Modifies picrust option to accept new unclassified format

Parent_unclassified #241
mothur · e41f1586a40745ead86b167082c9133624244568 · mothur-westcott committed Jun 30, 2016 · Jun 30, 2016 · e41f158
1 parent b3c223f
commit e41f1586a40745ead86b167082c9133624244568
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
@@ -1026,8 +1026,14 @@ int MakeBiomCommand::getGreenGenesOTUIDs(vector<SharedRAbundVector*>& lookup, ma
             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);