fixed some bugs found while testing 1.8

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 0dcdfc0143b12ae0c827086465a16bfb486dc66b..1fe2300387a96e81500a0b41c76190df02aba935 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -11,15 +11,19 @@
 
 //**********************************************************************************************************************
 
-SharedCommand::SharedCommand(){
+SharedCommand::SharedCommand(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
                
                //getting output filename
                filename = globaldata->inputFileName;
-               filename = getRootName(filename);
+               if (outputDir == "") { outputDir += hasPath(filename); }
+               
+               filename = outputDir + getRootName(getSimpleName(filename));
                filename = filename + "shared";
+               
                openOutputFile(filename, out);
+               pickedGroups = false;
                
                groupMap = globaldata->gGroupmap;
                
@@ -28,6 +32,7 @@ SharedCommand::SharedCommand(){
                        groups = groupMap->namesOfGroups;
                }else{ //they have specified groups
                        groups = globaldata->Groups;
+                       pickedGroups = true;
                }
                
                //fill filehandles with neccessary ofstreams
@@ -39,7 +44,7 @@ SharedCommand::SharedCommand(){
                }
                
                //set fileroot
-               fileroot = getRootName(globaldata->getListFile());
+               fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
                
                //clears file before we start to write to it below
                for (int i=0; i<groups.size(); i++) {
@@ -60,7 +65,7 @@ int SharedCommand::execute(){
                //lookup.clear();
                string errorOff = "no error";
                //errorOff = "";
-                       
+               
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -96,7 +101,7 @@ int SharedCommand::execute(){
                                groups += globaldata->Groups[i] + ".";
                        }
                
-                       string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+                       string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
                        ofstream outGroups;
                        openOutputFile(newGroupFile, outGroups);
                
@@ -114,12 +119,15 @@ int SharedCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;    
-               
+       
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
-                       
+               
                        if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       if (pickedGroups) { //check for otus with no seqs in them
+                                               eliminateZeroOTUS(lookup);
+                                       }
                                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
@@ -136,6 +144,9 @@ int SharedCommand::execute(){
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       if (pickedGroups) { //check for otus with no seqs in them
+                                               eliminateZeroOTUS(lookup);
+                                       }
                                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
@@ -170,6 +181,9 @@ int SharedCommand::execute(){
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                        lookup = SharedList->getSharedRAbundVector();
+                       if (pickedGroups) { //check for otus with no seqs in them
+                               eliminateZeroOTUS(lookup);
+                       }
                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                        
                        printSharedData(lookup); //prints info to the .shared file
@@ -186,6 +200,13 @@ int SharedCommand::execute(){
                }
 
                
+               //change format to shared  to speed up commands
+               globaldata->setFormat("sharedfile");
+               globaldata->setListFile("");
+               globaldata->setGroupFile("");
+               globaldata->setSharedFile(filename);
+
+               
                return 0;
        }
        catch(exception& e) {
@@ -216,10 +237,50 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
        }
 }
 //**********************************************************************************************************************
+void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+       try {
+               
+               vector<SharedRAbundVector*> newLookup;
+               for (int i = 0; i < thislookup.size(); i++) {
+                       SharedRAbundVector* temp = new SharedRAbundVector();
+                       temp->setLabel(thislookup[i]->getLabel());
+                       temp->setGroup(thislookup[i]->getGroup());
+                       newLookup.push_back(temp);
+               }
+               
+               //for each bin
+               for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+               
+                       //look at each sharedRabund and make sure they are not all zero
+                       bool allZero = true;
+                       for (int j = 0; j < thislookup.size(); j++) {
+                               if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
+                       }
+                       
+                       //if they are not all zero add this bin
+                       if (!allZero) {
+                               for (int j = 0; j < thislookup.size(); j++) {
+                                       newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+                               }
+                       }
+                       //else{  cout << "bin # " << i << " is all zeros" << endl;  }
+               }
+       
+               for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
+               thislookup = newLookup;
+       
+ 
+       }
+       catch(exception& e) {
+               errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 void SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;
-               string outputMisMatchName = getRootName(globaldata->inputFileName);
+               string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
                
                //you have sequences in your list file that are not in your group file
                if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
@@ -237,10 +298,10 @@ void SharedCommand::createMisMatchFile() {
                                        string name = names.substr(0,names.find_first_of(','));
                                        names = names.substr(names.find_first_of(',')+1, names.length());
                                        string group = groupMap->getGroup(name);
-                                       
+                               
                                        if(group == "not found") {      outMisMatch << name << endl;  }
                                }
-                               
+                       
                                //get last name
                                string group = groupMap->getGroup(names);
                                if(group == "not found") {      outMisMatch << names << endl;  }