GENOME <- "rheMac2"
ORGANISM <- "Macaca mulatta"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:20, "X"))
CIRC_SEQS <- character(0)
.order_seqlevels <- function(seqlevels)
{
ordered_seqlevels <- c(ASSEMBLED_MOLECULES, "chrUr")
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)
}
NCBI_LINKER <- list(
assembly_accession="GCA_000002255.2",
unmapped_seqs=list(`pseudo-scaffold`="chrUr")
)
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