inst/registered/UCSC_genomes/dm1.R

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

GENOME <- "dm1"
ORGANISM <- "Drosophila melanogaster"
ASSEMBLED_MOLECULES <- paste0("chr", c("2L", "2R", "3L", "3R", "4", "X"))
CIRC_SEQS <- character(0)

library(GenomeInfoDb)  # for fetch_chrom_sizes_from_UCSC()

.order_seqlevels <- function(seqlevels)
{
    het <- paste0("chr", c("2h", "3h", "Xh", "Yh"))
    ordered_seqlevels <- c(ASSEMBLED_MOLECULES, het, "chrU")
    stopifnot(length(seqlevels) == length(ordered_seqlevels))
    idx <- match(ordered_seqlevels, seqlevels)
    stopifnot(!anyNA(idx))
    idx
}

GET_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)
}