Pgenlib 0.92.0

Python wrapper for pgenlib's basic reader and writer.

This provides a basic Python API for pgenlib; see python_api.txt for details.

Build instructions

PyPI:

pip install 'pip>=20.3'
pip install Pgenlib

To build from GitHub instead, clone the repository:

# clone repo
git clone https://github.com/chrchang/plink-ng
# go to python folder
cd plink-ng/2.0/Python

Then install Cython and NumPy:

pip3 install "cython>=0.29.21" "numpy>=1.19.0"

and then build and install the package

python3 setup.py build_clib build_ext -i
python3 setup.py install

You can test the package with pytest.

Example usage:

#write a 2 sample file
import numpy as np
import pgenlib as pg

with pg.PgenWriter("test.pgen".encode("utf-8"), 2, variant_ct=3, nonref_flags=False) as writer:
	writer.append_alleles(np.array([0,1,1,1],dtype=np.int32))
	writer.append_alleles(np.array([0,1,0,0],dtype=np.int32))
	writer.append_alleles(np.array([0,0,0,0],dtype=np.int32))

See tests/test_pgenlib.py for more sophisticated examples.