulations.

What It Does

Population genetics QC and teaching workflows need chi-square and exact HWE tests for loci with 2–6 alleles, plus optional Wright-Fisher simulation under selection, drift, mutation, and migration. Rebuilding multinomial expected counts and Guo-Thompson exact tests in a notebook for each locus is slow and error-prone.

This package submits genotype counts, allele frequencies, or biallelic disease incidence to the same Pepkio Tools engine as the hosted HWE Equilibrium Studio web calculator. It returns observed-vs-expected genotypes, chi-square and exact p-values, inbreeding F, plain-language verdicts, simulator trajectories, and shareable run permalinks.

Programmatic runs require a network connection and a Pepkio API key. Calculations are not bundled for offline use.

Features

• Calculator: genotype_counts, allele_frequencies (expected only), or carrier_incidence (biallelic q² → 2pq)
• 2–6 alleles with scalable genotype keys (A1_A1, A1_A2, …)
• Chi-square and Guo-Thompson exact p-values; exact primary when expected counts < 5
• Inbreeding coefficient F and structured verdict
• Simulator: selection, drift (Ne), mutation, migration; 1–10000 generations
• Manifest examples: mn_blood_group, cystic_fibrosis_carrier, triallelic_counts, simulator_fixation, and more
• CLI: pepkio-hwe-equilibrium-studio manifest and run
• Configuration via PEPKIO_API_KEY, LOCAL_PEPKIO_API_KEY, and PEPKIO_API_BASE_URL

Installation

pip install pepkio-hwe-equilibrium-studio

Set an API key with tools:run scope before calling run():

export PEPKIO_API_KEY="your-key"

Create a key in your Pepkio account API keys settings.

Quick Example

from pepkio_hwe_equilibrium_studio import PepkioClient

with PepkioClient() as client:
    inp = client.get_example_input("mn_blood_group")
    result = client.run(inp)
    stats = result.result["stats"]
    print(result.permalink)
    print("chi-square p:", stats["chi_square_p"])
    print("verdict:", result.result["verdict"]["title"])

CLI:

pepkio-hwe-equilibrium-studio run --example mn_blood_group

Manifest inspection does not require an API key.

Typical Use Cases

• HWE test for a microsatellite or multiallelic SNP locus from genotype counts
• Carrier frequency from disease incidence (e.g. 1 in 2500 recessive incidence)
• Triallelic or higher-allele contingency tables without hand-built spreadsheets
• Wright-Fisher drift and selection simulations for teaching
• Automated reanalysis of genotype tables in notebooks or CI

Scientific Background

Under Hardy-Weinberg equilibrium, expected genotype frequencies follow the multinomial expansion from allele frequencies (biallelic: p² + 2pq + q² = 1). Chi-square goodness-of-fit uses df = k(k+1)/2 − k for k alleles. Guo-Thompson exact tests are preferred when expected counts are sparse. F = 1 − H_obs/H_exp measures inbreeding deviation. The simulator uses a discrete-generation Wright-Fisher model.

Web Application

For researchers who prefer a graphical interface, an interactive HWE Equilibrium Studio is available in the browser.

The web interface adds De Finetti ternary plots (2–3 alleles), bar charts (4+ alleles), observed-vs-expected tables, dynamic equation display, PNG/SVG export, CSV download, copy-ready methods text, animated simulator trajectories, and shareable permalinks.

Documentation and Resources

Source code and issue tracking: github.com/pepkio/pepkio-hwe-equilibrium-studio

Web calculator: pepkio.com/tools/hwe-equilibrium-studio

About Pepkio

Pepkio develops software tools and provides bioinformatics analysis services for life science research. See pepkio.com for additional calculators and analysis services.

Keywords

Hardy-Weinberg equilibrium, HWE test, multiallelic HWE, population genetics, Guo-Thompson exact test, inbreeding coefficient F, Wright-Fisher simulation, carrier frequency 2pq, genotype counts expected, chi-square Hardy-Weinberg, allele frequency drift, effective population size Ne, microsatellite HWE QC, MN blood group HWE, pepkio-hwe-equilibrium-studio, Python HWE API, REST API population genetics, disease incidence carrier risk, triallelic Hardy-Weinberg test, how to test Hardy-Weinberg for three alleles Python, carrier frequency from 1 in 2500 incidence API, multiallelic genotype HWE without R, Wright-Fisher selection drift simulation script, exact test when expected count below 5, automate Hardy-Weinberg notebook Pepkio, share HWE analysis permalink, population genetics teaching Hardy-Weinberg CLI