X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=ae242b6f56946c544aff5f389b026c2c93a50bee;hb=c53c53b0280452e1c3a087fbf807b2e508cd66c4;hp=e58cc883b26a33d2dec9526bb52bcbfb7de7741e;hpb=b9456b1087ade74251792e039f4e5021dbf32349;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index e58cc88..ae242b6 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -119,19 +119,30 @@ void GetSeqsCommand::readFasta(){
 		openInputFile(fastafile, in);
 		string name;
 		
+		bool wroteSomething = false;
+		
 		while(!in.eof()){
 			Sequence currSeq(in);
 			name = currSeq.getName();
 			
 			//if this name is in the accnos file
 			if (names.count(name) == 1) {
+				wroteSomething = true;
+				
 				currSeq.printSequence(out);
+				
+				names.erase(name);
 			}
 			
 			gobble(in);
 		}
 		in.close();	
-		out.close();	
+		out.close();
+		
+		if (wroteSomething == false) {
+			mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+			remove(outputFileName.c_str()); 
+		}
 
 	}
 	catch(exception& e) {
@@ -152,6 +163,8 @@ void GetSeqsCommand::readName(){
 		openInputFile(namefile, in);
 		string name, firstCol, secondCol;
 		
+		bool wroteSomething = false;
+		
 		
 		while(!in.eof()){
 
@@ -173,22 +186,31 @@ void GetSeqsCommand::readName(){
 			for (int i = 0; i < parsedNames.size(); i++) {
 				if (names.count(parsedNames[i]) == 1) {
 					validSecond.push_back(parsedNames[i]);
+					names.erase(parsedNames[i]);
 				}
 			}
 
 			
 			//if the name in the first column is in the set then print it and any other names in second column also in set
 			if (names.count(firstCol) == 1) {
+			
+				wroteSomething = true;
+				
 				out << firstCol << '\t';
 				
 				//you know you have at least one valid second since first column is valid
 				for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 				out << validSecond[validSecond.size()-1] << endl;
+				
+				names.erase(firstCol);
 			
 			//make first name in set you come to first column and then add the remaining names to second column
 			}else {
 				//you want part of this row
 				if (validSecond.size() != 0) {
+				
+					wroteSomething = true;
+					
 					out << validSecond[0] << '\t';
 				
 					//you know you have at least one valid second since first column is valid
@@ -202,6 +224,11 @@ void GetSeqsCommand::readName(){
 		in.close();
 		out.close();
 		
+		if (wroteSomething == false) {
+			mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+			remove(outputFileName.c_str()); 
+		}
+		
 	}
 	catch(exception& e) {
 		errorOut(e, "GetSeqsCommand", "readName");
@@ -221,6 +248,8 @@ void GetSeqsCommand::readGroup(){
 		openInputFile(groupfile, in);
 		string name, group;
 		
+		bool wroteSomething = false;
+		
 		while(!in.eof()){
 
 			in >> name;				//read from first column
@@ -228,13 +257,22 @@ void GetSeqsCommand::readGroup(){
 			
 			//if this name is in the accnos file
 			if (names.count(name) == 1) {
+				wroteSomething = true;
+				
 				out << name << '\t' << group << endl;
+				
+				names.erase(name);
 			}
 					
 			gobble(in);
 		}
 		in.close();
 		out.close();
+		
+		if (wroteSomething == false) {
+			mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+			remove(outputFileName.c_str()); 
+		}
 
 	}
 	catch(exception& e) {
@@ -255,6 +293,8 @@ void GetSeqsCommand::readAlign(){
 		openInputFile(alignfile, in);
 		string name, junk;
 		
+		bool wroteSomething = false;
+		
 		//read column headers
 		for (int i = 0; i < 16; i++) {  
 			if (!in.eof())	{	in >> junk;	 out << junk << '\t';	}
@@ -268,7 +308,8 @@ void GetSeqsCommand::readAlign(){
 			
 			//if this name is in the accnos file
 			if (names.count(name) == 1) {
-
+				wroteSomething = true;
+				
 				out << name << '\t';
 				
 				//read rest
@@ -278,6 +319,8 @@ void GetSeqsCommand::readAlign(){
 				}
 				out << endl;
 				
+				names.erase(name);
+				
 			}else {//still read just don't do anything with it
 				//read rest
 				for (int i = 0; i < 15; i++) {  
@@ -290,7 +333,11 @@ void GetSeqsCommand::readAlign(){
 		}
 		in.close();
 		out.close();
-
+		
+		if (wroteSomething == false) {
+			mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+			remove(outputFileName.c_str()); 
+		}
 		
 	}
 	catch(exception& e) {