ReFernment: Annotate RNA editing in for plastid genome submission

In TARobison/ReFernment: Automatically Adds RNA Editing Annotations To Plastome Genome Files

Description

Provides RNA editing annotations to satisfy GenBank submission requirements. Takes as input the paths to the folders containing required file inputs and the desired output path and the names of the files that the user wishes to annotate. Each filetype needn't be in separate folders, but it is recommended. This is especially true for output file path, because if it isn't separate from input gb files, the original files will be overwritten! Be sure that the file names for a respective genome are the same across file types!

Usage

ReFernment(gffFolderPath, fastaFolderPath = NULL, gbFolderPath = NULL,
  outFolderPath, genomes)

Arguments

gffFolderPath	this is the path to the folder containing the gff file(s) that you would like annotated.
fastaFolderPath	this is the path to the folder containing the fasta file(s) corresponding to the gff/gb files you would like annotated.
gbFolderPath	this is the path to the folder containing the gb file(s) that you would like annotated.
outFolderPath	this is the path to the folder where the new genome annotations will be produced. In addition to the preferred output file (gb or gff), the new annotations will produced as a feature table and a protein fasta file for BankIt submission. It is important to note that you should have the output file separate from your input files, as this prevents the script from overwriting the original files!
genomes	this should be a list containing the filenames of all the genomes that you would like to annotate. Note that you should not include the file endings of these files.

Value

an annotated gb or gff file file. In addition, a five column feature table will be produced, which can be used for BankIt submissions. This file will have the required misc_feature annotations as well as a translation corrected for RNA editing.

Author(s)

Tanner Robison

Examples

genomes <- c("Asplenium_pek", "Woodwardia_uni")
gbFolder <- "/home/travis/build/TARobison/ReFernment/examples/GB/"
gffFolder <- "/home/travis/build/TARobison/ReFernment/examples/GFF/"
outputFolder <- "/home/travis/build/TARobison/ReFernment/examples/"
ReFernment(gffFolder, fastaFolderPath=NULL, gbFolderPath=NULL, outputFolder, genomes)

TARobison/ReFernment documentation built on Jan. 9, 2022, 9:25 a.m.