inst/registered/UCSC_genomes/bosTau1.R

In Bioconductor/GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

GENOME <- "bosTau1"
ORGANISM <- "Bos taurus"
ASSEMBLED_MOLECULES <- character(0)
CIRC_SEQS <- character(0)

.order_seqlevels <- function(seqlevels)
{
    ordered_seqlevels <- paste0("SCAFFOLD", 1:449727)
    stopifnot(length(seqlevels) == length(ordered_seqlevels))
    idx <- match(ordered_seqlevels, seqlevels)
    stopifnot(!anyNA(idx))
    idx
}

FETCH_ORDERED_CHROM_SIZES <-
    function(goldenPath.url=getOption("UCSC.goldenPath.url"))
{
    chrom_sizes <- GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME,
                                              goldenPath.url=goldenPath.url)
    oo <- .order_seqlevels(chrom_sizes[ , "chrom"])
    S4Vectors:::extract_data_frame_rows(chrom_sizes, oo)
}