GENOME <- "mm9"
ORGANISM <- "Mus musculus"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:19, "X", "Y", "M"))
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
idx_chrUn <- match("chrUn_random", seqlevels)
stopifnot(!anyNA(idx_chrUn))
tmp <- IRanges::CharacterList(strsplit(seqlevels, "_"))
npart <- lengths(tmp)
stopifnot(all(npart <= 2L))
idx1 <- which(npart == 1L)
stopifnot(length(idx1) == length(ASSEMBLED_MOLECULES))
oo1 <- match(ASSEMBLED_MOLECULES, seqlevels[idx1])
stopifnot(!anyNA(oo1))
idx1 <- idx1[oo1]
idx2 <- which(npart == 2L & seqlevels != "chrUn_random")
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, 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_000001635.18",
AssemblyUnits=c("C57BL/6J", "non-nuclear"),
unmapped_seqs=list(
`pseudo-scaffold`=
paste0("chr", c(1, 3:5, 7:9, 13, 16:17, "X", "Y", "Un"), "_random")
)
)
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