changed normalize.shared and sub.sample commands to fix bug in normalize.shared and...

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index d5388896793adbd55c925480ec708e460cb14b71..e365441d69bfeebc826bff13f3be4728ae54a264 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -689,27 +689,17 @@ int SubSampleCommand::getSubSampleShared() {
                
                if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
                
-               string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
-               
-               ofstream out;
-               m->openOutputFile(outputFileName, out);
-               outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
-               
-               
                m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
                
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-                       if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; } out.close(); return 0;  }
+                       if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  return 0;  }
                        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                               processShared(lookup, out);
+                               processShared(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
@@ -723,8 +713,7 @@ int SubSampleCommand::getSubSampleShared() {
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                               processShared(lookup, out);
+                               processShared(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
@@ -742,7 +731,7 @@ int SubSampleCommand::getSubSampleShared() {
                }
                
                
-               if (m->control_pressed) {  out.close(); return 0;  }
+               if (m->control_pressed) {   return 0;  }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -764,14 +753,12 @@ int SubSampleCommand::getSubSampleShared() {
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
-                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
-                       processShared(lookup, out);
+                       processShared(lookup);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                }
                
                delete input;
-               out.close();  
                
                return 0;
                
@@ -782,9 +769,21 @@ int SubSampleCommand::getSubSampleShared() {
        }
 }
 //**********************************************************************************************************************
-int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
+int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
        try {
                
+               //save mothurOut's binLabels to restore for next label
+               vector<string> saveBinLabels = m->currentBinLabels;
+               
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
+               
+               
+               ofstream out;
+               m->openOutputFile(outputFileName, out);
+               outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+               
                int numBins = thislookup[0]->getNumBins();
                for (int i = 0; i < thislookup.size(); i++) {           
                        int thisSize = thislookup[i]->getNumSeqs();
@@ -811,7 +810,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
                                
                                for (int j = 0; j < size; j++) {
                                        
-                                       if (m->control_pressed) { delete order; return 0; }
+                                       if (m->control_pressed) { delete order; out.close(); return 0; }
                                        
                                        //get random number to sample from order between 0 and thisSize-1.
                                        int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
@@ -828,13 +827,20 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
                //subsampling may have created some otus with no sequences in them
                eliminateZeroOTUS(thislookup);
                
-               if (m->control_pressed) { return 0; }
+               if (m->control_pressed) { out.close(); return 0; }
+               
+               thislookup[0]->printHeaders(out);
                
                for (int i = 0; i < thislookup.size(); i++) {
                        out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
                        thislookup[i]->print(out);
                }
                
+               out.close();
+               
+               //save mothurOut's binLabels to restore for next label
+               m->currentBinLabels = saveBinLabels;
+               
                return 0;
                
        }
@@ -1517,6 +1523,7 @@ int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup)
                }
                
                //for each bin
+               vector<string> newBinLabels;
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -1531,6 +1538,11 @@ int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup)
                                for (int j = 0; j < thislookup.size(); j++) {
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
+                               //if there is a bin label use it otherwise make one
+                               string binLabel = "Otu" + (i+1);
+                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               
+                               newBinLabels.push_back(binLabel);
                        }
                }
                
@@ -1538,6 +1550,7 @@ int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup)
                thislookup.clear();
                
                thislookup = newLookup;
+               m->currentBinLabels = newBinLabels;
                
                return 0;