Use ensembl database server instead of biomart

scripts/ensembl_data.R

@@ -0,0 +1,77 @@
+# This script does post processing on the data from Ensembl and imports it into
+# the R package. Run this script after `ensembl_species.R` and
+# `ensembl_species.R`.
+
+library(data.table)
+
+species <- fread("species.csv")
+chromosomes <- fread("chromosomes.csv")
+genes <- fread("genes.csv")
+
+species_metadata <- chromosomes[,
+  .(
+    n_chromosomes = .N,
+    median_chromosome_length = as.double(stats::median(length))
+  ),
+  by = species
+]
+
+species <- merge(
+  species,
+  species_metadata,
+  by.x = "id",
+  by.y = "species",
+  sort = FALSE
+)
+
+# Remove duplicated genes within species.
+genes <- genes[!duplicated(genes, by = c("species", "gene"))]
+
+genes_chromosomes <- merge(
+  genes,
+  chromosomes,
+  by.x = c("species", "chromosome"),
+  by.y = c("species", "id"),
+  sort = FALSE
+)
+
+genes_chromosomes[, distance := ifelse(
+  start_position < length - end_position,
+  start_position,
+  length - end_position
+)]
+
+distances <- genes_chromosomes[, .(
+  species,
+  gene,
+  chromosome,
+  start_position,
+  end_position,
+  distance
+)]
+
+# This table will hold information on human genes.
+genes <- genes_chromosomes[
+  species == 9606,
+  .(
+    id = gene,
+    chromosome = name
+  )
+]
+
+genes[, name := gprofiler2::gconvert(
+  id,
+  target = "HGNC",
+  mthreshold = 1,
+  filter_na = FALSE
+)$target]
+
+# Previous versions of geposan used different species IDs. For backwards
+# compatibility, convert integer IDs to character.
+
+species[, id := as.character(id)]
+distances[, species := as.character(species)]
+
+usethis::use_data(species, overwrite = TRUE)
+usethis::use_data(genes, overwrite = TRUE)
+usethis::use_data(distances, overwrite = TRUE)