oma_organisms: adjusted to new column layout from OMA

saezlab · Sep 28, 2024 · ee7e7c3 · ee7e7c3
1 parent 9928e08
commit ee7e7c3
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/R/oma.R b/R/oma.R
@@ -29,6 +29,7 @@
 #'
 #' @importFrom readr cols
 #' @importFrom magrittr %>%
+#' @importFrom dplyr mutate
 #' @export
 #' @seealso \code{\link{ensembl_organisms}}
 oma_organisms <- function() {
@@ -38,16 +39,18 @@ oma_organisms <- function() {
         reader_param = list(
             col_names = c(
                 'oma_code',
-                'oma_tax_id',
                 'ncbi_tax_id',
-                'gtdb_genome',
                 'latin_name',
                 'genome_source',
                 'oma_version'
             ),
             col_types = cols(),
             skip = 3L
         )
+    ) %>%
+    mutate(
+        gtdb_tax_id = ifelse(ncbi_tax_id < 0L, -ncbi_tax_id, NA),
+        ncbi_tax_id = ifelse(ncbi_tax_id < 0L, NA, ncbi_tax_id)
     )
 
 }