X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.cpp;h=ef41ee1bab8853f6741938005f775076b60723ab;hb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178;hp=f36631a0590725867dffc402f74fd73af6168e20;hpb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;p=mothur.git

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index f36631a..ef41ee1 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -182,7 +182,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			else if (refTaxonomy == "not open") { abort = true; }
 	
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }	
+			if (namefile == "not open") { namefile = ""; abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -206,7 +206,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "51"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "probs", false);					if (temp == "not found"){	temp = "true";			}
 			probs = m->isTrue(temp);
@@ -214,6 +214,11 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			
 			if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true;  }
 			
+			if (namefile == ""){
+				vector<string> files; files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -470,6 +475,9 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
 				}
 				
 			}
+            
+            //phylotree adds an extra unknown so we want to remove that
+            if (bestChild.name == "unknown") { bestChildSize--; }
 				
 			//is this taxonomy above cutoff
 			int consensusConfidence = ceil((bestChildSize / (float) size) * 100);
@@ -536,7 +544,9 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 			taxaSum = new PhyloSummary(groupfile);
 		}
 		
+
 		//for each bin in the list vector
+        string snumBins = toString(processList->getNumBins());
 		for (int i = 0; i < processList->getNumBins(); i++) {
 			
 			if (m->control_pressed) { break; }
@@ -547,7 +557,15 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 			if (m->control_pressed) { out.close();  return 0; }
 			
 			//output to new names file
-			out << (i+1) << '\t' << size << '\t' << conTax << endl;
+            string binLabel = "Otu";
+            string sbinNumber = toString(i+1);
+            if (sbinNumber.length() < snumBins.length()) { 
+                int diff = snumBins.length() - sbinNumber.length();
+                for (int h = 0; h < diff; h++) { binLabel += "0"; }
+            }
+            binLabel += sbinNumber;
+
+			out << binLabel << '\t' << size << '\t' << conTax << endl;
 			
 			string noConfidenceConTax = conTax;
 			m->removeConfidences(noConfidenceConTax);