GENOME <- "galGal4"
ORGANISM <- "Gallus gallus"
ASSEMBLED_MOLECULES <- paste0("chr",
c(1:28, 32, "W", "Z",
"LGE22C19W28_E50C23", "LGE64",
"M"))
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
idx1 <- match(ASSEMBLED_MOLECULES, seqlevels)
stopifnot(!anyNA(idx1))
tmp <- IRanges::CharacterList(strsplit(seqlevels, "_"))
npart <- lengths(tmp)
stopifnot(all(npart <= 3L))
idx3 <- which(npart == 3L)
m3 <- matrix(unlist(tmp[idx3]), ncol=3L, byrow=TRUE)
assembled <- ASSEMBLED_MOLECULES
assembled[assembled == "chrLGE22C19W28_E50C23"] <- "chrLGE22C19W28"
m31 <- match(m3[ , 1L], assembled)
stopifnot(!anyNA(m31))
stopifnot(all(m3[ , 3L] == "random"))
oo3 <- order(m31, m3[ , 2L])
idx3 <- idx3[oo3]
idx2 <- which(npart == 2L & seqlevels != "chrLGE22C19W28_E50C23")
m2 <- matrix(unlist(tmp[idx2]), ncol=2L, byrow=TRUE)
stopifnot(all(m2[ , 1L] == "chrUn"))
oo2 <- order(m2[ , 2L])
idx2 <- idx2[oo2]
c(idx1, idx3, idx2)
}
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_000002315.2",
special_mappings=c(chrLGE22C19W28_E50C23="ChrE22C19W28_E50C23",
chrLGE64="ChrE64",
chrM="MT")
)
ENSEMBL_LINKER <- "ucscToEnsembl"
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