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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 21de6ac1f01e7ed4719443ecb578c0b4b9dac7b8..a8c3fc697ae10c1c6a117ce68c550a928281ec44 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -308,6 +308,7 @@ int TrimSeqsCommand::execute(){
                
                numFPrimers = 0;  //this needs to be initialized
                numRPrimers = 0;
+               createGroup = false;
                vector<vector<string> > fastaFileNames;
                vector<vector<string> > qualFileNames;
                vector<vector<string> > nameFileNames;
@@ -343,9 +344,11 @@ int TrimSeqsCommand::execute(){
                
                string outputGroupFileName;
                if(oligoFile != ""){
-                       outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
-                       outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
-                       getOligos(fastaFileNames, qualFileNames, nameFileNames);
+                       createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
+                       if (createGroup) {
+                               outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+                               outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+                       }
                }
                
                vector<unsigned long int> fastaFilePos;
@@ -505,7 +508,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                
                
                ofstream outGroupsFile;
-               if (oligoFile != ""){   m->openOutputFile(groupFileName, outGroupsFile);   }
+               if (createGroup){       m->openOutputFile(groupFileName, outGroupsFile);   }
                if(allFiles){
                        for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
                                for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
@@ -541,7 +544,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                
                        if (m->control_pressed) { 
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
-                               if (oligoFile != "") {   outGroupsFile.close();   }
+                               if (createGroup) {       outGroupsFile.close();   }
 
                                if(qFileName != ""){
                                        qFile.close();
@@ -646,30 +649,39 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
                                        }
                                        
-                                       if(barcodes.size() != 0){
-                                               string thisGroup = barcodeNameVector[barcodeIndex];
-                                               if (primers.size() != 0) { if (primerNameVector[primerIndex] != "") { thisGroup += "." + primerNameVector[primerIndex]; } }
-                                               
-                                               outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
-                                               
-                                               if (nameFile != "") {
-                                                       map<string, string>::iterator itName = nameMap.find(currSeq.getName());
-                                                       if (itName != nameMap.end()) { 
-                                                               vector<string> thisSeqsNames; 
-                                                               m->splitAtChar(itName->second, thisSeqsNames, ',');
-                                                               for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
-                                                                       outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
-                                                               }
-                                                       }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }                                                   
-                                               }
-                                               
-                                               map<string, int>::iterator it = groupCounts.find(thisGroup);
-                                               if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
-                                               else { groupCounts[it->first]++; }
+                                       if (createGroup) {
+                                               if(barcodes.size() != 0){
+                                                       string thisGroup = barcodeNameVector[barcodeIndex];
+                                                       if (primers.size() != 0) { 
+                                                               if (primerNameVector[primerIndex] != "") { 
+                                                                       if(thisGroup != "") {
+                                                                               thisGroup += "." + primerNameVector[primerIndex]; 
+                                                                       }else {
+                                                                               thisGroup = primerNameVector[primerIndex]; 
+                                                                       }
+                                                               } 
+                                                       }
                                                        
+                                                       outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+                                                       
+                                                       if (nameFile != "") {
+                                                               map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                                               if (itName != nameMap.end()) { 
+                                                                       vector<string> thisSeqsNames; 
+                                                                       m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                                                       for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                                                               outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+                                                                       }
+                                                               }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }                                                   
+                                                       }
+                                                       
+                                                       map<string, int>::iterator it = groupCounts.find(thisGroup);
+                                                       if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
+                                                       else { groupCounts[it->first]++; }
+                                                               
+                                               }
                                        }
                                        
-                                       
                                        if(allFiles){
                                                ofstream output;
                                                m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
@@ -728,7 +740,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                inFASTA.close();
                trimFASTAFile.close();
                scrapFASTAFile.close();
-               if (oligoFile != "") {   outGroupsFile.close();   }
+               if (createGroup) {       outGroupsFile.close();   }
                if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
                if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }
                
@@ -800,7 +812,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                 qLines[process]);
                                
                                //pass groupCounts to parent
-                               if(oligoFile != ""){
+                               if(createGroup){
                                        ofstream out;
                                        string tempFile = filename + toString(getpid()) + ".num.temp";
                                        m->openOutputFile(tempFile, out);
@@ -865,7 +877,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
                        }
                        
-                       if(oligoFile != ""){
+                       if(createGroup){
                                m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
                                m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
                        }
@@ -892,7 +904,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                }
                        }
                        
-                       if(oligoFile != ""){
+                       if(createGroup){
                                ifstream in;
                                string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
                                m->openInputFile(tempFile, in);
@@ -1044,7 +1056,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned
 
 //***************************************************************************************************************
 
-void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
+bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
        try {
                ifstream inOligos;
                m->openInputFile(oligoFile, inOligos);
@@ -1199,7 +1211,29 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                }
                numFPrimers = primers.size();
                numRPrimers = revPrimer.size();
-
+               
+               bool allBlank = true;
+               for (int i = 0; i < barcodeNameVector.size(); i++) {
+                       if (barcodeNameVector[i] != "") {
+                               allBlank = false;
+                               break;
+                       }
+               }
+               for (int i = 0; i < primerNameVector.size(); i++) {
+                       if (primerNameVector[i] != "") {
+                               allBlank = false;
+                               break;
+                       }
+               }
+               
+               if (allBlank) {
+                       m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
+                       allFiles = false;
+                       return false;
+               }
+               
+               return true;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "getOligos");