X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=89d78288639e6cca3e8eebca34dd01174c3963da;hb=4f3d46bdb42c23468a534486fd105180b030fc65;hp=5d8263c86e2a1f3eae24da047897e2c642d243eb;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5d8263c..89d7828 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -67,6 +67,13 @@ ShhherCommand::ShhherCommand(){
 
 ShhherCommand::ShhherCommand(string option) {
 	try {
+        
+#ifdef USE_MPI
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+		MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
+        
+		if(pid == 0){
+#endif
 		abort = false; calledHelp = false;   
 		
 		//allow user to run help
@@ -121,8 +128,10 @@ ShhherCommand::ShhherCommand(string option) {
 					if (path == "") {	parameters["file"] = inputDir + it->second;		}
 				}
 			}
-			
-			
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
+            
 			//check for required parameters
 			flowFileName = validParameter.validFile(parameters, "flow", true);
 			flowFilesFileName = validParameter.validFile(parameters, "file", true);
@@ -139,13 +148,15 @@ ShhherCommand::ShhherCommand(string option) {
 			}
 			else{
 				ofstream temp;
-
+                
+                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                
 				//flow.files = 9 character offset
-				compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+				compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
 				m->openOutputFile(compositeFASTAFileName, temp);
 				temp.close();
 				
-				compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+				compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
 				m->openOutputFile(compositeNamesFileName, temp);
 				temp.close();
 			}
@@ -207,17 +218,10 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
+                outputDir += m->hasPath(flowFileName);
                 flowFileVector.push_back(flowFileName);
             }
-
-			
-			//if the user changes the output directory command factory will send this info to us in the output parameter 
-			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
-				outputDir = "";	
-				outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it	
-			}
-			
-			
+		
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			string temp;
@@ -314,6 +318,9 @@ ShhherCommand::ShhherCommand(string option) {
 			}
 			
 		}
+#ifdef USE_MPI
+		}				
+#endif
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ShhherCommand", "ShhherCommand");
@@ -328,9 +335,7 @@ int ShhherCommand::execute(){
 		
 		int tag = 1976;
 		MPI_Status status; 
-		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-		MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
-        
+		        
 		if(pid == 0){
 
 			for(int i=1;i<ncpus;i++){
@@ -344,6 +349,22 @@ int ShhherCommand::execute(){
 			getSingleLookUp();	if (m->control_pressed) { return 0; }
 			getJointLookUp();	if (m->control_pressed) { return 0; }
 			
+            vector<string> flowFileVector;
+			if(flowFilesFileName != "not found"){
+				string fName;
+                
+				ifstream flowFilesFile;
+				m->openInputFile(flowFilesFileName, flowFilesFile);
+				while(flowFilesFile){
+					fName = m->getline(flowFilesFile);
+					flowFileVector.push_back(fName);
+					m->gobble(flowFilesFile);
+				}
+			}
+			else{
+				flowFileVector.push_back(flowFileName);
+			}
+            
 			int numFiles = flowFileVector.size();
 
 			for(int i=1;i<ncpus;i++){
@@ -719,6 +740,36 @@ int ShhherCommand::execute(){
 	}
 }
 /**************************************************************************************************/
+string ShhherCommand::createNamesFile(){
+	try{
+		
+		vector<string> duplicateNames(numUniques, "");
+		for(int i=0;i<numSeqs;i++){
+			duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
+		}
+		
+		string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+		
+		ofstream nameFile;
+		m->openOutputFile(nameFileName, nameFile);
+		
+		for(int i=0;i<numUniques;i++){
+			
+			if (m->control_pressed) { break; }
+			
+            //			nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+			nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+		}
+		
+		nameFile.close();
+		return  nameFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ShhherCommand", "createNamesFile");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 
 string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 	try{		
@@ -1823,7 +1874,7 @@ int ShhherCommand::execute(){
 		
         if (numFiles < processors) { processors = numFiles; }
         
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
         if (processors == 1) { driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName, 0, flowFileVector.size()); }
         else { createProcesses(flowFileVector); } //each processor processes one file
 #else
@@ -1869,7 +1920,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -3012,11 +3063,12 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
 			
 			if(otuCounts[i] > 0){
 				qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-				
+                	
 				int j=4;	//need to get past the first four bases
 				while(qualities[i][j] != -1){
-					qualityFile << qualities[i][j] << ' ';
-					j++;
+                    qualityFile << qualities[i][j] << ' ';
+                    if (j > qualities[i].size()) { break; }
+                    j++;
 				}
 				qualityFile << endl;
 			}