changed random forest output filename

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index f0fc6bff9da6d6d8b0ed8b368ad2422f25cd732a..3d671f98420e0fa7cf844aac647bd43feea959e8 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -219,12 +219,14 @@ int ConsensusSeqsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+        int start = time(NULL);
+        
                readFasta();
                
                if (m->control_pressed) { return 0; }
                
                if (namefile != "") { readNames(); }
-        if (countfile != "") { ct.readTable(countfile);  }
+        if (countfile != "") { ct.readTable(countfile, true);  }
                
                if (m->control_pressed) { return 0; }
                
@@ -310,7 +312,7 @@ int ConsensusSeqsCommand::execute(){
                
                }else {
                        
-                                               
+            
                        InputData* input = new InputData(listfile, "list");
                        ListVector* list = input->getListVector();
                        
@@ -391,6 +393,8 @@ int ConsensusSeqsCommand::execute(){
                        delete input;
                }
                
+        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus sequences.");
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }       
@@ -431,15 +435,24 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
                
                outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
                
+        string snumBins = toString(list->getNumBins());
                for (int i = 0; i < list->getNumBins(); i++) {
                        
                        if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
                        
                        string bin = list->get(i);
                        string consSeq = getConsSeq(bin, outSummary, i);
+            
+            string seqName = "Otu";
+            string sbinNumber = toString(i+1);
+            if (sbinNumber.length() < snumBins.length()) {
+                int diff = snumBins.length() - sbinNumber.length();
+                for (int h = 0; h < diff; h++) { seqName += "0"; }
+            }
+            seqName += sbinNumber;
                        
-                       outFasta << ">seq" << (i+1) << endl << consSeq << endl;
-                       outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << bin << endl;
+                       outFasta << ">" << seqName << endl << consSeq << endl;
+                       outName << seqName << '\t' << seqName << "," << bin << endl;
                }
                
                outSummary.close(); outName.close(); outFasta.close();