X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=bab5a634cd101507957dabc22e34e429c5ec5b1b;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=5888feedcf5f6d6c01438d5acecc5e65ba897c54;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 5888fee..bab5a63 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -45,6 +45,27 @@ string DeconvoluteCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DeconvoluteCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "unique" + m->getExtension(inputName); }
+            else if (type == "name") {  outputFileName =  "names"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 DeconvoluteCommand::DeconvoluteCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -125,9 +146,15 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
 			}
 			
 			oldNameMapFName = validParameter.validFile(parameters, "name", true);
-			if (oldNameMapFName == "not open") { abort = true; }
+			if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; }
 			else if (oldNameMapFName == "not found"){	oldNameMapFName = "";	}
 			else { m->setNameFile(oldNameMapFName); }
+			
+			if (oldNameMapFName == "") {
+				vector<string> files; files.push_back(inFastaName);
+				parser.getNameFile(files);
+			}
+			
 		}
 
 	}
@@ -143,12 +170,15 @@ int DeconvoluteCommand::execute() {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
 		//prepare filenames and open files
-		string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
-		string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
+		string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + getOutputFileNameTag("name");
+		string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + getOutputFileNameTag("fasta", inFastaName);
 		
 		map<string, string> nameMap;
 		map<string, string>::iterator itNames;
-		if (oldNameMapFName != "")  {  m->readNames(oldNameMapFName, nameMap); }
+		if (oldNameMapFName != "")  {  
+            m->readNames(oldNameMapFName, nameMap); 
+            if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique." + getOutputFileNameTag("name");   }
+        }
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -162,10 +192,11 @@ int DeconvoluteCommand::execute() {
 		map<string, string>::iterator itStrings;
 		set<string> nameInFastaFile; //for sanity checking
 		set<string>::iterator itname;
+		vector<string> nameFileOrder;
 		int count = 0;
 		while (!in.eof()) {
 			
-			if (m->control_pressed) { in.close(); outFasta.close(); remove(outFastaFile.c_str()); return 0; }
+			if (m->control_pressed) { in.close(); outFasta.close(); m->mothurRemove(outFastaFile); return 0; }
 			
 			Sequence seq(in);
 			
@@ -189,8 +220,9 @@ int DeconvoluteCommand::execute() {
 							m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
 						}else {
 							sequenceStrings[seq.getAligned()] = itNames->second;
+							nameFileOrder.push_back(seq.getAligned());
 						}
-					}else {	sequenceStrings[seq.getAligned()] = seq.getName();	}
+					}else {	sequenceStrings[seq.getAligned()] = seq.getName();	nameFileOrder.push_back(seq.getAligned()); }
 				}else { //this is a dup
 					if (oldNameMapFName != "") {
 						itNames = nameMap.find(seq.getName());
@@ -216,27 +248,32 @@ int DeconvoluteCommand::execute() {
 		in.close();
 		outFasta.close();
 		
-		if (m->control_pressed) { remove(outFastaFile.c_str()); return 0; }
+		if (m->control_pressed) { m->mothurRemove(outFastaFile); return 0; }
 		
 		//print new names file
 		ofstream outNames;
 		m->openOutputFile(outNameFile, outNames);
 		
-		for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
-			if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); outNames.close(); remove(outNameFile.c_str()); return 0; }
+		for (int i = 0; i < nameFileOrder.size(); i++) {
+		//for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+			if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); m->mothurRemove(outNameFile); return 0; }
 			
-			//get rep name
-			int pos = (itStrings->second).find_first_of(',');
+			itStrings = sequenceStrings.find(nameFileOrder[i]);
 			
-			if (pos == string::npos) { // only reps itself
-				outNames << itStrings->second << '\t' << itStrings->second << endl;
-			}else {
-				outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
-			}
+			if (itStrings != sequenceStrings.end()) {
+				//get rep name
+				int pos = (itStrings->second).find_first_of(',');
+			
+				if (pos == string::npos) { // only reps itself
+					outNames << itStrings->second << '\t' << itStrings->second << endl;
+				}else {
+					outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+				}
+			}else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; }
 		}
 		outNames.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); m->mothurRemove(outNameFile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();