Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy

Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy - Published in JOSS (2022)
https://github.com/ggonnella/fastsubtrees

Keywords

bioinformatics ncbi-taxonomy python subtree subtree-extraction subtree-query taxonomy tree

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 library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

Host: GitHub
URL: https://github.com/ggonnella/fastsubtrees
Owner: ggonnella
License: isc
Created: 2021-11-26T20:38:53.000Z (about 4 years ago)
Default Branch: main
Last Pushed: 2025-02-17T11:23:20.000Z (11 months ago)
Last Synced: 2025-10-24T01:39:47.826Z (2 months ago)
Topics: bioinformatics, ncbi-taxonomy, python, subtree, subtree-extraction, subtree-query, taxonomy, tree
Language: Python
Homepage:
Size: 834 KB
Stars: 4
Watchers: 4
Forks: 0
Open Issues: 0
Releases: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.txt
- License: LICENSE
- Citation: CITATION.cff
- Authors: AUTHORS.txt

Owner metadata

Name: Giorgio Gonnella
Login: ggonnella
Email:
Kind: user
Description:
Website:
Location: Goettingen, Germany
Twitter:
Company: Bioinformatics, University of Goettingen
Icon url: https://avatars.githubusercontent.com/u/21620?u=0c6ecc43ee0e4c7521759d29d4ffd1e6a28fac05&v=4
Repositories: 36
Last ynced at: 2023-04-11T19:32:21.185Z
Profile URL: https://github.com/ggonnella

GitHub Events

Total

Delete event: 3
Push event: 2
Create event: 1

Last Year

Delete event: 3
Push event: 2
Create event: 1

Committers metadata

Last synced: 2 months ago

Total Commits: 482
Total Committers: 4
Avg Commits per committer: 120.5
Development Distribution Score (DDS): 0.156

Commits in past year: 6
Committers in past year: 1
Avg Commits per committer in past year: 6.0
Development Distribution Score (DDS) in past year: 0.0

Name	Email	Commits
Giorgio Gonnella	g**a@z**e	407
aman.modi	a**i@s**e	73
Giorgio Gonnella	g**a@u**e	1
Aman Modi	a**o@t**e	1

Committer domains:

Issue and Pull Request metadata

Last synced: 4 months ago

Total issues: 25
Total pull requests: 2
Average time to close issues: 5 days
Average time to close pull requests: 3 months
Total issue authors: 2
Total pull request authors: 2
Average comments per issue: 3.24
Average comments per pull request: 0.0
Merged pull request: 0
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

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

Top Issue Authors

ggonnella (17)
KonradHoeffner (8)

Top Pull Request Authors

iamaman23 (1)
ggonnella (1)

Top Issue Labels

documentation (7)
enhancement (4)
bug (2)
question (1)

Top Pull Request Labels

Package metadata

Total packages: 5
Total downloads:
- pypi: 132 last-month
Total dependent packages: 6 (may contain duplicates)
Total dependent repositories: 2 (may contain duplicates)
Total versions: 27
Total maintainers: 1

pypi.org: ntmirror

Easily updatable local NCBI taxonomy database copy

Homepage: https://github.com/ggonnella/fastsubtrees/tree/main/ntmirror
Documentation: https://ntmirror.readthedocs.io/
Licenses: ISC
Latest release: 1.4.1 (published about 3 years ago)
Last Synced: 2025-10-26T02:38:09.183Z (2 months ago)
Versions: 6
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 33 Last month
Rankings:
- Dependent packages count: 3.244%
- Average: 20.324%
- Dependent repos count: 22.088%
- Forks count: 22.751%
- Stargazers count: 23.156%
- Downloads: 30.382%
Maintainers (1)
- gonnella

