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cool-seq-tool

https://github.com/genomicmedlab/cool-seq-tool

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found 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: ncbi.nlm.nih.gov, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

bioinformatics genomics

Keywords from Contributors

biomedical-informatics genetics precision-medicine
Last synced: 4 months ago · JSON representation ·

Repository

Basic Info
Statistics
  • Stars: 4
  • Watchers: 4
  • Forks: 0
  • Open Issues: 31
  • Releases: 59
Topics
bioinformatics genomics
Created over 4 years ago · Last pushed 5 months ago
Metadata Files
Readme License Citation

README.md

Cool-Seq-Tool

image DOI image image Actions status

Documentation · Installation · Usage · API reference

Overview

The Common Operations On Lots-Of Sequences Tool, Cool-Seq-Tool, provides:

  • A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, MANE transcript descriptions, and transcript alignment data from the Universal Transcript Archive
  • Augmented access to the SeqRepo database, including multiple additional methods and tools
  • Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined here, that combine the above to support translation between references sequences, annotation layers, and transcripts <!-- /description -->

Install

Cool-Seq-Tool is available on PyPI

shell python3 -m pip install cool-seq-tool

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

Usage

All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:

```pycon

from coolseqtool import CoolSeqTool from coolseqtool.schemas import AnnotationLayer, CoordinateType cst = CoolSeqTool() result = await cst.manetranscript.getmanetranscript( ... "NP004324.2", ... 599, ... AnnotationLayer.PROTEIN, ... coordinatetype=CoordinateType.INTERRESIDUE, ... ) result.gene, result.refseq, result.status ('EGFR', 'NM005228.5', <TranscriptPriority.MANESELECT: 'mane_select'>) ```

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: The Wagner/Chaudhari Laboratories at the Institute for Genomic Medicine
  • Login: GenomicMedLab
  • Kind: organization
  • Email: team@genomicmedlab.org
  • Location: Columbus, Ohio

The Wagner and Chaudhari Laboratories develop methods and tools for translating genomic variation in patients to clinical actionability

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Kuzma
    given-names: Kori
  - family-names: Stevenson
    given-names: James
  - family-names: Wagner
    given-names: Alex
title: Cool Seq Tool
version: v0.1.1
date-released: 2022-05-11

GitHub Events

Total
  • Create event: 34
  • Release event: 10
  • Issues event: 37
  • Delete event: 26
  • Issue comment event: 61
  • Push event: 56
  • Pull request review comment event: 51
  • Pull request review event: 70
  • Pull request event: 52
Last Year
  • Create event: 34
  • Release event: 10
  • Issues event: 37
  • Delete event: 26
  • Issue comment event: 61
  • Push event: 56
  • Pull request review comment event: 51
  • Pull request review event: 70
  • Pull request event: 52

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 331
  • Total Committers: 6
  • Avg Commits per committer: 55.167
  • Development Distribution Score (DDS): 0.19
Past Year
  • Commits: 103
  • Committers: 4
  • Avg Commits per committer: 25.75
  • Development Distribution Score (DDS): 0.437
Top Committers
Name Email Commits
korikuzma k****a@g****m 268
James Stevenson j****n@n****g 55
Kori Kuzma 4****a 3
Alex H. Wagner, PhD A****r@n****g 2
Jeremy Arbesfeld 5****d 2
katie stahl k****l@n****g 1
Committer Domains (Top 20 + Academic)
nationwidechildrens.org: 3

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 159
  • Total pull requests: 216
  • Average time to close issues: 5 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 4
  • Total pull request authors: 6
  • Average comments per issue: 2.14
  • Average comments per pull request: 0.47
  • Merged pull requests: 199
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 20
  • Pull requests: 47
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 10 days
  • Issue authors: 4
  • Pull request authors: 5
  • Average comments per issue: 2.05
  • Average comments per pull request: 0.43
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • korikuzma (93)
  • jsstevenson (43)
  • jarbesfeld (19)
  • katiestahl (1)
Pull Request Authors
  • korikuzma (173)
  • jsstevenson (83)
  • jarbesfeld (29)
  • katiestahl (3)
  • zealws (2)
  • ahwagner (1)
Top Labels
Issue Labels
enhancement (52) priority:low (48) priority:medium (45) bug (34) priority:high (29) technical debt (27) stale (17) keep-alive (13) closed-by-stale (7) documentation (7) test (6) performance (5) build (5) cleanup (3) stale-exempt (3) requirement (2) ci/cd (2) epic (2) wontfix (1) chore (1)
Pull Request Labels
priority:low (124) priority:medium (56) priority:high (51) enhancement (50) bug (28) technical debt (26) build (18) stale-exempt (13) chore (12) documentation (9) test (5) cleanup (4) ci/cd (3) stale (3) performance (2) keep-alive (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 3,872 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 1
  • Total versions: 40
  • Total maintainers: 2
pypi.org: cool-seq-tool

Common Operation on Lots of Sequences Tool

  • Homepage: https://github.com/genomicmedlab/cool-seq-tool
  • Documentation: https://coolseqtool.readthedocs.io/
  • License: MIT License Copyright (c) 2021-2024 Wagner Lab 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: 0.14.3
    published 5 months ago
  • Versions: 40
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 3,872 Last month
Rankings
Dependent packages count: 3.1%
Downloads: 9.7%
Average: 17.5%
Dependent repos count: 21.8%
Stargazers count: 23.1%
Forks count: 29.9%
Maintainers (2)
jsstevenson korikuzma
Last synced: 5 months ago