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Python Implementation of Codon Adaptation Index

Python Implementation of Codon Adaptation Index - Published in JOSS (2018)

https://github.com/benjamin-lee/codonadaptationindex

Science Score: 93.0%

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 8 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

bioinformatics codons genetics

Scientific Fields

Mathematics Computer Science - 84% confidence
Biology Life Sciences - 63% confidence
Last synced: 4 months ago · JSON representation

Repository

Python Implementation of Codon Adaption Index

Basic Info
  • Host: GitHub
  • Owner: Benjamin-Lee
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage: https://cai.readthedocs.io
  • Size: 34.8 MB
Statistics
  • Stars: 37
  • Watchers: 3
  • Forks: 11
  • Open Issues: 9
  • Releases: 8
Topics
bioinformatics codons genetics
Created over 8 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

Python Codon Adaptation Index

DOI Docs Travis CodeFactor PyPI

An implementation of Sharp and Li's 1987 formulation of the codon adaption index.

Installation

This module is available from PyPI and can be downloaded with the following command:

$ pip install CAI

To install the latest development version:

$ pip install git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git

Quickstart

Finding the CAI of a sequence is easy:

>>> from CAI import CAI
>>> CAI("ATG...", reference=["ATGTTT...", "ATGCGC...",...])
0.24948128951724224

Similarly, from the command line:

$ CAI -s sequence.fasta -r reference_sequences.fasta
0.24948128951724224

Determining which sequences to use as the reference set is left to the user, though the HEG-DB is a great resource of highly expressed genes.

Contributing and Getting Support

If you encounter any issues using CAI, feel free to create an issue.

To contribute to the project, please create a pull request. For more information on how to do so, please look at GitHub's documentation on pull requests.

Citation

Lee, B. D. (2018). Python Implementation of Codon Adaptation Index. Journal of Open Source Software, 3 (30), 905. https://doi.org/10.21105/joss.00905 :

@article{Lee2018,
  doi = {10.21105/joss.00905},
  url = {https://doi.org/10.21105/joss.00905},
  year  = {2018},
  month = {oct},
  publisher = {The Open Journal},
  volume = {3},
  number = {30},
  pages = {905},
  author = {Benjamin D. Lee},
  title = {Python Implementation of Codon Adaptation Index},
  journal = {Journal of Open Source Software}

Contact

I'm available for contact at .

Reference

Sharp, P. M., & Li, W. H. (1987). The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3), 1281–1295.

Owner

  • Name: Benjamin Lee
  • Login: Benjamin-Lee
  • Kind: user
  • Location: Tysons, VA

NIH-OxCam scholar at @ncbi & DPhil student at Oxford. Previously @Harvard CS '20 and @IQTLabs

JOSS Publication

Python Implementation of Codon Adaptation Index
Published
October 04, 2018
DOI
Volume 3, Issue 30, Page 905
Authors
Benjamin D. Lee ORCID
School of Engineering and Applied Sciences, Harvard University
Editor
George Githinji
Tags
bioinformatics computational biology codon adaptation index molecular biology
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 3
  • Issue comment event: 1
  • Pull request event: 1
  • Fork event: 2
Last Year
  • Watch event: 3
  • Issue comment event: 1
  • Pull request event: 1
  • Fork event: 2

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 111
  • Total Committers: 3
  • Avg Commits per committer: 37.0
  • Development Distribution Score (DDS): 0.153
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Benjamin Lee b****e@m****m 94
BjornFJohansson b****b@g****m 16
C. Titus Brown t****s@i****g 1
Committer Domains (Top 20 + Academic)
idyll.org: 1 me.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 11
  • Total pull requests: 6
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 months
  • Total issue authors: 8
  • Total pull request authors: 5
  • Average comments per issue: 2.18
  • Average comments per pull request: 0.67
  • Merged pull requests: 2
  • Bot issues: 1
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • BjornFJohansson (3)
  • ctb (2)
  • jrjhealey (1)
  • ante-turudic (1)
  • dependabot-preview[bot] (1)
  • celiosantosjr (1)
  • HarryMWinters (1)
  • Benjamin-Lee (1)
Pull Request Authors
  • BjornFJohansson (2)
  • cjwatson (2)
  • ctb (1)
  • ewallace (1)
  • renovate[bot] (1)
Top Labels
Issue Labels
enhancement (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 195 last-month
  • Total docker downloads: 21
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: cai

Python implementation of codon adaptation index

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 195 Last month
  • Docker Downloads: 21
Rankings
Docker downloads count: 3.5%
Dependent packages count: 10.0%
Stargazers count: 12.0%
Average: 12.7%
Forks count: 13.3%
Downloads: 15.9%
Dependent repos count: 21.7%
Maintainers (1)
Benjamin-Lee
Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi
  • sphinxcontrib-programoutput *
requirements.txt pypi
  • biopython >=1.79
  • click >=7
  • scipy >=1.7.1
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  • pypa/gh-action-pypi-publish master composite
.github/workflows/test_and_coverage_workflow.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • allenevans/set-env v2.0.0 composite
  • conda-incubator/setup-miniconda v2 composite