R/getAttributeField.R

In alyssafrazee/polyester: Simulate RNA-seq reads

#' extract a specific field of the "attributes" column of a data frame created 
#' from a GTF/GFF file
#'
#' @param x vector representing the "attributes" column of GTF/GFF file
#' @param field name of the field you want to extract from the "attributes" 
#'   column
#' @param attrsep separator for the fields in the attributes column.  Defaults 
#'   to '; ', 
#' the separator for GTF files outputted by Cufflinks.
#' @return vector of nucleotide positions included in the transcript
#' @seealso \url{http://useast.ensembl.org/info/website/upload/gff.html}, for
#'   specifics of the
#' GFF/GTF file format.
#' @author Wolfgang Huber, in the \code{davidTiling} package (LGPL license)
#' @export
#' @examples
#'   library(ballgown)
#'   gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
#'   gffdata = gffRead(gtfPath)
#'   gffdata$transcriptID = getAttributeField(gffdata$attributes, 
#'     field = "transcript_id")
#'
getAttributeField = function (x, field, attrsep = "; ") 
{
    s = strsplit(x, split = attrsep, fixed = TRUE)
    sapply(s, function(atts) {
        a = strsplit(atts, split = " ", fixed = TRUE)
        m = match(field, sapply(a, "[", 1))
        if (!is.na(m)) {
            rv = a[[m]][2]
        }
        else {
            rv = as.character(NA)
        }
        return(rv)
    })
}

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