# 🔥🦠 Pyrodigal-gv [](https://github.com/althonos/pyrodigal-gv/stargazers)
*A [Pyrodigal](https://github.com/althonos/pyrodigal) extension to predict genes in giant viruses and viruses with alternative genetic code.*
[](https://github.com/althonos/pyrodigal-gv/actions)
[](https://codecov.io/gh/althonos/pyrodigal-gv/)
[](https://choosealicense.com/licenses/gpl-3.0/)
[](https://pypi.org/project/pyrodigal-gv)
[](https://anaconda.org/bioconda/pyrodigal-gv)
[](https://aur.archlinux.org/packages/python-pyrodigal-gv)
[](https://pypi.org/project/pyrodigal-gv/#files)
[](https://pypi.org/project/pyrodigal/#files)
[](https://pypi.org/project/pyrodigal-gv/#files)
[](https://github.com/althonos/pyrodigal-gv/)
[](https://github.com/althonos/pyrodigal-gv/issues)
[](https://github.com/althonos/pyrodigal-gv/blob/main/CHANGELOG.md)
[](https://pepy.tech/project/pyrodigal-gv)
## 🗺️ Overview
[Pyrodigal](https://github.com/althonos/pyrodigal) is a Python module that provides
[Cython](https://cython.org/) bindings to [Prodigal](https://github.com/hyattpd/Prodigal/),
an efficient gene finding method for genomes and metagenomes based on dynamic programming.
`pyrodigal-gv` is a small extension module for `pyrodigal` which distributes
additional metagenomic models for giant viruses and viruses that use
alternative genetic codes, first provided by [Antônio Camargo](https://github.com/apcamargo)
in [`prodigal-gv`](https://github.com/apcamargo/prodigal-gv). The new models
are the following:
* Acanthamoeba polyphaga mimivirus
* Paramecium bursaria Chlorella virus
* Acanthocystis turfacea Chlorella virus
* [VirSorter2](https://github.com/jiarong/VirSorter2)'s NCLDV gene model
* [Topaz](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full) (genetic code 15)
* [Agate](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full) (genetic code 15)
* Gut phages (genetic code 15)
* Gut phages (genetic code 11) × 5
## 🔧 Installing
`pyrodigal-gv` can be installed directly from [PyPI](https://pypi.org/project/pyrodigal/)
as a universal wheel that contains all required data files:
```console
$ pip install pyrodigal-gv
```
<!--
Otherwise, `pyrodigal-gv` is also available as a [Bioconda](https://bioconda.github.io/)
package:
```console
$ conda install -c bioconda pyrodigal-gv
``` -->
## 💡 Example
Just use the provided `ViralGeneFinder` class instead of the usual `GeneFinder`
from `pyrodigal`, and the new viral models will be used automatically in
*meta* mode:
```python
import Bio.SeqIO
import pyrodigal_gv
record = Bio.SeqIO.read("sequence.gbk", "genbank")
orf_finder = pyrodigal_gv.ViralGeneFinder(meta=True)
for i, pred in enumerate(orf_finder.find_genes(bytes(record.seq))):
print(f">{record.id}_{i+1}")
print(pred.translate())
```
`ViralGeneFinder` has an additional keyword argument, `viral_only`, which can
be set to `True` to run gene calling using only viral models.
## 🔨 Command line
`pyrodigal-gv` comes with a very simple command line similar to Prodigal and `pyrodigal`:
```console
$ pyrodigal-gv -i <input_file.fasta> -a <gene_translations.fasta> -d <gene_sequences.fasta>
```
*Contrary to `prodigal` and `pyrodigal`, the `pyrodigal-gv` script runs in **meta** mode
by default! Running in **single** mode can be done with `pyrodigal-gv -p single` but
the results will be exactly the same as `pyrodigal`, so why would you ever do this ⁉️*
## 🔖 Citation
If you use the features provided by `pyrodigal-gv` beyond the base Pyrodigal functionality, please cite the original manuscript detailing these extensions:
> Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., ... and Kyrpides, N. C. (2023). [Identification of mobile genetic elements with geNomad](https://doi.org/10.1038/s41587-023-01953-y). Nature Biotechnology, *1-10*.
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
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue
tracker](https://github.com/althonos/pyrodigal-gv/issues) if you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.
### 🏗️ Contributing
Contributions are more than welcome! See
[`CONTRIBUTING.md`](https://github.com/althonos/pyrodigal-gv/blob/main/CONTRIBUTING.md)
for more details.
## 📋 Changelog
This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/pyrodigal-gv/blob/main/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
## ⚖️ License
This library is provided under the [GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/).
The Prodigal code was written by [Doug Hyatt](https://github.com/hyattpd) and is distributed under the
terms of the GPLv3 as well. See `vendor/Prodigal/LICENSE` for more information.
The giant virus and alternative genetic code virus parameters were created
by [Antônio Camargo](https://github.com/apcamargo).
