snputils 0.1.0

SNP utils

snputils

Installation

We recommend creating a fresh Python >= 3.8 conda environment. This package can be easily installed using pip after cloning the repository:

(base) $ conda create -n snputils python=3.10
(base) $ conda activate snputils
(snputils) $ git clone https://github.com/AI-sandbox/snputils.git && cd snputils
(snputils) $ pip install -e '.[testing,jupyter]'

Alternatively, you can install the package directly from the repository without cloning it:

(base) $ pip install git+https://github.com/AI-sandbox/snputils.git

Use snputils tools

PCA

To directly run Principal Component Analysis (PCA) on SNP data, plotting the results, and saving the principal components on a .npy file, simply call snputils pca with the required arguments, see snputils pca --help for more information.

An example of running PCA on a .vcf file, saving the plot in fig.png and the principal components in pc.npy:

> snputils pca --vcf_file /dataset/path/hapmap3.vcf --fig_path fig.png --npy_path pc.npy --backend sklearn