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https://github.com/cancervariants/fusor

Data classes and constructor tools supporting the VICC Gene Fusion Curation project

https://github.com/cancervariants/fusor

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords from Contributors

bioinformatics biomedical-informatics genetics precision-medicine genomics disease-classification bioinformatics-data
Last synced: 7 months ago · JSON representation

Repository

Data classes and constructor tools supporting the VICC Gene Fusion Curation project

Basic Info
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 2
  • Open Issues: 17
  • Releases: 40
Created over 4 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

FUSOR

image image image Actions status DOI

Documentation · Installation · Usage · API reference

Overview

FUSOR (FUSion Object Representation) provides modeling and validation tools for representing gene fusions in a precise, computable structure that adheres to the VICC Gene Fusion Specification. It also provides easy access to transcript selection and coordinate conversion tools, and enables generation of human-readable fusion nomenclature. <!-- /description -->

Install

FUSOR is available on PyPI:

shell python3 -m pip install fusor

See the installation instructions in the documentation for a description of dependency setup requirements.

Usage

Fusion and subcomponent constructors are provided through a core FUSOR class:

```pycon

from fusor import FUSOR f = FUSOR() fusion = f.fusion( ... structure=[ ... { ... "type": "GeneElement", ... "gene": { "primaryCoding": { ... "id": "hgnc:3508", "code": "HGNC:3508", "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgncid/" } "conceptType": "Gene", "name": "EWSR1" ... } ... }, ... { ... "type": "UnknownGeneElement" ... } ... ], ... assay={ ... "type": "Assay", ... "methodUri": "pmid:33576979", ... "assayId": "obi:OBI0003094", ... "assayName": "fluorescence in-situ hybridization assay", ... "fusionDetection": "inferred", ... }, ... ) fusion.type ```

See the usage section in the documentation for more features and code examples.

Feedback and contributing

We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.

Owner

  • Name: VICC
  • Login: cancervariants
  • Kind: organization

The Variant Interpretation for Cancer Consortium

GitHub Events

Total
  • Create event: 57
  • Release event: 3
  • Issues event: 76
  • Delete event: 46
  • Issue comment event: 70
  • Push event: 195
  • Pull request review event: 178
  • Pull request review comment event: 169
  • Pull request event: 98
  • Fork event: 1
Last Year
  • Create event: 57
  • Release event: 3
  • Issues event: 76
  • Delete event: 46
  • Issue comment event: 70
  • Push event: 195
  • Pull request review event: 178
  • Pull request review comment event: 169
  • Pull request event: 98
  • Fork event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 248
  • Total Committers: 6
  • Avg Commits per committer: 41.333
  • Development Distribution Score (DDS): 0.544
Top Committers
Name Email Commits
korikuzma k****a@g****m 113
James Stevenson j****n@n****g 108
Arbesfeld r****1@r****g 16
Arbesfeld r****1@r****t 8
Katie Stahl k****l@n****g 2
Kori Kuzma 4****a@u****m 1
Committer Domains (Top 20 + Academic)
nationwidechildrens.org: 2 resc02fw070md6r.columbuschildrens.net: 1 resc02fw070md6r.crii.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 116
  • Total pull requests: 242
  • Average time to close issues: 3 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 0.65
  • Average comments per pull request: 0.55
  • Merged pull requests: 195
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 52
  • Pull requests: 97
  • Average time to close issues: 10 days
  • Average time to close pull requests: 6 days
  • Issue authors: 5
  • Pull request authors: 5
  • Average comments per issue: 0.15
  • Average comments per pull request: 0.49
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jsstevenson (44)
  • jarbesfeld (43)
  • korikuzma (16)
  • katiestahl (10)
  • zealws (2)
  • ahwagner (1)
Pull Request Authors
  • jsstevenson (120)
  • jarbesfeld (76)
  • katiestahl (22)
  • korikuzma (19)
  • zealws (5)
Top Labels
Issue Labels
enhancement (49) priority:medium (28) priority:high (14) priority:low (12) bug (9) stale-exempt (9) documentation (7) technical debt (4) build (2) requirement (2) chore (2) stale (2) closed-by-stale (2) cleanup (1) good first issue (1) Epic (1) ci/cd (1)
Pull Request Labels
priority:low (64) priority:medium (64) enhancement (47) stale-exempt (37) priority:high (31) bug (19) build (9) documentation (4) ci/cd (3) help wanted (2) chore (2) keep-alive (2) stale (2) analysis (2) requirement (1) cleanup (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 438 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 40
  • Total maintainers: 3
pypi.org: fusor

Computable object representation and validation for gene fusions

  • Homepage: https://github.com/cancervariants/fusor
  • Documentation: https://github.com/cancervariants/fusor
  • License: MIT License Copyright (c) 2021-2024 VICC Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.8.0
    published 8 months ago
  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 438 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.5%
Average: 23.7%
Downloads: 28.0%
Forks count: 29.8%
Stargazers count: 38.8%
Maintainers (3)
alex.phd jsstevenson korikuzma
Last synced: 7 months ago

Dependencies

Pipfile pypi
  • coverage * develop
  • coveralls * develop
  • flake8 * develop
  • flake8-annotations * develop
  • flake8-docstrings * develop
  • flake8-quotes * develop
  • fusor * develop
  • ipykernel * develop
  • pre-commit * develop
  • pytest * develop
  • pytest-asyncio * develop
  • pytest-cov * develop
  • biocommons.seqrepo *
  • ga4gh.vrs ==0.7.6
  • ga4gh.vrsatile.pydantic ==0.0.11
  • gene-normalizer ==0.1.27
  • pydantic *
  • uta-tools >=0.1.2
.github/workflows/checks.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/close_issue.yml actions
  • ldez/gha-mjolnir v1.0.3 composite
.github/workflows/release.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite