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
GitHub:
pip install 'pip>=20.3'
pip install -e 'git+https://github.com/chrchang/plink-ng.git#egg=Pgenlib&subdirectory=2.0/Python'
Or install from a cloned copy:
# clone repo
git clone https://github.com/chrchang/plink-ng
# go to python folder
cd plink-ng/2.0/Python
# install the package
pip install -e .
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.
1 maintainer
Release files for Pgenlib 0.94.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pgenlib-0.94.1.tar.gz | 1.6 MB | Details |
Built distributions (wheels)
Total release size: 42.6 MB
Release files / pgenlib-0.94.1.tar.gz
| Download URL | pgenlib-0.94.1.tar.gz |
|---|---|
| Size | 1.6 MB |
| Tags | Source |
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