bug fix

Author: zachary-foster

R/parsers.R

@@ -471,7 +471,9 @@ parse_unite_general <- function(input = NULL, file = NULL, include_seqs = TRUE)
 
   # Remove unneeded columns
   output$data$tax_data$input <- NULL
-  output$data$tax_data$tax_string <- NULL
+  if ("tax_string" %in% names( output$data$tax_data)) {
+    output$data$tax_data$tax_string <- NULL
+  }
 
   # Add sequences 
   if (include_seqs) {

R/remove_ambiguous.R

@@ -6,16 +6,17 @@
 #'   placeholders for unknown taxa (e.g. "unknown ...").
 #' @param uncultured If \code{TRUE}, include names that suggest they are
 #'   assigned to uncultured organisms (e.g. "uncultured ...").
+#' @param regex If \code{TRUE}, includes regex syntax to make matching things like spaces more robust.
 #' @param case_variations If \code{TRUE}, include variations of letter case. 
 #'
 #' @export
-ambiguous_synonyms <- function(unknown = TRUE, uncultured = TRUE, case_variations = FALSE) {
+ambiguous_synonyms <- function(unknown = TRUE, uncultured = TRUE, regex = TRUE, case_variations = FALSE) {
   unknown_syns <- c(
     'unknown',
     'unidentified',
     'incertae sedis',
     'ambiguous',
-    'ambiguous_taxa',
+    'ambiguous taxa',
     'unassigned',
     'possible',
     'putative'
@@ -37,6 +38,9 @@ ambiguous_synonyms <- function(unknown = TRUE, uncultured = TRUE, case_variation
                 capitalize(output),
                 toupper(output))
   }
+  if (regex) {
+    output <- gsub(output, pattern = ' ', replacement = '[_ -]+')
+  }
   return(output)
 }