VCFPy: a Python 3 library with good support for both reading and writing VCF

VCFPy: a Python 3 library with good support for both reading and writing VCF - Published in JOSS (2016)
https://github.com/bihealth/vcfpy

Keywords

bioinformatics file-format parsing vcf writing

Keywords from Contributors

variant-filtration ontology reproducibility batteries simulations genome pypi robot

Last synced: 2 months ago
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Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

Python 3 library with good support for both reading and writing VCF

Host: GitHub
URL: https://github.com/bihealth/vcfpy
Owner: bihealth
License: mit
Created: 2016-09-15T07:59:19.000Z (over 9 years ago)
Default Branch: main
Last Pushed: 2025-10-02T06:37:31.000Z (3 months ago)
Last Synced: 2025-10-16T21:09:20.031Z (3 months ago)
Topics: bioinformatics, file-format, parsing, vcf, writing
Language: Python
Homepage:
Size: 1.41 MB
Stars: 109
Watchers: 4
Forks: 23
Open Issues: 11
Releases: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
- Authors: AUTHORS.rst
- Codemeta: codemeta.json

Owner metadata

Name: Berlin Institute of Health
Login: bihealth
Email:
Kind: organization
Description: BIH Core Unit Bioinformatics & BIH HPC IT
Website: https://www.cubi.bihealth.org/
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/11364301?v=4
Repositories: 215
Last ynced at: 2024-04-16T02:59:21.051Z
Profile URL: https://github.com/bihealth

GitHub Events

Total

Create event: 9
Release event: 2
Issues event: 7
Watch event: 12
Delete event: 16
Issue comment event: 7
Push event: 19
Pull request review event: 1
Pull request event: 15
Fork event: 4

Last Year

Create event: 9
Release event: 2
Issues event: 6
Watch event: 10
Delete event: 16
Issue comment event: 7
Push event: 19
Pull request review event: 1
Pull request event: 15
Fork event: 4

Name	Email	Commits
Manuel Holtgrewe	m**e@b**e	164
Manuel Holtgrewe	z**i@g**m	28
pyup-bot	g**t@p**o	22
varfish-bot	1****t	5
hylkedonker	4****r	1
ericblanc20	e**c@b**e	1
Katie Chen	k**n@g**m	1
Arfon Smith	a****n	1

Issue and Pull Request metadata

Last synced: 3 months ago

Total issues: 40
Total pull requests: 120
Average time to close issues: 6 months
Average time to close pull requests: about 1 month
Total issue authors: 31
Total pull request authors: 11
Average comments per issue: 1.25
Average comments per pull request: 0.49
Merged pull request: 39
Bot issues: 0
Bot pull requests: 1

Past year issues: 5
Past year pull requests: 16
Past year average time to close issues: 6 days
Past year average time to close pull requests: 18 days
Past year issue authors: 3
Past year pull request authors: 3
Past year average comments per issue: 0.2
Past year average comments per pull request: 0.19
Past year merged pull request: 10
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/bihealth/vcfpy

Top Issue Authors

holtgrewe (7)
stolpeo (2)
JarvisVon (2)
parlar (2)
martha-garasky-genedx (1)
jsstevenson (1)
dgomezpere (1)
msnyder424 (1)
Akazhiel (1)
marissa97 (1)
SAI-EL (1)
keiranmraine (1)
ok-gitr (1)
lczech (1)
ShadiKhoury (1)

Top Pull Request Authors

pyup-bot (67)
holtgrewe (25)
varfish-bot (15)
JarvisVon (3)
ericblanc20 (2)
Grarie (2)
effigies (2)
hylkedonker (1)
k8iechen (1)
dependabot[bot] (1)
robertopreste (1)

Top Issue Labels

Top Pull Request Labels

autorelease: pending (10)
autorelease: tagged (5)
dependencies (1)

Package metadata

Total packages: 1
Total downloads:
- pypi: 26,176 last-month
Total docker downloads: 675
Total dependent packages: 14
Total dependent repositories: 37
Total versions: 30
Total maintainers: 1

pypi.org: vcfpy

Python 3 VCF library with good support for both reading and writing

Homepage:
Documentation: https://github.com/bihealth/vcfpy
Licenses: MIT License
Latest release: 0.14.2 (published 3 months ago)
Last Synced: 2025-10-26T03:01:13.926Z (2 months ago)
Versions: 30
Dependent Packages: 14
Dependent Repositories: 37
Downloads: 26,176 Last month
Docker Downloads: 675
Rankings:
- Dependent packages count: 0.951%
- Dependent repos count: 2.411%
- Docker downloads count: 2.78%
- Downloads: 4.657%
- Average: 4.721%
- Stargazers count: 7.955%
- Forks count: 9.572%
Maintainers (1)
- Manuel.Holtgrewe

Dependencies

requirements/base.txt pypi

pysam >=0.10.0

requirements/dev.txt pypi

Babel >=2.3.4 development
Jinja2 >=2.9.5 development
MarkupSafe >=0.23 development
Pygments >=2.2.0 development
Sphinx >=1.5.2 development
alabaster >=0.7.9 development
docutils >=0.13.1 development
imagesize >=0.7.1 development
pytest-sugar >=0.8.0 development
pytz >=2016.10 development
requests >=2.13.0 development
six >=1.10.0 development
snowballstemmer >=1.2.1 development
termcolor >=1.1.0 development
twine >=1.12.1 development

requirements/pre36.txt pypi

cyordereddict >=1.0.0

requirements/test.txt pypi

apipkg >=1.4 test
codacy-coverage >=1.3.6 test
coverage >=4.3.4 test
execnet >=1.4.1 test
flake8 >=3.6.0 test
py >=1.4.32 test
pytest >=3.0.6 test
pytest-cache >=1.0 test
pytest-cov >=2.4.0 test

requirements/test_black.txt pypi

black ==22.3.0 test

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requirements.txt pypi

setup.py pypi

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Score: 17.067075039247996

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