Re-evaluating Introgression site Patterns Through Ancestral alleles

NOTE: This is a beta version of RIPTA and is subject to change, all equations implemented are described in appendix/RIPTA-equations.pdf and the weighted-block Jackknife procedure is described in appendix/RIPTA-weighted-block-jackknife-procedure.pdf. If you have any questions or feature requests, please leave a detailed issue. If you use RIPTA in your work, please cite doi: https://doi.org/10.1101/2022.12.02.518851.

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Installation

These steps only need to be performed once.

1. Create the virtual environment

python -m venv RIPTA
source RIPTA/bin/activate

2. Install all dependencies

python -m pip install -r requirements.txt

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Usage

Command line

source RIPTA/bin/activate
ripta --yaml_path config.yaml

Python

from ripta import read_config, process_vcfs, compile_results

config = read_config("config.yaml")
blocks = process_vcfs(config)
compile_results(config, blocks)