R/read_gff.R

In biomartr: Genomic Data Retrieval

#' @title Import GFF File
#' @description This function reads an organism specific CDS stored
#' in a defined file format.
#' @param file a character string specifying the path to the file
#' storing the CDS.
#' @author Hajk-Georg Drost
#' @details This function takes a string specifying the path to the GFF file
#' of interest (e.g. the path returned by \code{\link{getGFF}}).
#' @return Either a \code{Biostrings} or \code{data.table} object.
#' @family gff
#' @family readers
#' @export
read_gff <- function(file) {
    # read gff file content
        gff.input <-
            readr::read_delim(
                file = file,
                delim = "\t",
                col_names = FALSE,
                comment = "#",
                col_types = readr::cols(
                  "X1" = readr::col_character(),
                  "X2" = readr::col_character(),
                  "X3" = readr::col_character(),
                  "X4" = readr::col_integer(),
                  "X5" = readr::col_integer(),
                  "X6" = readr::col_character(),
                  "X7" = readr::col_character(),
                  "X8" = readr::col_character(),
                  "X9" = readr::col_character()
                )
            )

    if (!file.exists(file))
        stop("The file path you specified does not seem to exist: '", file,"'.", call. = FALSE)

    if (ncol(gff.input) > 9)
        stop("The gff file format can not store more than 9 columns!", call. = FALSE)

    # name standardized columns
    gffNames <- c("seqid",
                  "source",
                  "type",
                  "start",
                  "end",
                  "score",
                  "strand",
                  "phase",
                  "attribute")

    names(gff.input) <- gffNames

    return(gff.input)
}