VCFPy

VCFPy: a Python 3 library with good support for both reading and writing VCF - Published in JOSS (2016)

https://github.com/bihealth/vcfpy

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

bioinformatics file-format parsing vcf writing

Keywords from Contributors

genome

Last synced: 4 months ago · JSON representation

Repository

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

Basic Info

Host: GitHub
Owner: bihealth
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 1.25 MB

Statistics

Stars: 110
Watchers: 5
Forks: 24
Open Issues: 19
Releases: 2

Topics

bioinformatics file-format parsing vcf writing

Created over 9 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Contributing License Authors Codemeta

VCFPy

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

Free software: MIT license
Documentation: https://vcfpy.readthedocs.io.

Features

Support for reading and writing VCF v4.3
Interface to INFO and FORMAT fields is based on OrderedDict allows for easier modification than PyVCF (also I find this more pythonic)
Read (and jump in) and write BGZF files just using vcfpy

Why another VCF parser for Python!

I've been using PyVCF with quite some success in the past. However, the main bottleneck of PyVCF is when you want to modify the per-sample genotype information. There are some issues in the tracker of PyVCF but none of them can really be considered solved. I tried several hours to solve these problems within PyVCF but this never got far or towards a complete rewrite...

For this reason, VCFPy was born and here it is!

What's the State?

VCFPy is the result of two full days of development plus some maintenance work later now (right now). I'm using it in several projects but it is not as battle-tested as PyVCF.

Why Python 3 Only?

As I'm only using Python 3 code, I see no advantage in carrying around support for legacy Python 2 and maintaining it. At a later point when VCFPy is known to be stable, Python 2 support might be added if someone contributes a pull request.

Owner

Name: Berlin Institute of Health
Login: bihealth
Kind: organization

Website: https://www.cubi.bihealth.org/
Repositories: 215
Profile: https://github.com/bihealth

BIH Core Unit Bioinformatics & BIH HPC IT

JOSS Publication

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

Published

October 25, 2016

DOI

10.21105/joss.00085

Volume 1, Issue 6, Page 85

Authors

Manuel Holtgrewe

Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin

Dieter Beule

Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin

Editor

Pjotr Prins

CodeMeta (codemeta.json)

{
  "@context": "https://raw.githubusercontent.com/mbjones/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": "https://orcid.org/0000-0002-3051-1763",
      "@type": "Person",
      "email": "manuel.holtgrewe@bihealth.de",
      "name": "Manuel Holtgrewe",
      "affiliation": "Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin"
    },
    {
      "@id": "https://orcid.org/0000-0002-3284-0632",
      "@type": "Person",
      "email": "dieter.beule@bihealth.de",
      "name": "Dieter Beule",
      "affiliation": "Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin"
    }
  ],
  "identifier": "https://figshare.com/articles/vcfpy-0_7_0/3863583",
  "codeRepository": "https://github.com/bihealth/vcfpy",
  "datePublished": "2016-09-28",
  "dateModified": "2016-09-28",
  "dateCreated": "2016-09-28",
  "description": "Python 3 library with good support for both reading and writing VCF",
  "keywords": "VCF, Python, software library",
  "license": "MIT",
  "title": "VCFPy",
  "version": "v0.7.0"
}

GitHub Events

Total

Issues event: 2
Watch event: 12
Issue comment event: 1
Pull request event: 1
Fork event: 4

Last Year

Issues event: 2
Watch event: 12
Issue comment event: 1
Pull request event: 1
Fork event: 4

Committers

Last synced: 5 months ago

All Time

Total Commits: 209
Total Committers: 7
Avg Commits per committer: 29.857
Development Distribution Score (DDS): 0.263

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Manuel Holtgrewe	m**e@b**e	154
Manuel Holtgrewe	z**i@g**m	28
pyup-bot	g**t@p**o	22
varfish-bot	1****t	2
hylkedonker	4****r	1
Katie Chen	k**n@g**m	1
Arfon Smith	a****n	1

Committer Domains (Top 20 + Academic)

pyup.io: 1 bihealth.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 37
Total pull requests: 92
Average time to close issues: 3 months
Average time to close pull requests: 22 days
Total issue authors: 31
Total pull request authors: 11
Average comments per issue: 1.32
Average comments per pull request: 0.57
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 3
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

holtgrewe (4)
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)

Pull Request Authors

pyup-bot (67)
holtgrewe (14)
varfish-bot (12)
JarvisVon (3)
ericblanc20 (2)
effigies (2)
Grarie (2)
k8iechen (1)
hylkedonker (1)
dependabot[bot] (1)
robertopreste (1)

Top Labels

Issue Labels

Pull Request Labels

autorelease: pending (7) autorelease: tagged (5) dependencies (1)

Packages

Total packages: 1
Total downloads:
- pypi 7,934 last-month
Total docker downloads: 675

Total dependent packages: 14
Total dependent repositories: 37
Total versions: 27
Total maintainers: 1

pypi.org: vcfpy

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

Homepage: https://github.com/bihealth/vcfpy
Documentation: https://vcfpy.readthedocs.io/
License: MIT license
Latest release: 0.13.8
published almost 2 years ago

Versions: 27
Dependent Packages: 14
Dependent Repositories: 37
Downloads: 7,934 Last month
Docker Downloads: 675

Rankings

Dependent packages count: 1.0%

Dependent repos count: 2.4%

Docker downloads count: 2.8%

Downloads: 4.7%

Average: 4.7%

Stargazers count: 8.0%

Forks count: 9.6%

Maintainers (1)

Manuel.Holtgrewe

Last synced: 4 months ago

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

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/checkout v1 composite
actions/setup-python v2 composite
khan/pull-request-workflow-cancel 1.0.0 composite
marocchino/sticky-pull-request-comment v1.1.0 composite

requirements.txt pypi

setup.py pypi

.github/workflows/conventional-prs.yml actions

amannn/action-semantic-pull-request v3.4.0 composite

.github/workflows/release-please.yml actions

GoogleCloudPlatform/release-please-action v3 composite
actions/checkout v2 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish master composite

VCFPy

Science Score: 93.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

VCFPy

Features

Why another VCF parser for Python!

What's the State?

Why Python 3 Only?

Owner

JOSS Publication

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

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: vcfpy

Rankings

Maintainers (1)

Dependencies