GENOME <- "panTro2"
ORGANISM <- "Pan troglodytes"
ASSEMBLED_MOLECULES <- paste0("chr", c(1, "2a", "2b", 3:22, "X", "Y", "M"))
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
idx_chrUn <- match("chrUn", seqlevels)
stopifnot(!anyNA(idx_chrUn))
tmp <- IRanges::CharacterList(strsplit(seqlevels, "_"))
npart <- lengths(tmp)
stopifnot(all(npart <= 3L))
idx1 <- which(npart == 1L & seqlevels != "chrUn")
stopifnot(length(idx1) == length(ASSEMBLED_MOLECULES))
oo1 <- match(ASSEMBLED_MOLECULES, seqlevels[idx1])
stopifnot(!anyNA(oo1))
idx1 <- idx1[oo1]
idx3 <- which(npart == 3L)
stopifnot(length(idx3) == 1L, seqlevels[idx3] == "chr6_hla_hap1")
idx2 <- which(npart == 2L)
m2 <- matrix(unlist(tmp[idx2]), ncol=2L, byrow=TRUE)
m21 <- match(m2[ , 1L], ASSEMBLED_MOLECULES)
stopifnot(!anyNA(m21))
stopifnot(all(m2[ , 2L] == "random"))
oo2 <- order(m21)
idx2 <- idx2[oo2]
c(idx1, idx3, idx2, idx_chrUn)
}
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_000001515.3",
special_mappings=c(chrM="MT"),
unmapped_seqs=list(
`pseudo-scaffold`=
c("chr6_hla_hap1",
paste0("chr", c(1, "2a", "2b", 3:20, 22, "X", "Y"), "_random"),
"chrUn")
)
)
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