R/fasta_cleaner.R

In brouwern/dayoff: Bioinformatics in R

#' Function to convert a FASTA file stored as an object into a vector
#'
#' @param fasta_object R object with FASTA character data to clean
#' @param parse Parse data to character vector?
#'
#' @examples
#'
#' header. <- ">NC_001477.1 Dengue virus 1, complete genome"
#' fasta_cleaner(dengueseq_fasta, parse = TRUE)
#'
#' @export

fasta_cleaner <- function(fasta_object, parse = TRUE){

         #header <- gsub("\\|","",header)
         #header <- gsub("\\+","",header)
         #header <- gsub("\\=","",header)
         #header <- gsub("\\:","",header)
         #header <- gsub("\\;","",header)

         #fasta_object <- gsub("\\|","",fasta_object)
         #fasta_object <- gsub("\\+","",fasta_object)
         #fasta_object <- gsub("\\=","",fasta_object)
         #fasta_object <- gsub("\\:","",fasta_object)
         #fasta_object <- gsub("\\;","",fasta_object)


         #fasta_object <- gsub(header, "", fasta_object)

        fasta_object <- sub("^(>)(.*?)(\\n)(.*)(\\n\\n)","\\4",fasta_object)
        fasta_object <- gsub("\n", "", fasta_object)

         if(parse == TRUE){
         fasta_object <- stringr::str_split(fasta_object,
                                   pattern = "",
                                   simplify = FALSE)
         }


         return(fasta_object[[1]])
 }