WIP make.biom reftaxonomy change

mothur · b3c223ff193e6d1281c2fbc0c0ff5b8905c3ae2e · mothur-westcott committed Jun 30, 2016 · Jun 30, 2016 · b3c223f
1 parent b598f39
commit b3c223ff193e6d1281c2fbc0c0ff5b8905c3ae2e
Unified Split

Showing with 8 additions and 2 deletions.

+8 −2 source/commands/makebiomcommand.cpp
diff --git a/source/commands/makebiomcommand.cpp b/source/commands/makebiomcommand.cpp
@@ -1192,8 +1192,14 @@ int MakeBiomCommand::getGreenGenesOTUIDs(vector<SharedRAbundFloatVector*>& looku
             m->removeConfidences(OTUTaxonomy);
             
             //remove unclassifieds to match template
-            int thisPos = OTUTaxonomy.find("unclassified;");
-            if (thisPos != string::npos) {  OTUTaxonomy = OTUTaxonomy.substr(0, thisPos);  }
+            int thisPos = OTUTaxonomy.find("unclassified;"); //"Porphyromonadaceae"_unclassified;
+            if (thisPos != string::npos) {
+                OTUTaxonomy = OTUTaxonomy.substr(0, thisPos);
+                thisPos = OTUTaxonomy.find_last_of(";"); //remove rest of parent taxon
+                if (thisPos != string::npos) {
+                    OTUTaxonomy = OTUTaxonomy.substr(0, thisPos);
+                }
+            }
             
             //get list of reference ids that map to this taxonomy
             vector<string> referenceIds = phylo.getSeqs(OTUTaxonomy);