X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getotuscommand.cpp;h=3ca7f5d575db0a7e3a065ebcf371128698d5056b;hp=8d20e63b65b9a99b6476608fe4a108ce233718f0;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index 8d20e63..3ca7f5d 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -15,13 +15,13 @@
 //**********************************************************************************************************************
 vector<string> GetOtusCommand::setParameters(){	
 	try {
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
+		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -54,25 +54,20 @@ string GetOtusCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string GetOtusCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string GetOtusCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
-            else if (type == "list")        {   outputFileName = "pick" + m->getExtension(inputName);  }
-            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, "GetOtusCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){	
@@ -249,26 +244,33 @@ int GetOtusCommand::execute(){
 //**********************************************************************************************************************
 int GetOtusCommand::readListGroup(){
 	try {
-		string thisOutputDir = outputDir;
+		InputData* input = new InputData(listfile, "list");
+		ListVector* list = input->getListVector();
+		string lastLabel = list->getLabel();
+		
+		//using first label seen if none is provided
+		if (label == "") { label = lastLabel; }
+        
+        string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
+        map<string, string> variables;
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+		string outputFileName = getOutputFileName("list", variables);
 		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
-		
-		string GroupOutputDir = outputDir;
+        
+        string GroupOutputDir = outputDir;
 		if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-		string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
+        variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+		string outputGroupFileName = getOutputFileName("group", variables);
 		
 		ofstream outGroup;
 		m->openOutputFile(outputGroupFileName, outGroup);
-			
-		InputData* input = new InputData(listfile, "list");
-		ListVector* list = input->getListVector();
-		string lastLabel = list->getLabel();
-		
-		//using first label seen if none is provided
-		if (label == "") { label = lastLabel; }
+
 		
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> labels; labels.insert(label);
@@ -365,6 +367,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
 		
 		int numOtus = 0;
 		//for each bin
+        vector<string> binLabels = list->getLabels();
+        vector<string> newBinLabels;
 		for (int i = 0; i < list->getNumBins(); i++) {
 			if (m->control_pressed) { return 0; }
 			
@@ -398,7 +402,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
 			
 			//if there are sequences from the groups we want in this bin add to new list, output to groupfile
 			if (keepBin) {  
-				newList.push_back(binnames);	
+				newList.push_back(binnames);
+                newBinLabels.push_back(binLabels[i]);
 				outGroup << groupFileOutput;
 				numOtus++;
 			}
@@ -407,7 +412,9 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
 		//print new listvector
 		if (newList.getNumBins() != 0) {
 			wroteSomething = true;
-			newList.print(out);
+			newList.setLabels(newBinLabels);
+            newList.printHeaders(out);
+            newList.print(out);
 		}
 		
 		m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();