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

Build instructions

PyPI: 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.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.95.1)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for chrchang523 from gravatar.com chrchang523

Credits

Author: Christopher Chang

License

GNU Lesser General Public License v3 (LGPLv3)

Requires

Python >=3.5

Classifiers

Report project as malware

Metadata

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.95.1)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for chrchang523 from gravatar.com chrchang523

Credits

Author: Christopher Chang

License

GNU Lesser General Public License v3 (LGPLv3)

Requires

Python >=3.5

Classifiers

Report project as malware

Release files for pgenlib 0.90.1

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Source distribution (sdist)

Source distribution for pgenlib 0.90.1
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Pgenlib-0.90.1.tar.gz 1.0 MB Details

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Table of built distributions (wheels) for pgenlib 0.90.1
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Pgenlib-0.90.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 416.2 kB PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 416.5 kB PyPy 3.8 PyPy 3.8 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 421.6 kB PyPy 3.7 PyPy 3.7 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.6 MB CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.6 MB CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.6 MB CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.7 MB CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.5 MB CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.5 MB CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.17+ x86-64 Details

Total release size: 17.9 MB

Release files / Pgenlib-0.90.1.tar.gz

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