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Sugar

Sugar: A Python framework for bioinformatics - Published in JOSS (2025)

https://github.com/rnajena/sugar

Science Score: 98.0%

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 7 DOI reference(s) in README and JOSS metadata
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    Academic publication links
    Links to: joss.theoj.org
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    Academic email domains
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    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 8 months ago · JSON representation ·

Repository

S*R -- A Python framework for bioinformatics

Basic Info
  • Host: GitHub
  • Owner: rnajena
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.38 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 10
Created about 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

logo

A Python framework for bioinformatics

build status docs status codecov pypi version python version DOI

The sugar project aims to provide a lightweight framework to facilitate rapid application development for bioinformatics.

It thus provides classes and functions for working with DNA and RNA sequences, as well as related annotations, and it provides parsers and writers for various file formats using a plugin interface.

Installation

Sugar requires a Python version >=3.11. Use pip to install the package, e.g.

pip install rnajena-sugar

Other installation options are described in the documentation.

Run tests with the sugar test command. Note that tests that require an Internet connection are skipped by default, this behavior can be turned off with the --web option. Also, depending on the installation and platform, some tests may be skipped or have an expected failure, to see details about the reasons please use the --verbose flag.

Getting started

Read about how to get started in the tutorial section of the documentation.

python from sugar import read seqs = read() # load example GenBank file print(seqs) print(seqs[1].fts) # show features attached to second sequence seqs.plot_ftsviewer(show=True) # plot attached features aas = seqs['cds'].translate() print(aas) aas.write('translated_cds.fasta')

Documentation and Changelog

Documentation can be found at Read the Docs. The detailed changelog is available here.

Contributions

Contributions are welcome! -- e.g. report or fix bugs, discuss or add features, improve the documentation. See the CONTRIBUTING.md file for details.

Citation

If you found this package useful, please consider citing it.

Eulenfeld T (2025), Sugar: A Python framework for bioinformatics, Journal of Open Source Software, 10(111), 8122, doi:10.21105/joss.08122

Owner

  • Name: RNA Bioinformatics and Highthroughput Analysis Jena
  • Login: rnajena
  • Kind: user
  • Location: Jena

JOSS Publication

Sugar: A Python framework for bioinformatics
Published
July 24, 2025
DOI
Volume 10, Issue 111, Page 8122
Authors
Tom Eulenfeld ORCID
Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, Germany
Editor
Olexandr Konovalov ORCID
Tags
bioinformatics genomics annotations
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
title: "Sugar: A Python framework for bioinformatics"
authors:
- family-names: Eulenfeld
  given-names: Tom
doi: 10.5281/zenodo.11388074
message: If you find this software useful, please cite it.
preferred-citation:
  authors:
  - family-names: Eulenfeld
    given-names: Tom
  date-published: 2025-07-24
  doi: 10.21105/joss.08122
  issn: 2475-9066
  issue: 111
  journal: Journal of Open Source Software
  start: 8122
  title: "Sugar: A Python framework for bioinformatics"
  type: article
  volume: 10

GitHub Events

Total
  • Create event: 8
  • Issues event: 10
  • Release event: 5
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 22
  • Push event: 425
  • Pull request event: 3
  • Gollum event: 3
Last Year
  • Create event: 8
  • Issues event: 10
  • Release event: 5
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 22
  • Push event: 425
  • Pull request event: 3
  • Gollum event: 3

Issues and Pull Requests

Last synced: 8 months ago

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 30 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 11
  • Total maintainers: 1
pypi.org: rnajena-sugar

A Python framework for bioinformatics

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 30 Last month
Rankings
Dependent packages count: 10.9%
Average: 36.1%
Dependent repos count: 61.2%
Maintainers (1)
lorchel
Last synced: 8 months ago

Dependencies

.github/workflows/logo.yml actions
  • actions/checkout v4 composite
  • conda-incubator/setup-miniconda v3 composite
.github/workflows/tests.yml actions
  • actions/checkout v4 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v3 composite
pyproject.toml pypi
  • matplotlib *
  • pandas *
  • pytest *
  • requests *
  • seaborn *
docs/requirements.txt pypi
  • furo *
  • sphinx *
setup.py pypi