R/detectGFF-internal.R

In acidgenomics/freerange: Generate and Manipulate Genomic Ranges

## Report the source of the gene annotations.
.detectGFFSource <- function(object) {
    assert(is(object, "GRanges"))
    mcols <- mcols(object)
    source <- mcols[["source"]]
    if (
        ## UCSC (e.g. hg38_knownGene)
        any(grepl(pattern = "_knownGene$", x = source, ignore.case = FALSE))
    ) {
        ## nocov start
        stop(
            "UCSC is intentionally not supported.\n",
            "Use a pre-built TxDb package instead ",
            "(e.g. 'TxDb.Hsapiens.UCSC.hg38.knownGene')"
        )
        ## nocov end
    } else if (
        ## Check for GENCODE prior to Ensembl.
        any(source == "ENSEMBL") &&
        any(source == "HAVANA") &&
        "gene_type" %in% colnames(mcols)
    ) {
        "GENCODE"
    } else if (
        any(grepl(pattern = "FlyBase", x = source, ignore.case = FALSE))
    ) {
        "FlyBase"
    } else if (
        any(grepl(pattern = "WormBase", x = source, ignore.case = FALSE))
    ) {
        "WormBase"
    } else if (
        any(grepl(pattern = "RefSeq", x = source, ignore.case = FALSE))
    ) {
        "RefSeq"
    } else if (
        any(grepl(
            pattern = "ensembl|havana",
            x = source,
            ignore.case = FALSE
        ))
    ) {
        "Ensembl"
    } else {
        ## nocov start
        stop(sprintf(
            fmt = paste(
                "Failed to detect valid GFF/GTF source.",
                "Supported: %s",
                sep = "\n"
            ),
            toString(c(
                "Ensembl", "GENCODE", "RefSeq",
                "FlyBase", "WormBase"
            ))
        ))
        ## nocov end
    }
}



## Determine if GFF or GTF.
.detectGFFType <- function(object) {
    assert(is(object, "GRanges"))
    if (any(c("ID", "Name", "Parent") %in% colnames(mcols(object)))) {
        "GFF3"
    } else {
        "GTF"
    }
}



.slotGFFDetectInfo <- function(object) {
    source <- .detectGFFSource(object)
    type <- .detectGFFType(object)
    message(sprintf("%s %s detected.", source, type))
    metadata(object)[["detect"]] <- c(
        source = source,
        type = type
    )
    object
}