genespeak

A library to encode text as DNA and decode DNA to text.

https://github.com/sugatoray/genespeak

Science Score: 67.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary

Keywords

decoding dna-to-text encoding genespeak python text-to-dna

Last synced: 4 months ago · JSON representation ·

Repository

A library to encode text as DNA and decode DNA to text.

Basic Info

Host: GitHub
Owner: sugatoray
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 1.1 MB

Statistics

Stars: 12
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 10

Topics

decoding dna-to-text encoding genespeak python text-to-dna

Created almost 4 years ago · Last pushed about 3 years ago

Metadata Files

Readme License Citation

GeneSpeak 🧬

genespeak-banner

A library to encode text as DNA and decode DNA to text.

GeneSpeak allows you to encode regular text as DNA using base-pairs (A, T, G, C) and convert back to the original text. Text encoding is done for both ascii and utf-8 characters based on the strategy keyword argument. The encoding scheme could be any combination of A, T, G, C.

Installation 📜

You can install the library via pip or conda.

Install with pip

sh pip install genespeak

Install with conda

sh conda install -c conda-forge genespeak

Quickstart ⚡

See the quickstart guide here.

Demo App ✨

You can play around with GeneSpeak in this streamlit app: https://tinyurl.com/genespeak-demo

Usage ✋

```python import genespeak as gp print(f'{gp.name} version: {gp.version}')

schema = "ATCG" # (1) strategy = "ascii" # (2) text = "Hello World!"

dna = gp.texttodna(text, schema=schema) textfromdna = gp.dnatotext(dna, schema=schema) print(f'Text: {text}\nEncoded DNA: {dna}\nDecoded Text: {textfromdna}\nSuccess: {text == textfromdna}') ```

Output

```sh genespeak version: 0.0.5 Text: Hello World! Encoded DNA: TACATCTTTCGATCGATCGGACAATTTGTCGGTGACTCGATCTAACAT

Text: Hello World! Encoded DNA: TACATCTTTCGATCGATCGGACAATTTGTCGGTGACTCGATCTAACAT Decoded Text: Hello World! ```

Documentation 📚

The genespeak docs are maintained here.

License 📑

The library is available under MIT license.

Citation 🔖

You may cite this library as follows.

bibtex @software{ray2022genespeak, author = {Ray, Sugato}, title = {GeneSpeak - A library to encode text as DNA and decode DNA to text}, url = {https://github.com/sugatoray/genespeak}, doi = {10.5281/zenodo.5885777}, month = {1}, year = {2022} }

GeneSpeak Thumb Print 👍

Let's have some fun! ✨ The following is a GeneSpeak thumbprint of genespeak itself.

| schema | strategy | thumbprint | |:---:|:---:|:---| | ATCG | ascii | TCTGTCTTTCGCTCTTTGAGTGAATCTTTCATTCCG |

Repository Health Metrics 💟

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Owner

Name: Sugato Ray
Login: sugatoray
Kind: user
Location: Wisconsin, USA
Company: University of Wisconsin - Milwaukee

Website: https://www.linkedin.com/in/sugatoray/
Twitter: sugatoray
Repositories: 50
Profile: https://github.com/sugatoray

I am a Physicist (PhD ongoing). Research Interests: Data Science, ML, DL, Statistics, Math, Computing.

Citation (CITATION.cff)

# file: CITATION.cff

cff-version: 1.2.0
title: "GeneSpeak - A library to encode text as DNA and decode DNA to text"
message: "If you use this software, please cite it using these metadata."
type: "software"
authors:
  - family-names: "Ray"
    given-names: "Sugato"
    #email: "author@email.com"
    affiliation: "University of Wisconsin Milwaukee"
    orcid: "https://orcid.org/0000-0002-9886-2324"
    alias: "sugatoray"
repository-code: "https://github.com/sugatoray/genespeak"
url: "https://sugatoray.github.io/genespeak"
repository: "https://doi.org/10.5281/zenodo.5885777"
repository-artifact: "https://pypi.org/project/genespeak/"
# version: 1.0.0
doi: "10.5281/zenodo.5885777"
# date-released: 2022-01-21
keywords:
  - "python"
  - "encoding"
  - "decoding"
  - "genespeak"
  - "text-to-dna"
  - "dna-to-text"
license: "MIT"

