GENOME <- "panTro5"
ORGANISM <- "Pan troglodytes"
ASSEMBLED_MOLECULES <- paste0("chr", c(1, "2A", "2B", 3:22, "X", "Y", "M"))
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
tmp <- IRanges::CharacterList(strsplit(seqlevels, "_"))
npart <- lengths(tmp)
stopifnot(all(npart %in% c(1L, 3L, 4L)))
idx1 <- which(npart == 1L)
stopifnot(length(idx1) == length(ASSEMBLED_MOLECULES))
oo1 <- match(ASSEMBLED_MOLECULES, seqlevels[idx1])
stopifnot(!anyNA(oo1))
idx1 <- idx1[oo1]
idx4 <- which(npart == 4L)
m4 <- matrix(unlist(tmp[idx4]), ncol=4L, byrow=TRUE)
m41 <- match(m4[ , 1L], ASSEMBLED_MOLECULES)
stopifnot(!anyNA(m41))
stopifnot(all(m4[ , 2L] == "NW"))
stopifnot(all(m4[ , 4L] == "random"))
oo4 <- order(m41, m4[ , 3L])
idx4 <- idx4[oo4]
idx3 <- which(npart == 3L)
m3 <- matrix(unlist(tmp[idx3]), ncol=3L, byrow=TRUE)
stopifnot(all(m3[ , 1L] == "chrUn"))
stopifnot(all(m3[ , 2L] == "NW"))
oo3 <- order(m3[ , 3L])
idx3 <- idx3[oo3]
c(idx1, idx4, idx3)
}
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_000001515.7",
special_mappings=c(chrM="MT")
)
ENSEMBL_LINKER <- "chromAlias"
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