#' @title Generate the bash command of RNAfold
#'
#' @description RNAfold is a RNA secondary structure prediction software in ViennaRNA package.
#' This R function is used to generate the single bash command of RNAfold, which is used to predict the MEA RNA secondary structures of the full length transcripts.
#'
#' @param Group_num The number of the group of the fasta file.
#' This value corresponds to the \code{divide_num} argument of the \code{\link{tx_seq_extraction}}.
#'
#' @param Size The size of the transcript.
#' Can be one of the "Small", "Middle", and "Large".
#' @param outPutNames The name of the output files of RNA fold.
#'
#' @return This function will return the code of RNAfold that can directly run in the terminal.
#'
#' @seealso \code{\link{tx_seq_extraction}}, \code{\link{RNAfold}}, and \code{\link{rfold_assembly_tx}}
#'
#' @examples
#' cat(Single_RNAfold(1,"Small","gsmall"))
#'
#' @export
#'
#' \dontrun{
#' tx_seq_extraction(MMusculus,txdb,getwd())
#' system(Single_RNAfold(1,"Small","gsmall"))
#'}
#'
Single_RNAfold <-
function(Group_num,Size = "Small",outPutNames="Foo") {
RNAfold = c(
'RNAfold',
paste0('--infile=','./',Size,"_d",Group_num,".fasta"),
paste0('--outfile=',outPutNames),
'--maxBPspan=150',
'--MEA=.1',
'--temp=70',
'--noconv',
'--noPS'
)
paste(RNAfold, collapse = " \\\n")
}
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