R/gffRead.R

In alyssafrazee/ballgown: Flexible, isoform-level differential expression analysis

#' read in GTF/GFF file as a data frame
#'
#' @param gffFile name of GTF/GFF on disk
#' @param nrows number of rows to read in (default -1, which means read all 
#'    rows)
#' @param verbose if TRUE, print status info at beginning and end of file read.
#'    Default FALSE.
#' 
#' @return data frame representing the GTF/GFF file
#' 
#' @seealso \code{\link{getAttributeField}} to extract data from "attributes" 
#'  column; \url{http://useast.ensembl.org/info/website/upload/gff.html} for
#'   more information on the GTF/GFF file format.
#' 
#' @author Kasper Hansen
#' 
#' @export
#' @examples
#' gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
#' annot = gffRead(gtfPath)
gffRead = function (gffFile, nrows = -1, verbose=FALSE) 
{
    if(verbose){
        cat("Reading ", gffFile, ": ", sep = "")    
    }
    gff = read.table(gffFile, sep = "\t", as.is = TRUE, quote = "", 
        header = FALSE, comment.char = "#", nrows = nrows, 
        colClasses = c("character", "character", "character", "integer", 
            "integer", "character", "character", "character", "character"))
    colnames(gff) = c("seqname", "source", "feature", "start", 
        "end", "score", "strand", "frame", "attributes")
    if(verbose){
        cat("found", nrow(gff), "rows with classes:", paste(sapply(gff, 
            class), collapse = ", "), "\n")
    }
    stopifnot(!any(is.na(gff$start)), !any(is.na(gff$end)))
    return(gff)
}

# source: https://stat.ethz.ch/pipermail/bioconductor/2008-October/024669.html