Commit 81b5bbf5 authored by Martin Larralde's avatar Martin Larralde
Browse files

Update documentation and project metadata with JOSS paper references

parent 8a5c8e05
......@@ -17,7 +17,7 @@ finder for genomes and metagenomes. **Now with SIMD!***
[![Docs](https://img.shields.io/readthedocs/pyrodigal/latest?style=flat-square&maxAge=600)](https://pyrodigal.readthedocs.io)
[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyrodigal/blob/main/CHANGELOG.md)
[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fpyrodigal)](https://pepy.tech/project/pyrodigal)
[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.4015169-purple?style=flat-square&maxAge=86400)](https://doi.org/10.5281/zenodo.4015169)
[![Paper](https://img.shields.io/badge/paper-JOSS-darkblue?style=flat-square&maxAge=86400)](https://doi.org/10.21105/joss.04296)
## 🗺️ Overview
......@@ -131,8 +131,8 @@ format.
### 🔬 [Biopython](https://github.com/biopython/biopython)
To use the [`OrfFinder`](https://pyrodigal.readthedocs.io/en/stable/api/orf_finder.html#pyrodigal.OrfFinder)
in single mode (corresponding to `prodigal -p single`, the default operation mode of Prodigal),
To use the [`OrfFinder`](https://pyrodigal.readthedocs.io/en/stable/api/orf_finder.html#pyrodigal.OrfFinder)
in single mode (corresponding to `prodigal -p single`, the default operation mode of Prodigal),
you must explicitly call the
[`train`](https://pyrodigal.readthedocs.io/en/stable/api/orf_finder.html#pyrodigal.OrfFinder.train) method
with the sequence you want to use for training before trying to find genes,
......@@ -183,6 +183,20 @@ for i, pred in enumerate(orf_finder.find_genes(seq.values.view('B'))):
method to get the sequence viewable by Cython as an array of `unsigned char`.*
## 🔖 Citation
Pyrodigal is scientific software, with a
[published paper](https://doi.org/10.21105/joss.04296)
in the [Journal of Open-Source Software](https://joss.theoj.org/). Please
cite both [Pyrodigal](https://doi.org/10.21105/joss.04296)
and [Prodigal](https://doi.org/10.1186/1471-2105-11-119) if you are using it in
an academic work, for instance as:
> Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt *et al.*, 2010).
Detailed references are available on the [Publications page](https://pyrodigal.readthedocs.io/en/stable/publications.html) of the
[online documentation](https://pyrodigal.readthedocs.io/).
## 💭 Feedback
### ⚠️ Issue Tracker
......
@article{larralde_pyrodigal_2022,
title = {Pyrodigal: {Python} bindings and interface to {Prodigal}, an efficient method for gene prediction in prokaryotes},
volume = {7},
copyright = {All rights reserved},
issn = {2475-9066},
shorttitle = {Pyrodigal},
url = {https://joss.theoj.org/papers/10.21105/joss.04296},
doi = {10.21105/joss.04296},
abstract = {Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296, https://doi.org/10.21105/joss.04296},
language = {en},
number = {72},
urldate = {2022-04-26},
journal = {Journal of Open Source Software},
author = {Larralde, Martin},
month = apr,
year = {2022},
pages = {4296},
file = {Snapshot:/home/althonos/.local/share/zotero/storage/RF7FCM8E/joss.html:text/html},
}
@article{hyatt_prodigal_2010,
title = {Prodigal: prokaryotic gene recognition and translation initiation site identification},
volume = {11},
issn = {1471-2105},
shorttitle = {Prodigal},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119},
doi = {10.1186/1471-2105-11-119},
language = {en},
number = {1},
urldate = {2022-04-26},
journal = {BMC Bioinformatics},
author = {Hyatt, Doug and Chen, Gwo-Liang and LoCascio, Philip F and Land, Miriam L and Larimer, Frank W and Hauser, Loren J},
month = dec,
year = {2010},
pages = {119},
file = {Full Text:/home/althonos/.local/share/zotero/storage/5UGJWWR8/Hyatt et al. - 2010 - Prodigal prokaryotic gene recognition and transla.pdf:application/pdf},
}
......@@ -221,6 +221,6 @@ nbsphinx_execute_arguments = [
extlinks = {
'doi': ('https://doi.org/%s', 'doi:'),
'pmid': ('https://pubmed.ncbi.nlm.nih.gov/%s', 'PMID:'),
'pmc': ('https://pubmed.ncbi.nlm.nih.gov/%s', 'PMID:'),
'pmc': ('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s', 'PMC'),
'isbn': ('https://www.worldcat.org/isbn/%s', 'ISBN:'),
}
......@@ -7,7 +7,7 @@ Pyrodigal |Stars|
*Cython bindings and Python interface to* `Prodigal <https://github.com/hyattpd/Prodigal/>`_,
*an ORF finder for genomes and metagenomes*. **Now with SIMD!**
|Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Mirror| |Issues| |Docs| |Changelog| |Downloads| |DOI|
|Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Mirror| |Issues| |Docs| |Changelog| |Downloads| |Paper|
.. |Actions| image:: https://img.shields.io/github/workflow/status/althonos/pyrodigal/Test/main?logo=github&style=flat-square&maxAge=300
:target: https://github.com/althonos/pyrodigal/actions
......@@ -57,8 +57,8 @@ Pyrodigal |Stars|
.. |Downloads| image:: https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fpyrodigal
:target: https://pepy.tech/project/pyrodigal
.. |DOI| image:: https://img.shields.io/badge/doi-10.5281%2Fzenodo.4015169-purple?style=flat-square&maxAge=86400
:target: https://doi.org/10.5281/zenodo.4015169
.. |Paper| image:: https://img.shields.io/badge/paper-JOSS-darkblue?style=flat-square&maxAge=86400
:target: https://doi.org/10.21105/joss.04296
Overview
......
