added qvalues to metastats. fixed bug with chimera.uchime location. fixed windows...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index e08909bc89993db47ed80836a417b7020f68d068..40b3f2683fbdc47770dd3a4292df5ae8cc6fbf75 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -509,7 +509,7 @@ int ChimeraUchimeCommand::execute(){
                                if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
                                        nameFile = nameFileNames[s];
                                }else { nameFile = getNamesFile(fastaFileNames[s]); }
-                                                                       
+                                                                               
                                map<string, string> seqs;  
                                readFasta(fastaFileNames[s], seqs);  if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  return 0; }
 
@@ -560,12 +560,19 @@ int ChimeraUchimeCommand::execute(){
                        
                                int numSeqs = 0;
                                int numChimeras = 0;
-       //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
                                if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
                                else{   numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
-       //#else
-       //                      numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras);
-       //#endif
+                               
+                               //add headings
+                               ofstream out;
+                               m->openOutputFile(outputFileName+".temp", out); 
+                               out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
+                               out.close();
+                               
+                               m->appendFiles(outputFileName, outputFileName+".temp");
+                               m->mothurRemove(outputFileName); rename((outputFileName+".temp").c_str(), outputFileName.c_str());
+                               
                                if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        } return 0; }
                        
                                //remove file made for uchime
@@ -653,6 +660,7 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp
                
                ofstream out;
                m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+               out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
                
                float temp1;
                string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag;
@@ -979,23 +987,35 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
+               
+               outputFName = m->getFullPathName(outputFName);
+               filename = m->getFullPathName(filename);
+               alns = m->getFullPathName(alns);
+               
                //to allow for spaces in the path
                outputFName = "\"" + outputFName + "\"";
                filename = "\"" + filename + "\"";
                alns = "\"" + alns + "\"";
                                
                vector<char*> cPara;
-       
-               char* tempUchime;
+               
+               string path = m->argv;
+               string tempPath = path;
+               for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+               path = path.substr(0, (tempPath.find_last_of('m')));
+               
+               string uchimeCommand = path;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               tempUchime= new char[10];  
-               *tempUchime = '\0';
-               strncat(tempUchime, "./uchime ", 9); 
+               uchimeCommand += "uchime ";
 #else
-               tempUchime= new char[8]; 
-               *tempUchime = '\0';
-               strncat(tempUchime, "uchime ", 7); 
+               uchimeCommand += "uchime";
+               uchimeCommand = "\"" + uchimeCommand + "\"";
 #endif
+               
+               char* tempUchime;
+               tempUchime= new char[uchimeCommand.length()+1]; 
+               *tempUchime = '\0';
+               strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
                cPara.push_back(tempUchime);
                
                char* tempIn = new char[8]; 
@@ -1223,6 +1243,10 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                //uchime_main(numArgs, uchimeParameters); 
                //cout << "commandString = " << commandString << endl;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+               commandString = "\"" + commandString + "\"";
+#endif
                system(commandString.c_str());
                
                //free memory
@@ -1514,7 +1538,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                                
 #else
                //////////////////////////////////////////////////////////////////////////////////////////////////////
-               //Windows version shared memory, so be careful when passing variables through the preClusterData struct. 
+               //Windows version shared memory, so be careful when passing variables through the uchimeData struct. 
                //Above fork() will clone, so memory is separate, but that's not the case with windows, 
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                
@@ -1534,7 +1558,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                        pDataArray.push_back(tempUchime);
                        processIDS.push_back(i);
                        
-                       //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+                       //MyUchimeThreadFunction is in header. It must be global or static to work with the threads.
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
                        hThreadArray[i-1] = CreateThread(NULL, 0, MyUchimeThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);   
                }