geposan/scripts/chromosome_names.R

library(data.table)
library(httr)

ensembl_api_url <- "https://rest.ensembl.org"

#' Perform a request to the Ensembl REST API.
ensembl_request <- function(api_path) {
  content(stop_for_status(GET(
    paste0(ensembl_api_url, api_path),
    content_type_json()
  )))
}

#' Get IDs of all available vertebrates.
get_species_ids <- function() {
  species <- ensembl_request("/info/species")$species
  sapply(species, function(species) species$name)
}

#' Get all chromosomes names for a species.
get_species_chromosomes <- function(species_id) {
  chromosomes <- unlist(ensembl_request(
    paste0("/info/assembly/", species_id)
  )$karyotype)
}

#' Get a vector of all available unqiue chromosome names.
#'
#' There are multiple names for mitochondrial DNA which have to be removed
#' manually, unfortunately.
get_all_chromosomes <- function() {
  chromosomes <- sapply(get_species_ids(), get_species_chromosomes)
  unique(unlist(chromosomes))
}