inst/registered/UCSC_genomes/hg17.R

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

GENOME <- "hg17"
ORGANISM <- "Homo sapiens"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:22, "X", "Y", "M"))
CIRC_SEQS <- "chrM"

.hap_sequences <- paste0("chr6_hla_hap", 1:2)
.random_sequences <- paste0("chr", c(1:10, 12:13, 15:19, 22, "X"), "_random")

library(GenomeInfoDb)  # for fetch_chrom_sizes_from_UCSC()

.order_seqlevels <- function(seqlevels)
{
    ordered_seqlevels <- c(ASSEMBLED_MOLECULES,
                           .hap_sequences,
                           .random_sequences)
    stopifnot(length(seqlevels) == length(ordered_seqlevels))
    idx <- match(ordered_seqlevels, seqlevels)
    stopifnot(!anyNA(idx))
    idx
}

GET_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_000001405.11",
    special_mappings=c(chr6_hla_hap1="NG_002392.2",
                       chr6_hla_hap2="NG_002433.1"),
    unmapped_seqs=list(
        `assembled-molecule`="chrM",
        `pseudo-scaffold`=.random_sequences)
)