GENOME <- "loxAfr3"
ORGANISM <- "Loxodonta africana"
ASSEMBLED_MOLECULES <- "chrM"
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
scaffolds <- paste0("scaffold_", 0:2351)
ordered_seqlevels <- c(ASSEMBLED_MOLECULES, scaffolds)
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="GCF_000001905.1",
special_mappings=c(chrM="MT"),
## For some mysterious reason NCBI and UCSC disagree on the length
## of the scaffold_750 sequence. According to the former (Loxafr3.0
## assembly) it's 16799 but for the latter (loxAfr3 genome) it's 22731.
## This means that the scaffold_750 sequence in one is not the same as
## the scaffold_750 sequence in the other so we must not map them.
## We also assume that scaffold_750 in loxAfr3 is an "unplaced-scaffold"
## (and not an "unlocalized-scaffold" like reported in Loxafr3.0) so it's
## no different from all the other scaffolds in the assembly.
unmapped_seqs=list(`unplaced-scaffold`="scaffold_750")
)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.