Add some initial utilities

R/non-biomart-utils.R

@@ -0,0 +1,89 @@
+## The Ensembl BioMart isn't always fit for purpose, and some operations can also be achieved using the 
+## Ensembl REST API.  This file contains some functions that may be useful to biomaRt users,
+## but which don't actually interact with BioMart.
+
+createNameToAliasMap <- function() {
+  url <- "https://rest.ensembl.org/info/species?"
+
+  req <- httr2::request(url) |>
+    httr2::req_headers("Accept" = "application/json")
+  json <- req_perform(req) |>
+    resp_body_json()
+
+  names <- vapply(json$species, FUN = \(x) { x$name }, FUN.VALUE = character(1))
+
+  aliases <- lapply(json$species, 
+                    FUN = \(x) { 
+                      all <- c(x$display_name, unlist(x$aliases), x$common_name) 
+                      return(unique(tolower(all)))
+                    })
+
+  names(aliases) <- names
+  return(aliases)
+}
+
+pickReferenceStrain <- function(genomes_to_choose_from) {
+  url <- "https://rest.ensembl.org/info/species?"
+
+  req <- httr2::request(url) |>
+    httr2::req_headers("Accept" = "application/json")
+  json <- req_perform(req) |>
+    resp_body_json()
+
+  names <- vapply(json$species, FUN = \(x) { x$name }, FUN.VALUE = character(1))
+
+  idx <- which(names %in% genomes_to_choose_from)
+
+  strains <- vapply(json$species[idx], 
+                    FUN = \(x) { 
+                      unique(tolower(x$strain))
+                    },
+                    FUN.VALUE = character(1))
+
+  idx2 <- which(strains == "reference")
+
+  message("Your search term was ambigous and multiple strains matching this term were found\n",
+          "Selecting the reference geneome for this organism.")
+
+  return(names[idx][idx2])
+}
+
+## Given an input string, try to identify the genome name for the organism
+findGenomeName <- function(input) {
+
+  input <- tolower(input)
+  aliases <- createNameToAliasMap()
+
+  if(input %in% names(aliases)) {
+    res <- input
+  } else {
+    search <- vapply(aliases, FUN = \(x, input) { 
+      any(grepl(pattern = input, x = x))
+    }, input = paste0("^", input, "$"), 
+    FUN.VALUE = logical(1))
+    if(any(search) && (sum(search) == 1)) {
+      res <- names(aliases)[which(search)]
+    } else if (any(search) && (sum(search) > 1)) {
+      res <- pickReferenceStrain(genomes_to_choose_from = names(aliases)[which(search)])
+    } else {
+      stop('Unable to match the search term to a genome')
+    }
+  }
+  return(res)
+}
+
+## use the Ensembl Rest API to get the current Ensembl version
+getCurrentEnsemblRelease <- function() {
+
+  req <- httr2::request("https://rest.ensembl.org/info/data/") |>
+    httr2::req_headers("Accept" = "application/json")
+
+  version <- req |> 
+    httr2::req_perform() |>
+    httr2::resp_body_json() |>
+    unlist() |>
+    as.integer()
+
+  return(version)
+}
+