change_id.rb in rbbt-util-5.19.30

- old
+ new
@@ -51,12 +51,20 @@
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
 
     identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
     identifiers = tsv.identifier_files.first if identifiers.nil?
     identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace and Organism.identifiers(tsv.namespace).exists?
+    identifiers.namespace ||= tsv.namespace
 
     fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
-    index = identifiers.index :target => format, :fields => fields, :persist => persist_input
+    #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
+
+    grep = Organism.blacklist_genes(tsv.namespace).list  if identifiers.namespace and Organism.blacklist_genes(tsv.namespace).exists?
+    if fields.nil?
+      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
+    else
+      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :fields => fields, :order => true, :unnamed => true, :persist => true, :data_persist => true)
+    end
 
     orig_type = tsv.type 
     tsv = tsv.to_double if orig_type != :double
 
     pos = tsv.fields.index field