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fqfa

fqfa: A pure Python package for genomic sequence files - Published in JOSS (2020)

https://github.com/countess-project/fqfa

Science Score: 100.0%

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 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation ·

Repository

A lightweight Python library for handling FASTQ and FASTA files.

Basic Info
  • Host: GitHub
  • Owner: CountESS-Project
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Size: 158 KB
Statistics
  • Stars: 6
  • Watchers: 2
  • Forks: 2
  • Open Issues: 2
  • Releases: 11
Created over 6 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Code of conduct Citation

README.md

DOI Documentation Status Code style: black

fqfa

A pure Python library for handling FASTQ and FASTA files.

Install fqfa from PyPI using pip:

pip3 install fqfa

To set up the package for development purposes, include the optional dependencies and install pre-commit:

pip3 install fqfa[dev]
pre-commit install

Building the documentation requires the following additional packages:

pip3 install sphinx
pip3 install sphinx-rtd-theme

Online documentation including usage examples is available on Read the Docs.

To report a problem or request a new feature, please use the GitHub issue tracker.

To cite this package please refer to "fqfa: A pure Python package for genomic sequence files".

Contributions via pull request are welcome. Contributed code should have full unit test coverage, NumPy-style docstrings, black formatting, and type hints.

Owner

  • Name: CountESS
  • Login: CountESS-Project
  • Kind: organization

JOSS Publication

fqfa: A pure Python package for genomic sequence files
Published
March 01, 2020
DOI
Volume 5, Issue 47, Page 2076
Authors
Alan F. Rubin ORCID
The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne
Editor
Lorena Pantano ORCID
Tags
genomics bioinformatics
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Rubin"
  given-names: "Alan F"
  orcid: "https://orcid.org/0000-0003-1474-605X"
title: "fqfa"
version: 1.2.1
doi: 10.5281/zenodo.4346283
date-released: 2020-12-18
url: "https://github.com/CountESS-Project/fqfa"
preferred-citation:
  type: article
  authors:
  - family-names: "Rubin"
    given-names: "Alan F"
    orcid: "https://orcid.org/0000-0003-1474-605X"
  doi: "10.21105/joss.02076"
  journal: "Journal of Open Source Software"
  month: 3
  start: 2076
  title: "fqfa: A pure Python package for genomic sequence files"
  issue: 47
  volume: 5
  year: 2020

Papers & Mentions

Total mentions: 1

fqfa: A pure Python package for genomic sequence files
Last synced: 4 months ago

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 194
  • Total Committers: 2
  • Avg Commits per committer: 97.0
  • Development Distribution Score (DDS): 0.01
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alan Rubin a****n@w****u 192
Nick Moore n****k@z****g 2
Committer Domains (Top 20 + Academic)
zoic.org: 1 wehi.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 16
  • Average time to close issues: 5 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.06
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • genomematt (1)
  • FlorianThibord (1)
  • natir (1)
  • afrubin (1)
Pull Request Authors
  • afrubin (13)
  • nickzoic (3)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 9,058 last-month
  • Total dependent packages: 3
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 2
pypi.org: fqfa

A lightweight Python library for handling FASTQ and FASTA files.

  • Versions: 10
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 9,058 Last month
Rankings
Dependent packages count: 3.1%
Downloads: 11.9%
Average: 12.2%
Dependent repos count: 21.7%
Maintainers (2)
nickzoic afrubin
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • ipython *