R/getAttributeField.R

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

#' 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 \code{\link{gffRead}} for creating a data frame from a GTF/GFF file,
#'   and \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} R package (LGPL license)
#' 
#' @export
#' @examples
#' 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