......@@ -4,19 +4,33 @@ Publications
Citation
--------
Cite ``pyrodigal`` as well as the Prodigal paper as:
*Pyrodigal (Larralde, 2022), a Cythonized version of Prodigal (Hyatt et al, 2011)*.
When citing Pyrodigal, please additionally cite the original Prodigal paper,
which developed the actual method. You can for instance cite both papers as:
*Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt et al., 2010).*
Use the following for the bibliography:
- `Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). doi:10.1186/1471-2105-11-119 <https://doi.org/10.1186/1471-2105-11-119>`_.
- `Larralde, M. (2022). althonos/pyrodigal (v0.6.4). Zenodo. doi:10.5281/zenodo.4015169. <https://doi.org/10.5281/zenodo.4015169>`_
- `Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296. doi:10.21105/joss.04296 <https://doi.org/10.21105/joss.04296>`_.
Or just grab the `BibTex file <_static/bibtex/citation.bib>`_ with these two papers.
JOSS
----
Pyrodigal has been published in the `Journal of Open-Source Science <https://joss.theoj.org>`_.
JOSS is a community-run journal and relies upon volunteer effort. If you'd like
to support us please consider doing either one (or both) of the the following:
- Volunteering to review for JOSS sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
- Making a small donation to support running costs here: https://numfocus.org/donate-to-joss
Users
-----
``pyrodigal`` is being used in the following works:
Pyrodigal is being used in the following research works:
- `Carroll, L. M., Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio, E., Zeller, G. Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv 2021.05.03.442509; doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`_.
- `Sirén K., Millard, A., Petersen, B., Gilbert, M. T. P., Clokie, M. RJ., Sicheritz-Pontén, T. Rapid discovery of novel prophages using biological feature engineering and machine learning. bioRxiv 2020.08.09.243022; doi:10.1101/2020.08.09.243022 <https://doi.org/10.1101/2020.08.09.243022>`_.
......
......@@ -37,11 +37,22 @@ Caution:
symbol will be treated as an unknown nucleotide. Be careful to remove
the gap characters if loading sequences from a multiple alignment file.
Note:
To cite Pyrodigal, please cite both the original method and the short
paper for the Python library itself, for instance as:
Pyrodigal (Larralde, 2022), a Python library binding to Prodigal
(Hyatt *et al.*, 2010).
References:
- Larralde, M.
*Pyrodigal: Python bindings and interface to Prodigal, an efficient
method for gene prediction in prokaryotes*. Journal of Open Source
Software 7, no. 72 (25 April 2022): 4296. :doi:`10.21105/joss.04296`.
- Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.
*Prodigal: prokaryotic gene recognition and translation initiation
site identification.* BMC Bioinformatics. 2010 Mar 8;11:119.
doi:10.1186/1471-2105-11-119. PMID:20211023. PMCID:PMC2848648.
*Prodigal: prokaryotic gene recognition and translation initiation site
identification. BMC Bioinformatics 11, no. 1 (December 2010): 119.
:doi:`10.1186/1471-2105-11-119`. :pmid:`20211023`. :pmc:`2848648`.
"""
......
......@@ -35,7 +35,7 @@ project_urls =
Changelog = https://github.com/althonos/pyrodigal/blob/master/CHANGELOG.md
Coverage = https://codecov.io/gh/althonos/pyrodigal/
Builds = https://github.com/althonos/pyrodigal/actions
Zenodo = https://doi.org/10.5281/zenodo.4015169
Paper = https://doi.org/10.21105/joss.04296
PyPI = https://pypi.org/project/pyrodigal
[options]
......
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