aortizsax / nyemtaay

Nyemtaay is a CLI python package for calcuating pop-gen stats and information theory metrics from fasta files.

Nyemtaay

Introduction

Nyemtaay is a python library for population genetics caluclations. The name nyemtaay is from a Kumeyaay (Ipai) word for "cougar", in homage to the inigenous peole of Southern California, on whose land we live and wok.

Requirements and Installation

Nyemtaay runs under python3 (>3.9)

We recommend that you install directly from the main GitHub repository using pip (which works with an Anaconda environment as well):

$ python3 -m pip install --user --upgrade git+https://github.com/aortizsax/nyemtaay.git

Applications

Below I will outline the applications icluding traditional popgen stats, information theory analysis, and tissue of origin for a cancer dataset.

Once cloned locally, check the help page

nyemtaay -h

Information Theory

The greek bears data will be used to show the functionality of Nyemtaay.

Normailzed JSD

cd nyemtaay/tests/testdata/greekbears
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc norm-jsd -dm

Directionality

nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc directionality -dm

Partitioning based on normailzed JSD

nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc norm-jsd-cluster -dm

Overlay of both Partitioning and Directionality

nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc directionality norm-jsd-cluster -dm

Population Genetics

nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc nei-fst