ORF code, from https://support.bioconductor.org/p/100570/#100612

orf.R

dna <- getFastaSeq()
## function for finding orfs. Returned as IRanges.
ORFdef <- find_in_frame_ORFs(dna, longestORF = FALSE, minimumLength = 8)
ORFdef <- ORFdef[lengths(ORFdef) > 0]

## Map (mapply) on each five prime leader
uORFs <- Map(
    function(granges, tx_name, ORFdef) {
        map_granges(ORFdef, granges, tx_name)
    },
    fiveUTRs, names(fiveUTRs),
    MoreArgs=list(ORFdef = ORFdef)
)

## ?? not sure what map_granges returns
## uORFs <- GRangesList(unlist(uORFs))