R/read.tabout.R

In HajkD/LTRpred: De novo functional annotation of retrotransposons

#' @title Import information sheet returned by LTRdigest
#' @description This function imports the \code{*-ltrdigest_tabout.csv} file generated by \code{\link{LTRdigest}}.
#' @param tabout.file path to the tabout.csv file generated by the
#'   \code{\link{LTRdigest}} function.
#' @examples 
#' # example tabout file generated by LTRdigest for A thaliana
#' tabout.file <- system.file("TAIR10_chr_all-ltrdigest_tabout.csv",package = "LTRpred")
#' # import tabout file
#' imported.tabout <- read.tabout(tabout.file)
#' # look at the imported tabout file.
#' head(imported.tabout)      
#' @author Hajk-Georg Drost
#' @export

read.tabout <- function(tabout.file){
    
    LTRdigest.tabout.header <- readr::read_lines(tabout.file, n_max = 1)
    LTRdigest.tabout.header.names <-
        stringr::str_replace_all(unlist(stringr::str_split(LTRdigest.tabout.header, "\t")), " ", "_")
    
    LTRdigest.tabout <-
        readr::read_tsv(
            tabout.file,
            skip = 1,
            col_names = FALSE,
            col_types = readr::cols(
                "X1" = readr::col_integer(),
                "X2" = readr::col_integer(),
                "X3" = readr::col_integer(),
                "X4" = readr::col_character(),
                "X5" = readr::col_integer(),
                "X6" = readr::col_integer(),
                "X7" = readr::col_integer(),
                "X8" = readr::col_integer(),
                "X9" = readr::col_integer(),
                "X10" = readr::col_integer(),
                "X11" = readr::col_integer(),
                "X12" = readr::col_integer(),
                "X13" = readr::col_character(),
                "X14" = readr::col_integer(),
                "X15" = readr::col_integer(),
                "X16" = readr::col_character(),
                "X17" = readr::col_integer(),
                "X18" = readr::col_integer(),
                "X19" = readr::col_character(),
                "X20" = readr::col_character(),
                "X21" = readr::col_integer(),
                "X22" = readr::col_integer(),
                "X23" = readr::col_integer(),
                "X24" = readr::col_character(),
                "X25" = readr::col_character(),
                "X26" = readr::col_character(),
                "X27" = readr::col_integer(),
                "X28" = readr::col_integer(),
                "X29" = readr::col_integer(),
                "X30" = readr::col_character()
            )
        )
    
    colnames(LTRdigest.tabout) <-
        c(LTRdigest.tabout.header.names, "protein_domain")
    
    return(LTRdigest.tabout)
}