data: Add more chromosomes

scripts/chromosome_names.R

@@ -0,0 +1,34 @@
+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))
+}