Package: pyrodigal-gv
🔥🦠 Pyrodigal-gvAPyrodigalextension to predict genes in giant viruses and viruses with alternative genetic code.🗺️ OverviewPyrodigalis a Python module that providesCythonbindings toProdigal,
an efficient gene finding method for genomes and metagenomes based on dynamic programming.pyrodigal-gvis a small extension module forpyrodigalwhich distributes
additional metagenomic models for giant viruses and viruses that use
alternative genetic codes, first provided byAntônio Camargoinprodigal-gv. The new models
are the following:Acanthamoeba polyphaga mimivirusParamecium bursaria Chlorella virusAcanthocystis turfacea Chlorella virusVirSorter2's NCLDV gene modelTopaz(genetic code 15)Agate(genetic code 15)Gut phages (genetic code 15)Gut phages (genetic code 11) × 5🔧 Installingpyrodigal-gvcan be installed directly fromPyPIas a universal wheel that contains all required data files:$pipinstallpyrodigal-gv💡 ExampleJust use the providedViralGeneFinderclass instead of the usualGeneFinderfrompyrodigal, and the new viral models will be used automatically inmetamode:importBio.SeqIOimportpyrodigal_gvrecord=Bio.SeqIO.read("sequence.gbk","genbank")orf_finder=pyrodigal_gv.ViralGeneFinder(meta=True)fori,predinenumerate(orf_finder.find_genes(bytes(record.seq))):print(f">{record.id}_{i+1}")print(pred.translate())ViralGeneFinderhas an additional keyword argument,viral_only, which can
be set toTrueto run gene calling using only viral models.🔨 Command linepyrodigal-gvcomes with a very simple command line similar to Prodigal andpyrodigal:$pyrodigal-gv-i<input_file.fasta>-a<gene_translations.fasta>-d<gene_sequences.fasta>Contrary toprodigalandpyrodigal, thepyrodigal-gvscript runs inmetamode
by default! Running insinglemode can be done withpyrodigal-gv -p singlebut
the results will be exactly the same aspyrodigal, so why would you ever do this ⁉️🔖 CitationPyrodigal is scientific software, with apublished paperin theJournal of Open-Source Software. Please
cite bothPyrodigalandProdigalif you are using it in
an academic work, for instance as:Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyattet al., 2010).Detailed references are available on thePublications pageof theonline documentation.💭 Feedback⚠️ Issue TrackerFound a bug ? Have an enhancement request ? Head over to theGitHub issue
trackerif 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.🏗️ ContributingContributions are more than welcome! SeeCONTRIBUTING.mdfor more details.📋 ChangelogThis project adheres toSemantic Versioningand provides achangelogin theKeep a Changelogformat.⚖️ LicenseThis library is provided under theGNU General Public License v3.0.
The Prodigal code was written byDoug Hyattand is distributed under the
terms of the GPLv3 as well. Seevendor/Prodigal/LICENSEfor more information.
The giant virus and alternative genetic code virus parameters were created
byAntônio Camargo.This project is in no way not affiliated, sponsored, or otherwise endorsed
by theoriginal Prodigal authors. It was developed
byMartin Larraldeduring his PhD project
at theEuropean Molecular Biology Laboratoryin
theZeller team.