*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [original Prodigal authors](https://github.com/hyattpd). It was developed
by [Martin Larralde](https://github.com/althonos/) during his PhD project
at the [European Molecular Biology Laboratory](https://www.embl.de/) in
the [Zeller team](https://github.com/zellerlab).*
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"description": "# \ud83d\udd25\ud83e\udda0 Pyrodigal-gv [](https://github.com/althonos/pyrodigal-gv/stargazers)\n\n*A [Pyrodigal](https://github.com/althonos/pyrodigal) extension to predict genes in giant viruses and viruses with alternative genetic code.*\n\n[](https://github.com/althonos/pyrodigal-gv/actions)\n[](https://codecov.io/gh/althonos/pyrodigal-gv/)\n[](https://choosealicense.com/licenses/gpl-3.0/)\n[](https://pypi.org/project/pyrodigal-gv)\n[](https://anaconda.org/bioconda/pyrodigal-gv)\n[](https://aur.archlinux.org/packages/python-pyrodigal-gv)\n[](https://pypi.org/project/pyrodigal-gv/#files)\n[](https://pypi.org/project/pyrodigal/#files)\n[](https://pypi.org/project/pyrodigal-gv/#files)\n[](https://github.com/althonos/pyrodigal-gv/)\n[](https://github.com/althonos/pyrodigal-gv/issues)\n[](https://github.com/althonos/pyrodigal-gv/blob/main/CHANGELOG.md)\n[](https://pepy.tech/project/pyrodigal-gv)\n\n\n## \ud83d\uddfa\ufe0f Overview\n\n[Pyrodigal](https://github.com/althonos/pyrodigal) is a Python module that provides \n[Cython](https://cython.org/) bindings to [Prodigal](https://github.com/hyattpd/Prodigal/), \nan efficient gene finding method for genomes and metagenomes based on dynamic programming.\n\n`pyrodigal-gv` is a small extension module for `pyrodigal` which distributes\nadditional metagenomic models for giant viruses and viruses that use\nalternative genetic codes, first provided by [Ant\u00f4nio Camargo](https://github.com/apcamargo)\nin [`prodigal-gv`](https://github.com/apcamargo/prodigal-gv). The new models\nare the following:\n\n* Acanthamoeba polyphaga mimivirus\n* Paramecium bursaria Chlorella virus\n* Acanthocystis turfacea Chlorella virus\n* [VirSorter2](https://github.com/jiarong/VirSorter2)'s NCLDV gene model\n* [Topaz](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full) (genetic code 15)\n* [Agate](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full) (genetic code 15)\n* Gut phages (genetic code 15)\n* Gut phages (genetic code 11) \u00d7 5\n\n## \ud83d\udd27 Installing\n\n`pyrodigal-gv` can be installed directly from [PyPI](https://pypi.org/project/pyrodigal/)\nas a universal wheel that contains all required data files:\n```console\n$ pip install pyrodigal-gv\n```\n\n<!--\nOtherwise, `pyrodigal-gv` is also available as a [Bioconda](https://bioconda.github.io/)\npackage:\n```console\n$ conda install -c bioconda pyrodigal-gv\n``` -->\n\n## \ud83d\udca1 Example\n\nJust use the provided `ViralGeneFinder` class instead of the usual `GeneFinder`\nfrom `pyrodigal`, and the new viral models will be used automatically in\n*meta* mode:\n\n```python\nimport Bio.SeqIO\nimport pyrodigal_gv\n\nrecord = Bio.SeqIO.read(\"sequence.gbk\", \"genbank\")\n\norf_finder = pyrodigal_gv.ViralGeneFinder(meta=True)\nfor i, pred in enumerate(orf_finder.find_genes(bytes(record.seq))):\n print(f\">{record.id}_{i+1}\")\n print(pred.translate())\n```\n\n`ViralGeneFinder` has an additional keyword argument, `viral_only`, which can\nbe set to `True` to run gene calling using only viral models.\n\n## \ud83d\udd28 Command line\n\n`pyrodigal-gv` comes with a very simple command line similar to Prodigal and `pyrodigal`:\n```console\n$ pyrodigal-gv -i <input_file.fasta> -a <gene_translations.fasta> -d <gene_sequences.fasta>\n```\n\n*Contrary to `prodigal` and `pyrodigal`, the `pyrodigal-gv` script runs in **meta** mode\nby default! Running in **single** mode can be done with `pyrodigal-gv -p single` but \nthe results will be exactly the same as `pyrodigal`, so why would you ever do this \u2049\ufe0f*\n\n\n## \ud83d\udd16 Citation\n\nIf you use the features provided by `pyrodigal-gv` beyond the base Pyrodigal functionality, please cite the original manuscript detailing these extensions:\n\n> Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., ... and Kyrpides, N. C. (2023). [Identification of mobile genetic elements with geNomad](https://doi.org/10.1038/s41587-023-01953-y). Nature Biotechnology, *1-10*.\n\nPyrodigal is scientific software, with a\n[published paper](https://doi.org/10.21105/joss.04296)\nin the [Journal of Open-Source Software](https://joss.theoj.org/). Please\ncite both [Pyrodigal](https://doi.org/10.21105/joss.04296)\nand [Prodigal](https://doi.org/10.1186/1471-2105-11-119) if you are using it in\nan academic work, for instance as:\n\n> Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt *et al.*, 2010).\n\nDetailed references are available on the [Publications page](https://pyrodigal.readthedocs.io/en/stable/publications.html) of the\n[online documentation](https://pyrodigal.readthedocs.io/).\n\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/althonos/pyrodigal-gv/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! 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See `vendor/Prodigal/LICENSE` for more information.\nThe giant virus and alternative genetic code virus parameters were created\nby [Ant\u00f4nio Camargo](https://github.com/apcamargo).\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [original Prodigal authors](https://github.com/hyattpd). It was developed\nby [Martin Larralde](https://github.com/althonos/) during his PhD project\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in\nthe [Zeller team](https://github.com/zellerlab).*\n",
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