Replace "-" with "_" in gene IDs before SBML export

Otherwise, libSBML reports an error: `Error: basic_string::substr: __pos (which is 2) > this->size() (which is 0)`
Waschina · Oct 7, 2024 · 05ec80e · 05ec80e
1 parent 95ba6cc
commit 05ec80e
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/io.R b/R/io.R
@@ -189,9 +189,9 @@ writeSBMLmod <- function(model, file_path = NULL) {
     model@subSys_id <- paste0("subsys_",model@subSys_id)
   model@met_id <- sub("\\[(.*)\\]$", "_\\1", model@met_id)
 
-  # libSBML seems not to allow "." nor ":" in gene IDs... replacing them here
+  # libSBML seems not to allow ".", ":", "-" in gene IDs... replacing them here
   # with underscores
-  regrepl <- "\\.|\\:"
+  regrepl <- "\\.|\\:|-"
   if(any(grepl(regrepl,model@allGenes))) {
     model@allGenes <- gsub(regrepl,"_",model@allGenes)
     model@genes <- lapply(model@genes, FUN = function(x) gsub(regrepl,"_",x))