JOSS: https://github.com/ggonnella/fastsubtrees
bioinformatics ncbi-taxonomy python subtree subtree-extraction subtree-query taxonomy tree
Score: 7.543273346705446
Last synced: about 10 hours ago
JSON representation
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 (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-02-17T11:23:20.000Z (over 1 year ago)
- Last Synced: 2026-02-28T07:47:19.038Z (4 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
-
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 Synced at: 2023-04-11T19:32:21.185Z
- Profile URL: https://github.com/ggonnella
GitHub Events
Total
- Create event: 1
- Delete event: 3
- Push event: 2
- Total: 6
Last Year
- Create event: 1
- Delete event: 3
- Push event: 2
- Total: 6
Committers metadata
Last synced: 8 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 | 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 |
Issue and Pull Request metadata
Last synced: 10 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
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: 109 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 over 3 years ago)
- Last Synced: 2025-10-31T05:07:03.997Z (8 months ago)
- Versions: 6
- Dependent Packages: 1
- Dependent Repositories: 1
- Downloads: 20 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)
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 over 3 years ago)
- Last Synced: 2025-10-31T05:07:22.426Z (8 months ago)
- Versions: 11
- Dependent Packages: 2
- Dependent Repositories: 1
- Downloads: 38 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)
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 over 3 years ago)
- Last Synced: 2025-10-31T05:06:35.775Z (8 months ago)
- Versions: 5
- Dependent Packages: 3
- Dependent Repositories: 0
- Downloads: 20 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)
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 over 3 years ago)
- Last Synced: 2025-10-31T05:06:36.384Z (8 months ago)
- Versions: 3
- Dependent Packages: 0
- Dependent Repositories: 0
- Downloads: 19 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)
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 over 3 years ago)
- Last Synced: 2025-10-31T05:06:35.779Z (8 months ago)
- Versions: 2
- Dependent Packages: 0
- Dependent Repositories: 0
- Downloads: 12 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)
Dependencies
- loguru *
- sqlalchemy *
- docopt >=0.6.2
- loguru >=0.5.1
- schema >=0.7.4
- tqdm >=4.57.0
- actions/checkout v2 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
- actions/checkout v3 composite
- actions/setup-python v3 composite
- ubuntu 22.04 build
- docopts *
- sh *
- myst_parser *
- Flask ==2.1.2
- dash-bootstrap-components ==1.0.2
- dash-html-components ==2.0.0
- fastsubtrees >=2.0
- loguru *
- schema *
- snacli *
- loguru *
- PyYAML *
- loguru *
- mariadb *
- mysql *
- ntdownload *
- schema *
- snacli *
- sqlalchemy *
- sqlalchemy_repr *
- docopt >=0.6.2
- loguru >=0.5.1
- ntdownload *
- schema >=0.7.4
- tqdm >=4.57.0
- docopt >=0.6.2
- loguru >=0.5.1
- ntdownload >=1.6
- schema >=0.7.4
- sh >=1.14.2
- tqdm >=4.57.0