fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index ee7add9ebd4ff55ea37312d3194bbd4df91270e2..54b1d9b4caace40335934db39c6306687ddafdf5 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -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;
@@ -985,17 +993,24 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                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 +1238,10 @@ 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