prodigal_training {bifrost} R Documentation

Train the gene prediction model in an unsupervised manner

Description

Usage

prodigal_training(x);

Arguments

x

input target fasta sequence collection for make prodigal training, it should be a set of the genomics contigs assembly sequence, which can be a FastaFile object, a collection of the @T:SMRUCC.genomics.SequenceModel.FASTA.FastaSeq

env

[as Environment]

Details

Authors

seqtoolkit

Value

a trained prodigal TrainingModel object, which can be used for the gene prediction of the other genomics contigs assembly sequence that come from the same or a close related species, via the model parameter of the prodigal function.

this function returns a R# error message object if the input sequence data is nothing or can not be cast to a fasta sequence collection.

clr value class

Examples

 imports "bioseq.fasta" from "seqtoolkit";
 imports "bifrost" from "seqtoolkit";
 
 # train the gene prediction model from a well assembled 
 # genomics contigs sequence, and then apply the trained 
 # model on the other MAGs contigs of the same species
 let model <- prodigal_training(read.fasta("./genome.fasta"));
 let genes <- prodigal(read.fasta("./MAGs_contigs.fasta"), model = model);
[Package bifrost version 1.0.0.0 Index]