pypi.org: fastsubtrees

Tree representation for fast subtree queries

Homepage: https://github.com/ggonnella/fastsubtrees
Documentation: https://fastsubtrees.readthedocs.io/
Licenses: ISC
Latest release: 1.6.1 (published about 3 years ago)
Last Synced: 2025-10-26T02:38:08.667Z (2 months ago)
Versions: 11
Dependent Packages: 2
Dependent Repositories: 1
Downloads: 41 Last month
Rankings:
- Dependent packages count: 2.138%
- Average: 20.419%
- Dependent repos count: 22.088%
- Forks count: 22.751%
- Stargazers count: 23.156%
- Downloads: 31.962%
Maintainers (1)
- gonnella

pypi.org: ntdownload

Easily updatable local NCBI taxonomy dumps file copy

Homepage: https://github.com/ggonnella/fastsubtrees/tree/main/ntdowload
Documentation: https://ntdownload.readthedocs.io/
Licenses: ISC
Latest release: 1.7.1 (published about 3 years ago)
Last Synced: 2025-10-26T02:37:54.310Z (2 months ago)
Versions: 5
Dependent Packages: 3
Dependent Repositories: 0
Downloads: 30 Last month
Rankings:
- Dependent packages count: 1.428%
- Average: 20.425%
- Forks count: 23.201%
- Stargazers count: 23.317%
- Downloads: 23.569%
- Dependent repos count: 30.611%
Maintainers (1)
- gonnella

pypi.org: genomes-attributes-viewer

Example application of fastsubtrees

Homepage: https://github.com/ggonnella/fastsubtrees/"+ "tree/main/genomes_attributes_viewer
Documentation: https://genomes-attributes-viewer.readthedocs.io/
Licenses: ISC
Latest release: 1.3 (published about 3 years ago)
Last Synced: 2025-10-26T02:38:08.658Z (2 months ago)
Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 15 Last month
Rankings:
- Dependent packages count: 6.633%
- Average: 22.86%
- Forks count: 23.201%
- Stargazers count: 23.317%
- Downloads: 30.539%
- Dependent repos count: 30.611%
Maintainers (1)
- gonnella

pypi.org: ntsubtree

Tree representation for fast queries of the subtree of a taxon in the NCBI taxonomy tree

Homepage: https://github.com/ggonnella/fastsubtrees/tree/main/ntsubtree
Documentation: https://ntsubtree.readthedocs.io/
Licenses: ISC
Latest release: 1.1 (published about 3 years ago)
Last Synced: 2025-10-26T02:38:09.169Z (2 months ago)
Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 13 Last month
Rankings:
- Dependent packages count: 6.633%
- Forks count: 23.201%
- Stargazers count: 23.317%
- Average: 23.616%
- Dependent repos count: 30.611%
- Downloads: 34.319%
Maintainers (1)
- gonnella

Dependencies

ntmirror/setup.py pypi

loguru *
sqlalchemy *

setup.py pypi

docopt >=0.6.2
loguru >=0.5.1
schema >=0.7.4
tqdm >=4.57.0

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actions/checkout v2 composite
actions/upload-artifact v1 composite
openjournals/openjournals-draft-action master composite

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actions/setup-python v3 composite

Dockerfile docker

ubuntu 22.04 build

data/requirements.txt pypi

docopts *
sh *

docs/requirements.txt pypi

myst_parser *

genomes_attributes_viewer/setup.py pypi

Flask ==2.1.2
dash-bootstrap-components ==1.0.2
dash-html-components ==2.0.0
fastsubtrees >=2.0

ntdownload/requirements.txt pypi

loguru *
schema *
snacli *

ntdownload/setup.py pypi

loguru *

ntmirror/requirements.txt pypi

PyYAML *
loguru *
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ntdownload *
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ntsubtree/setup.py pypi

docopt >=0.6.2
loguru >=0.5.1
ntdownload *
schema >=0.7.4
tqdm >=4.57.0

requirements.txt pypi

docopt >=0.6.2
loguru >=0.5.1
ntdownload >=1.6
schema >=0.7.4
sh >=1.14.2
tqdm >=4.57.0

Score: 7.72134861261795

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