GENOME <- "galGal3"
ORGANISM <- "Gallus gallus"
ASSEMBLED_MOLECULES <- paste0("chr",
c(1:28, 32, "W", "Z",
"E22C19W28_E50C23", "E64",
"M"))
CIRC_SEQS <- "chrM"
.random_sequences <- paste0("chr",
c(1:2, 4:8, 10:13, 16:18, 20, 22, 25, 28, "W", "Z",
"E22C19W28_E50C23", "E64", "Un"), "_random")
.order_seqlevels <- function(seqlevels)
{
ordered_seqlevels <- c(ASSEMBLED_MOLECULES, .random_sequences)
stopifnot(length(seqlevels) == length(ordered_seqlevels))
idx <- match(ordered_seqlevels, seqlevels)
stopifnot(!anyNA(idx))
idx
}
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_000002315.2",
special_mappings=c(chrE22C19W28_E50C23="LGE22C19W28_E50C23",
chrE64="LGE64",
chrM="MT"),
unmapped_seqs=list(`pseudo-scaffold`=.random_sequences)
)
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