parse_karyotypes <- function(species_name, lst) {
tibble::tibble(
species_name = species_name,
chromosome = lst$karyotype,
) %>%
dplyr::left_join(lst$top_level_region, by = c(chromosome = 'name')) %>%
dplyr::relocate('species_name', 'coord_system', 'chromosome', 'length')
}
#' Get the karyotype of a species
#'
#' This function retrieves the set of chromosomes of a species.
#'
#' @param species_name The species name, i.e., the scientific name, all letters
#' lowercase and space replaced by underscore. Examples: \code{'homo_sapiens'}
#' (human), \code{'ovis_aries'} (Domestic sheep) or \code{'capra_hircus'}
#' (Goat).
#' @param verbose Whether to be chatty.
#' @param warnings Whether to print warnings.
#' @param progress_bar Whether to show a progress bar.
#'
#' @return A \code{\link[tibble]{tibble}}, each row being a chromosome,
#' of 4 variables:
#' \describe{
#' \item{`species_name`}{Ensembl species name: this is the name used internally
#' by Ensembl to uniquely identify a species by name. It is the scientific
#' name but formatted without capitalisation and spacing converted with an
#' underscore, e.g., \code{'homo_sapiens'}.}
#' \item{`coord_system`}{Coordinate system type.}
#' \item{`chromosome`}{Chromosome name.}
#' \item{`length`}{Genomic length of the chromsome in base pairs.}
#' }
#'
#' @examples
#' # Get the karyotype of Caenorhabditis elegans
#' get_karyotypes('caenorhabditis_elegans')
#'
#' # Get the karyotype of the Giant panda
#' get_karyotypes('ailuropoda_melanoleuca')
#'
#' @md
#' @export
get_karyotypes <- function(species_name = 'homo_sapiens',
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
resource_urls <- glue::glue('/info/assembly/',
'{species_name}?bands=0')
responses <-
request_parallel(
resource_urls,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar
)
# Only keep those responses that responded successfully, i.e. with status == "OK".
responses_ok <-
purrr::keep(responses,
~ identical(.x$status, 'OK') &&
!rlang::is_empty(.x$content))
if (rlang::is_empty(responses_ok))
return(
tibble::tibble(
species_name = character(),
coord_system = character(),
chromosome = character(),
length = integer()
)
)
return(purrr::imap_dfr(
.x = responses_ok,
.f = ~ parse_karyotypes(species_name = species_name[.y],
lst = .x$content)
))
}
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