pgstats - Population Genetics Statistics Toolkit

Installation

Requirements

• Python >=3.8, <3.13
• Dependencies: numba, numpy, xarray, zarr, scipy, pandas, dask, pyranges, bio2zarr

From Source

git clone https://github.com/SolomonAPS/pgstats.git
cd pgstats

# Create conda environment with dependencies
conda env create -f environment.yml
conda activate pgstats

# Install package
pip install -e .

# Verify installation
pgstats --version

Quick Start

Command-Line Interface

# Genome-wide statistics
pgstats stats input.vcf.gz --output results.csv

# Windowed analysis (100kb windows, 50kb step)
pgstats stats input.vcf.gz --output results.csv \
    --window-size 100000 --step-size 50000

# With callable sites masking
pgstats stats input.vcf.gz --output results.csv \
    --bed non_callable.bed --window-size 50000

Python API

import pgstats as pg
from pgstats.core import GenomicDataset, WindowConfig

# Load VCF data
dataset = GenomicDataset("input.vcf.gz")

# Configure windowing
dataset.window_config = WindowConfig(
    window_size=100000,
    step_size=50000,
    min_variants=10
)

# Create windows and calculate statistics
dataset.create_windows()
results = dataset.calculate_windowed_stats(
    stats=['tajima_d', 'theta_pi', 'theta_w']
)

# Save results
dataset.save_results("results.csv")