This provides a basic Python API for pgenlib (See python_api.txt for details.)

Build instructions

To build from GitHub, 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
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 0.90.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pgenlib 0.90.0
File Size Uploaded
Pgenlib-0.90.0.tar.gz 1.1 MB Details

Built distributions (wheels)

Table of built distributions (wheels) for pgenlib 0.90.0
File
Pgenlib-0.90.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 414.9 kB PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 415.9 kB PyPy 3.8 PyPy 3.8 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 421.0 kB PyPy 3.7 PyPy 3.7 7.3 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.0-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-0.90.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.5 MB CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.0-cp310-cp310-macosx_13_0_arm64.whl 383.0 kB CPython 3.10 CPython 3.10 macOS 13.0+ ARM64 Details
Pgenlib-0.90.0-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-0.90.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.6 MB CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
Pgenlib-0.90.0-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-0.90.0-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: 18.1 MB

Release files / Pgenlib-0.90.0.tar.gz

Download URL Pgenlib-0.90.0.tar.gz
Size 1.1 MB
Tags Source
SHA-256 checksum
How to use checksums 		c39dcd824e6cb5445915b64345b63aafe69b4a01ae39118799e8c4182481031d
BLAKE2b-256 checksum
How to use checksums 		dc263150424408411a6f326db5b2f61a5accf900dfe3d287f4452e73d62b0b01
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.10.9

Release files / Pgenlib-0.90.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 414.9 kB
Tags Linux glibc 2.17+ x86-64 PyPy 3.9 PyPy 3.9 7.3
SHA-256 checksum
How to use checksums 		adc48ab98cb70e9c303cb7764d0cc7d416acac9de0d164b756514797ad64a2e6
BLAKE2b-256 checksum
How to use checksums 		4560dd584321eedc419f7b1aee92fc15110070714ca949ee012bf5dddffec6cf
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 415.9 kB
Tags Linux glibc 2.17+ x86-64 PyPy 3.8 PyPy 3.8 7.3
SHA-256 checksum
How to use checksums 		2f279914c09a7721479efc775313af204490016266f2b25fff5d09e6c5900b4f
BLAKE2b-256 checksum
How to use checksums 		05cc185166c604f18f1d60291fd0d407d6c02b26e712af8e39bfaabfe9be57ce
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 421.0 kB
Tags Linux glibc 2.17+ x86-64 PyPy 3.7 PyPy 3.7 7.3
SHA-256 checksum
How to use checksums 		1e63d5f3b7fc91cbf3f9f70afc866525e040e253144990d1411323c11a903b19
BLAKE2b-256 checksum
How to use checksums 		f3b001e1c04e3fe156252d1ebb82f362da5642a128d72c5a67c481b26986d450
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.6 MB
Tags CPython 3.11 Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		bb2c64c50511141161674d5b568e054f0e012b3bd2d8f21c829aa3f34f11c6c0
BLAKE2b-256 checksum
How to use checksums 		95af14f03aa5e6568810347aef280eb57b82a5a45e03f33c9653d56685a5157c
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.5 MB
Tags CPython 3.10 Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		d124da3e8ab9ad66a0248e664502fb110c87acece1ea5826844da8361415c6ac
BLAKE2b-256 checksum
How to use checksums 		4345b23b200529cc05e27de60c6623e3c272f3babacd46ba7ca04f8ba8cee212
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp310-cp310-macosx_13_0_arm64.whl

Download URL Pgenlib-0.90.0-cp310-cp310-macosx_13_0_arm64.whl
Size 383.0 kB
Tags CPython 3.10 macOS 13.0+ ARM64
SHA-256 checksum
How to use checksums 		de846a2c389cadb6c098603f736c44f8f6d7c6356a54bd4855004c7a8ed7a288
BLAKE2b-256 checksum
How to use checksums 		16245e5f3f751fc014e67c567073089e5ff22887c890ddcb33b2eee234b2ff66
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.10.9

Release files / Pgenlib-0.90.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.6 MB
Tags CPython 3.9 Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		89f22566a61bca2e12acab41a389ab353c4853fa55994704d81d112a1d4782da
BLAKE2b-256 checksum
How to use checksums 		da25eef614e9ea13964aed3aa93211d44fc0a53591fe59901def7f0842c26259
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.6 MB
Tags CPython 3.8 Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		165c46b7c3c6dea1533f80baac3354e38abe6c897d8a56c27ff34fb5a2866734
BLAKE2b-256 checksum
How to use checksums 		7f7503cbd46f9f1cb21c22745c4548f85b5e548b1e5a5cbb4d69064f111c3f77
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.5 MB
Tags CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		1e3088375ca0fe3c1d87d0d1cb43a3a950c78a7ef5fc5ea4f6ae18ed32756fa3
BLAKE2b-256 checksum
How to use checksums 		4b623d03109e3a79b4981cde01c00f7d63b2f850599d3b4c06125e0561b0dbd7
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release files / Pgenlib-0.90.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL Pgenlib-0.90.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size 2.5 MB
Tags CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.17+ x86-64
SHA-256 checksum
How to use checksums 		53c638d30126b4cfddda0968b9734748c66fb1b33c615bec68ae97dd4c618548
BLAKE2b-256 checksum
How to use checksums 		59d67157c61da0ebb0d2f05ba178ef1c57e567054192e47153ea29952de377c9
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/4.0.2 CPython/3.11.2

Release history Release notifications | RSS feed

0.95.1

16 release files

0.95.0

16 release files

0.94.1

16 release files

0.94.0

16 release files

0.93.0

19 release files

0.92.1

19 release files

0.92.0

8 release files

0.91.0

22 release files

0.90.2

10 release files

0.90.1

10 release files

This release

0.90.0 This release

11 release files

0.83.0

11 release files

0.82.1

10 release files

0.82.0

1 release file

0.81.3

1 release file

0.81.2

2 release files

0.81.1

1 release file

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page