X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=902cc07c2d6e8768e5aa9d1bacd3d9586e9196d9;hb=df905918ace8537273616b4120d404ebd29dc9cc;hp=d40dcc6a30d20080770ac806855295f98ed83df3;hpb=de67504f85e091a3049ef4c5df8e77f7dcb1d814;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index d40dcc6..902cc07 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> GetSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -69,10 +68,10 @@ vector<string> GetSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 				
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -188,8 +187,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 			if (accnosfile == "not open") { abort = true; }
 			else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }	
 			
-			accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
-			if (accnosfile2 == "not open") { abort = true; }
+			if (accnosfile2 == "not found") { accnosfile2 = ""; }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
@@ -258,7 +256,7 @@ void GetSeqsCommand::help(){
 int GetSeqsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get names you want to keep
 		readAccnos();
@@ -779,6 +777,30 @@ int GetSeqsCommand::compareAccnos(){
 		set<string> namesDups;
 		set<string> namesAccnos = names;
 		
+		map<string, int> nameCount;
+		
+		if (namefile != "") {
+			ifstream inName;
+			m->openInputFile(namefile, inName);
+			
+			
+			while(!inName.eof()){
+				
+				if (m->control_pressed) { inName.close(); return 0; }
+				
+				string thisname, repnames;
+				
+				inName >> thisname;		m->gobble(inName);		//read from first column
+				inName >> repnames;			//read from second column
+				
+				int num = m->getNumNames(repnames);
+				nameCount[thisname] = num;
+				
+				m->gobble(inName);
+			}
+			inName.close();	
+		}
+		
 		while(!in.eof()){
 			in >> name;
 			
@@ -797,21 +819,27 @@ int GetSeqsCommand::compareAccnos(){
 		m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
 		
 		for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
-			out << (*it) << endl;
+			out << (*it);
+			if (namefile != "") { out << '\t' << nameCount[(*it)]; }
+			out << endl;
 		}
 		
 		out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
 		m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
 		
 		for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
-			out << (*it) << endl;
+			out << (*it);
+			if (namefile != "") { out << '\t' << nameCount[(*it)]; }
+			out << endl;
 		}
 		
 		out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
 		m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
 		
 		for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
-			out << (*it) << endl;
+			out << (*it);
+			if (namefile != "") { out << '\t' << nameCount[(*it)]; }
+			out << endl;
 		}
 
 		out.close();