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
Metadata
1 maintainer
Release files for pgenlib 0.93.0
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-0.93.0.tar.gz | 1.4 MB | Details |
Built distributions (wheels)
Total release size: 36.8 MB
Release files / pgenlib-0.93.0.tar.gz
| Download URL | pgenlib-0.93.0.tar.gz |
|---|---|
| Size | 1.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
b51c2aa6099c76bc7d77021d107146cd90a6e40f22bf3b703527a7cf07213794
|
|
BLAKE2b-256 checksum How to use checksums |
fdb523eb6aa256128c83ae1792cadcf387b834671c8ce2de41d9c1ccd845e70b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pgenlib-0.93.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 3.1 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
cf1e6f96e297d09998fbdec618a72b92d2f78e9e8a0d31b657ab00c34110224e
|
|
BLAKE2b-256 checksum How to use checksums |
7bf84d7cc7f49631c00a4733e804c89f2d9e7962c8d50e53e69e89fc3ff5b3fa
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | pgenlib-0.93.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
74de2ff2d6d4e6bc36be16f06aa8e289f775901f66dc4a70062c5aabcfc4b697
|
|
BLAKE2b-256 checksum How to use checksums |
644c35b09ee6a5ab9f6cd06f13827c28dca53f6f621b573683ba301451560e23
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp313-cp313-macosx_10_13_universal2.whl
| Download URL | pgenlib-0.93.0-cp313-cp313-macosx_10_13_universal2.whl |
|---|---|
| Size | 896.7 kB |
| Tags | CPython 3.13 macOS 10.13+ universal2 (ARM64, x86-64) |
|
SHA-256 checksum How to use checksums |
2451d5011989e769ff65e36b43523eb025a3f756709f65abddae38b37f434b7e
|
|
BLAKE2b-256 checksum How to use checksums |
83769239a5d35d3d31f8250bb7e60cc0c5ef6ab2fb1c4ab3cb28b31d3104ee70
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pgenlib-0.93.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 3.1 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
3f027e36a633b0a5da9abea2c130ab9517895ed19665b5b847aae44a13c4de95
|
|
BLAKE2b-256 checksum How to use checksums |
96b2b5d342944cce1cd9ea4dd4ba16e70f77d99a915137bbb364e0bbc188f2a1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | pgenlib-0.93.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
684a12a0d724d24db06797dbbd8db4fd91419116bca8eb23076ee46cf9a46990
|
|
BLAKE2b-256 checksum How to use checksums |
6cdac3077ab9f29764abd20298a9a5fcc6d3458c446a75043f1c9e1cddde63be
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp312-cp312-macosx_10_13_universal2.whl
| Download URL | pgenlib-0.93.0-cp312-cp312-macosx_10_13_universal2.whl |
|---|---|
| Size | 898.7 kB |
| Tags | CPython 3.12 macOS 10.13+ universal2 (ARM64, x86-64) |
|
SHA-256 checksum How to use checksums |
5666bee17c1d8edb86f6f6878582877ad72be99a4857795acd2dda07ff992eaf
|
|
BLAKE2b-256 checksum How to use checksums |
8a7d684fa89ae48c2b61fdfb91ec576ba044b08a7dd65f11e06d21a692e21adf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pgenlib-0.93.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
bfc3baf2f1892ec1d0f18f1df5b73199b9ff3a482a9ffbd3a3e5ab746c3f9b73
|
|
BLAKE2b-256 checksum How to use checksums |
38be8f232caaabc024de6746363e8171fd354b55299f09e54071ee035b83dab4
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | pgenlib-0.93.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
84372c62c8c1cabf6ec6fd72f5a721da93c7a2869468e34ed0839ed3ef5a075e
|
|
BLAKE2b-256 checksum How to use checksums |
ec1339a59cd5778de12940d3e39771d15a0fabee4981417b48e83307098d5567
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp311-cp311-macosx_10_9_universal2.whl
| Download URL | pgenlib-0.93.0-cp311-cp311-macosx_10_9_universal2.whl |
|---|---|
| Size | 909.9 kB |
| Tags | CPython 3.11 macOS 10.9+ universal2 (ARM64, x86-64) |
|
SHA-256 checksum How to use checksums |
634ae9f3059f80a3d41bf285edf56fb0cbc5b069b0ff27088964a613e0a435fa
|
