gffutils

GFF and GTF file manipulation and interconversion

https://github.com/daler/gffutils

Science Score: 23.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
4 of 22 committers (18.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (3.3%) to scientific vocabulary

Keywords from Contributors

bioinformatics ngs usegalaxy workflow-engine phylogenetics sequence-alignment nextflow bioconda multiqc pypi

Last synced: 10 months ago · JSON representation

Repository

GFF and GTF file manipulation and interconversion

Basic Info

Host: GitHub
Owner: daler
License: mit
Language: Python
Default Branch: master
Homepage: http://daler.github.io/gffutils
Size: 30.9 MB

Statistics

Stars: 305
Watchers: 13
Forks: 79
Open Issues: 23
Releases: 1

Created almost 15 years ago · Last pushed over 2 years ago

Metadata Files

Readme License

README.rst

gffutils
========

``gffutils`` is a Python package for working with and manipulating the GFF and
GTF format files typically used for genomic annotations.

Files are loaded into a sqlite3 database, allowing much more complex
manipulation of hierarchical features (e.g., genes, transcripts, and exons)
than is possible with plain-text methods alone.

See documentation at https://daler.github.io/gffutils, and GitHub repo at
https:/github.com/daler/gffutils.

Owner

Name: Ryan Dale
Login: daler
Kind: user
Location: Bethesda, MD
Company: National Institutes of Health (NIH), National Institute of Child Health and Human Development (NICHD)

Repositories: 55
Profile: https://github.com/daler

GitHub Events

Total

Issues event: 4
Watch event: 16
Issue comment event: 12
Pull request event: 1
Fork event: 1

Last Year

Issues event: 4
Watch event: 16
Issue comment event: 12
Pull request event: 1
Fork event: 1

Committers

Last synced: about 1 year ago

All Time

Total Commits: 672
Total Committers: 22
Avg Commits per committer: 30.545
Development Distribution Score (DDS): 0.122

Past Year

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

Top Committers

Name	Email	Commits
daler	d**r@n**v	590
Yarden Katz	y**z@g**m	30
Andrew Lando	d**l@g**m	14
Jacques Dainat	j**t@i**r	8
Nolan Woods	i**t@g**m	6
Gabriel Pratt	g**t@u**u	3
Rintze M. Zelle	r**e@g**m	3
Abishek.k	j**k@g**m	3
Rory Kirchner	r**r@g**m	2
Vladimir Mladenovic	v**c@s**m	1
Edward S. Rice	e**e@m**u	1
Husen M. Umer	h****g	1
Matt Shirley	m**5@g**m	1
Michael R. Crusoe	c**e@d**g	1
Rob Beagrie	r**b@b**m	1
Stefano Rivera	g**b@r**t	1
Steven Brown	s**n@g**m	1
Trent Hauck	t**t@t**m	1
Viktor Kerkez	a**a@g**m	1
lowdanie	l**e@g**m	1
moritzbuck	m**k@g**m	1
njohnso6	n**6@u**u	1

Committer Domains (Top 20 + Academic)

uccs.edu: 1 trenthauck.com: 1 rivera.za.net: 1 beagrie.com: 1 debian.org: 1 missouri.edu: 1 sbgenomics.com: 1 ucsd.edu: 1 ird.fr: 1 niddk.nih.gov: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 75
Total pull requests: 52
Average time to close issues: over 1 year
Average time to close pull requests: 5 months
Total issue authors: 54
Total pull request authors: 21
Average comments per issue: 2.69
Average comments per pull request: 1.04
Merged pull requests: 37
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 2
Average time to close issues: 16 days
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 2
Average comments per issue: 3.67
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

innovate-invent (5)
daler (4)
dariober (4)
mictadlo (3)
yurivict (3)
yarden (3)
scimerc (2)
novigit (2)
YeHW (2)
z626093820 (2)
olgabot (2)
p-polacek (1)
msarrias (1)
soungalo (1)
bbimber (1)

Pull Request Authors

daler (25)
mr-c (4)
innovate-invent (4)
Juke34 (3)
a-detiste (2)
stevendbrown (2)
AMDmi3 (2)
aliciaaevans (2)
EFraim (1)
roryk (1)
smoe (1)
lowdanie (1)
stefanor (1)
DevangThakkar (1)
pbradz (1)

Top Labels

Issue Labels

v0.11 (10) feature request (7) needs-discussion (3) design (2)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- pypi 17,079 last-month
Total docker downloads: 1,035

Total dependent packages: 33
(may contain duplicates)
Total dependent repositories: 96
(may contain duplicates)
Total versions: 29
Total maintainers: 2

pypi.org: gffutils

Work with GFF and GTF files in a flexible database framework

Homepage: https://github.com/daler/gffutils
Documentation: https://gffutils.readthedocs.io/
License: MIT License
Latest release: 0.11.1
published almost 4 years ago

Versions: 21
Dependent Packages: 31
Dependent Repositories: 96
Downloads: 17,079 Last month
Docker Downloads: 1,035

Rankings

Dependent packages count: 0.5%

Docker downloads count: 1.3%

Dependent repos count: 1.5%

Average: 2.6%

Downloads: 3.3%

Stargazers count: 4.0%

Forks count: 5.2%

Maintainers (1)

daler

Last synced: 11 months ago

proxy.golang.org: github.com/daler/gffutils

Documentation: https://pkg.go.dev/github.com/daler/gffutils#section-documentation
License: mit
Latest release: v0.11.1
published almost 4 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 11 months ago

GFF and GTF file manipulation and interconversion gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. Files are loaded into a sqlite3 database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.

Homepage: https://github.com/daler/gffutils
License: []
Latest release: 0.10.1
published over 4 years ago

Versions: 1
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Average: 11.4%

Forks count: 12.8%

Stargazers count: 14.0%

Dependent packages count: 19.0%

Maintainers (1)

dorton21

Last synced: 11 months ago

Dependencies

docs-requirements.txt pypi

make *
numpydoc *
sphinx *
sphinx-autoapi *
sphinx_rtd_theme *

optional-requirements.txt pypi

bedtools >=2.27.1
biopython >=1.73
pybedtools >=0.8.0

requirements.txt pypi

argcomplete >=1.9.4
argh >=0.26.2
pyfaidx >=0.5.5.2
simplejson *
six >=1.12.0

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/upload-artifact v2 composite

gffutils

Science Score: 23.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

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: gffutils

Rankings

Maintainers (1)

proxy.golang.org: github.com/daler/gffutils

Rankings

spack.io: py-gffutils

Rankings

Maintainers (1)

Dependencies