pyrodigal-gv 0.3.2

Description:

pyrodigalgv 0.3.2

🔥🦠 Pyrodigal-gv
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.













🗺️ Overview
Pyrodigal is a Python module that provides
Cython bindings to 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
in prodigal-gv. The new models
are the following:

Acanthamoeba polyphaga mimivirus
Paramecium bursaria Chlorella virus
Acanthocystis turfacea Chlorella virus
VirSorter2's NCLDV gene model
Topaz (genetic code 15)
Agate (genetic code 15)
Gut phages (genetic code 15)
Gut phages (genetic code 11) × 5

🔧 Installing
pyrodigal-gv can be installed directly from PyPI
as a universal wheel that contains all required data files:
$ pip install 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:
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:
$ 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. Nature Biotechnology, 1-10.

Pyrodigal is scientific software, with a
published paper
in the Journal of Open-Source Software. Please
cite both Pyrodigal
and Prodigal 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 of the
online documentation.
💭 Feedback
⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the GitHub issue
tracker 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
for more details.
📋 Changelog
This project adheres to Semantic Versioning
and provides a changelog
in the Keep a Changelog format.
⚖️ License
This library is provided under the GNU General Public License v3.0.
The Prodigal code was written by Doug Hyatt 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.
This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original Prodigal authors. It was developed
by Martin Larralde during his PhD project
at the European Molecular Biology Laboratory in
the Zeller team.