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#' 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
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