Use ensembl database server instead of biomart

scripts/ensembl_species.R

@@ -0,0 +1,119 @@
+# This is an *interactive* script for retrieving information on species from the
+# Ensembl database. There are taxons with more than one entry in the database.
+# For each species that has already been seen, the script asks whether to keep
+# it or replace it. We recommend to choose the most generic entry in most
+# cases.
+
+library(data.table)
+library(DBI)
+library(glue)
+
+# These are the output tables of this script:
+
+species <- data.table(
+  id = integer(),
+  name = character(),
+  scientific_name = character(),
+  table_name = character()
+)
+
+chromosomes <- data.table(
+  species = integer(),
+  id = integer(),
+  name = character(),
+  length = integer()
+)
+
+rlog::log_info("Connecting to Ensembl database server")
+db <- dbConnect(
+  RMariaDB::MariaDB(),
+  host = "ensembldb.ensembl.org",
+  port = 5306,
+  user = "anonymous"
+)
+
+rlog::log_info("Retrieving list of databases")
+tables <- dbGetQuery(db, "SHOW DATABASES LIKE '%_core_110_%'")[, 1]
+
+# Populates the species and chromosomes tables using data from each species'
+# table within the Ensembl database. Species without a karyotype will be skipped
+# without adding any information to the tables.
+for (table in tables) {
+  rlog::log_info(glue("Reading species information from {table}"))
+  dbExecute(db, glue_sql("USE {`table`}", .con = db))
+
+  species_id <- db |>
+    dbGetQuery("
+      SELECT meta_value FROM meta
+        WHERE meta_key = 'species.taxonomy_id'") |>
+    as.integer()
+
+  species_name <- db |>
+    dbGetQuery("
+      SELECT meta_value FROM meta
+        WHERE meta_key = 'species.display_name'") |>
+    as.character()
+
+  species_scientific_name <- db |>
+    dbGetQuery("
+      SELECT meta_value FROM meta
+        WHERE meta_key = 'species.scientific_name'") |>
+    as.character()
+
+  rlog::log_info(glue(
+    "Found species {species_name} ({species_scientific_name})"
+  ))
+
+  if (species[id == species_id, .N] > 0) {
+    old_name <- species[id == species_id, name]
+    old_scientific_name <- species[id == species_id, scientific_name]
+    input <- readline(glue("\\
+      Taxon already present ({old_name}, {old_scientific_name}). \\
+      Replace with {species_name} ({species_scientific_name})? [y/N] "))
+
+    if (input == "y") {
+      species <- species[id != species_id]
+      chromosomes <- chromosomes[species != species_id]
+    } else {
+      next
+    }
+  }
+
+  species_chromosomes <- db |>
+    dbGetQuery(glue("
+      SELECT seq_region_id, seq_region.name, length
+      FROM seq_region
+        JOIN seq_region_attrib USING (seq_region_id)
+        JOIN attrib_type USING (attrib_type_id)
+      WHERE code = 'karyotype_rank'
+        AND NOT EXISTS
+          (SELECT * FROM seq_region_attrib AS chromosome_attrib
+            JOIN attrib_type USING (attrib_type_id)
+            WHERE chromosome_attrib.seq_region_id = seq_region.seq_region_id
+              AND code = 'sequence_location'
+              AND chromosome_attrib.value != 'nuclear_chromosome');
+    ")) |>
+    as.data.table() |>
+    setnames("seq_region_id", "id")
+
+  species_chromosomes[, species := species_id]
+
+  if (nrow(species_chromosomes) == 0) {
+    rlog::log_info("Skipping (no karyotype)")
+    next
+  }
+
+  species <- rbind(species, data.table(
+    id = species_id,
+    name = species_name,
+    scientific_name = species_scientific_name,
+    table_name = table
+  ))
+
+  chromosomes <- rbind(chromosomes, species_chromosomes)
+}
+
+dbDisconnect(db)
+
+fwrite(species, "species.csv")
+fwrite(chromosomes, "chromosomes.csv")