#### Citations file related resources:
##
## - [x] GitHub Blog: https://github.blog/2021-08-19-enhanced-support-citations-github/
## - [x] Docs: https://citation-file-format.github.io/
##   - [x] Generate CITATION file: https://citation-file-format.github.io/cff-initializer-javascript/
##   - [x] The `.cff` format and fields: https://github.com/citation-file-format/citation-file-format/blob/main/README.md
##   - [x] The cff schema-guide: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
## - [x] LinkedIn Post: https://www.linkedin.com/posts/github_enhanced-citation-support-on-github-activity-6834161054352850944-LRDT
## - [x] Others:
##   - [x] https://guides.github.com/activities/citable-code/
##   - [x] https://docs.ropensci.org/cffr/articles/bibtex_cff.html
## - [x] Tools for working with CITATION.cff files
##   - All tools: https://github.com/citation-file-format/citation-file-format#tools-to-work-with-citationcff-files-wrench
##   - [x] doi2cff: 
##     - [x] GitHub: https://github.com/citation-file-format/doi2cff
##   - [x] cffconvert: 
##     - [x] PyPI: https://pypi.org/project/cffconvert/
##     - [x] GitHub: https://github.com/citation-file-format/cff-converter-python
##     - [x] Docker: https://github.com/citation-file-format/citation-file-format#validation-heavy_check_mark
##
##
## This CITATION.cff file was generated with cffinit.
## Visit https://bit.ly/cffinit to generate yours today!

GitHub Events

Total

Watch event: 4

Last Year

Watch event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 169
Total Committers: 3
Avg Commits per committer: 56.333
Development Distribution Score (DDS): 0.278

Past Year

Commits: 9
Committers: 2
Avg Commits per committer: 4.5
Development Distribution Score (DDS): 0.111

Top Committers

Name	Email	Commits
Sugato Ray	r**o@g**m	122
Sugato Ray	s**y@u**m	46
dependabot[bot]	4**]@u**m	1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 0
Total pull requests: 10
Average time to close issues: N/A
Average time to close pull requests: about 2 hours
Total issue authors: 0
Total pull request authors: 3
Average comments per issue: 0
Average comments per pull request: 2.2
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 2

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

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Top Authors

Issue Authors

Pull Request Authors

sugatoray (8)
imgbot[bot] (1)
dependabot[bot] (1)

Top Labels

Issue Labels

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dependencies (1)

Packages

Total packages: 2
Total downloads:
- pypi 380 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 13
Total maintainers: 1

pypi.org: genespeak

A library to encode text as DNA and decode DNA to text.

Homepage: https://github.com/sugatoray/genespeak/
Documentation: https://sugatoray.github.io/genespeak/
License: MIT License
Latest release: 0.0.9
published almost 4 years ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 380 Last month

Rankings

Dependent packages count: 10.1%

Stargazers count: 17.1%

Dependent repos count: 21.6%

Average: 24.8%

Forks count: 29.8%

Downloads: 45.2%

Maintainers (1)

sugatoray

Last synced: 12 months ago

conda-forge.org: genespeak

<a href="https://github.com/sugatoray/genespeak/"> <img src="https://raw.githubusercontent.com/sugatoray/genespeak/master/docs/assets/images/genespeak_banner_01.png" alt="genespeak-banner" /> </a> GeneSpeak allows you to encode regular text as DNA using base-pairs (`A`, `C`, `G`, `T`) and convert back to the original text. Text encoding is done for both `ascii` and `utf-8` characters based on the `strategy` keyword argument. PyPI: [https://pypi.org/project/genespeak/](https://pypi.org/project/genespeak/)

Homepage: https://github.com/sugatoray/genespeak/
License: MIT
Latest release: 0.0.9
published almost 4 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 49.5%

Dependent packages count: 51.2%

Stargazers count: 51.9%

Forks count: 61.1%

Last synced: 5 months ago

Dependencies

requirements/docs.txt pypi

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mdx_truly_sane_lists >=1.2
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mkdocs-awesome-pages-plugin >=2.5.0
mkdocs-bibtex >=1.0.0
mkdocs-coverage >=0.2.4
mkdocs-drawio-exporter >=0.8.0
mkdocs-enumerate-headings-plugin >=0.4.5
mkdocs-exclude >=1.0.2
mkdocs-gen-files >=0.3.3
mkdocs-git-revision-date-plugin >=0.3.1
mkdocs-include-markdown-plugin >=3.2.3
mkdocs-jupyter >=0.18.2
mkdocs-kroki-plugin >=0.2.0
mkdocs-macros-plugin >=0.6.0
mkdocs-markdownextradata-plugin >=0.2.4
mkdocs-markmap >=2.1.2
mkdocs-material ==8.1.3
mkdocs-material-extensions >=1.0.3
mkdocs-minify-plugin >=0.4.1
mkdocs-pdf-export-plugin >=0.5.9
mkdocs-redirects >=1.0.3
mkdocs-table-reader-plugin >=0.6
mkdocs-tooltips >=0.1.0
mkdocs-tooltipster-links-plugin >=0.1.0
mkdocstrings >=0.16.2
pygments *
pymdown-extensions >=9.0

pyproject.toml pypi

setup.py pypi