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.
1 maintainer
Metadata
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Release files for pgenlib 0.91.0
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-0.91.0.tar.gz | 1.3 MB | Details |
Built distributions (wheels)
Total release size: 40.2 MB
Release files / pgenlib-0.91.0.tar.gz
| Download URL | pgenlib-0.91.0.tar.gz |
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| Size | 1.3 MB |
| Tags | Source |
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Release files / Pgenlib-0.91.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / Pgenlib-0.91.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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