|
BLAKE2b-256 checksum How to use checksums |
79154729d89f42bb6b60eaaffd37226111e5e9c7dd33ba2901fb34c457f0c43d
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pgenlib-0.93.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
bc29b5e6aaa4b7a3dd34be7c8e8e377bbd25ab68959b08bc49bab587b5009a7b
|
|
BLAKE2b-256 checksum How to use checksums |
0677e580c19e0fb183c9c8a4ecac294e158e3aa79e81746d62faf0ce2292484f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | pgenlib-0.93.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
7b0607a2e85bf54a61c826140a84d4ccbf6c79be341a91efdf123b723462ada7
|
|
BLAKE2b-256 checksum How to use checksums |
26252715613beb8240484fc323ec48e2c90dc5d2852c57dcf8d1fc6035c15eeb
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp310-cp310-macosx_10_9_universal2.whl
| Download URL | pgenlib-0.93.0-cp310-cp310-macosx_10_9_universal2.whl |
|---|---|
| Size | 898.6 kB |
| Tags | CPython 3.10 macOS 10.9+ universal2 (ARM64, x86-64) |
|
SHA-256 checksum How to use checksums |
74a02b09cc907be1c7d6f99cc2df0274d556b072bceb79123772660078d395fd
|
|
BLAKE2b-256 checksum How to use checksums |
9818291d0d5a6eb661f34ee84835050e4cd5b96951e405468c0de285d2959873
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pgenlib-0.93.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
d311bc4ae0e4cef24d3a7c9d7b6cc1aad6048b2b1e9074e94531a21a45d34add
|
|
BLAKE2b-256 checksum How to use checksums |
a1e05429f3c11aea15d7ca474956a2c988f36f647886680c53a5534ccde52b44
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | pgenlib-0.93.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
5ddacea458924268b9b71a690b4d8e6bb3cfd0626518805ad938232432d13f9c
|
|
BLAKE2b-256 checksum How to use checksums |
e5ab39e25c49ddd1397739d7c008e698ba4a46a934e79564f721f6501c420fd9
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / pgenlib-0.93.0-cp39-cp39-macosx_10_9_universal2.whl
| Download URL | pgenlib-0.93.0-cp39-cp39-macosx_10_9_universal2.whl |
|---|---|
| Size | 899.9 kB |
| Tags | CPython 3.9 macOS 10.9+ universal2 (ARM64, x86-64) |
|
SHA-256 checksum How to use checksums |
87c1bc26bf251a147ff1eb2b9fe2aa52ee416b3e2fdad82797a28c45fd40b6e3
|
|
BLAKE2b-256 checksum How to use checksums |
72831c5b5861fa9ba4a87ad55f3889be86fd4190094fdb35f207197e905f4d37
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / Pgenlib-0.93.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | Pgenlib-0.93.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 451.4 kB |
| Tags | Linux glibc 2.17+ x86-64 PyPy 3.11 PyPy 3.11 7.3 |
|
SHA-256 checksum How to use checksums |
02756b246b72164799380ceaf6f93d0623e6df5be039be2fb7c4f1133337fcdf
|
|
BLAKE2b-256 checksum How to use checksums |
f34cfc297297d6caa1b2e044b62445c0c24cf2bc9327d9ba0e763b6db325c4a5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / Pgenlib-0.93.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | Pgenlib-0.93.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 446.3 kB |
| Tags | Linux glibc 2.17+ x86-64 PyPy 3.10 PyPy 3.10 7.3 |
|
SHA-256 checksum How to use checksums |
f7e72703474ccb9f28bf9db2021a4d728e4bcbcd6693f3140d5d572626089b71
|
|
BLAKE2b-256 checksum How to use checksums |
52d8b482e2a3b502ea38ec411432df1e11dd317fc97227ccc301674b5cf0f795
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency logRelease files / Pgenlib-0.93.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | Pgenlib-0.93.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 446.7 kB |
| Tags | Linux glibc 2.17+ x86-64 PyPy 3.9 PyPy 3.9 7.3 |
|
SHA-256 checksum How to use checksums |
63a49f76ceb597321e2ef5857d13e6955d3642e0a05de23c3351eef3011571cf
|
|
BLAKE2b-256 checksum How to use checksums |
44131f15c3e8e1c5e58fab90d83c15a09f5ea2424c4245f943e93d858d355c72
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jun 10, 2025.
Transparency log
