X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=0d53c1a95ed5b968d0a8281f1f3d612d7d4c2047;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=abd3c23eaadb0001b518ac226e34148a9bcb2f07;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index abd3c23..0d53c1a 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -53,7 +53,32 @@ string RemoveSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string RemoveSeqsCommand::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 =  "pick" + m->getExtension(inputName);   }
+            else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "alignreport") {   outputFileName =  "pick.align.report";                   }
+            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, "RemoveSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 RemoveSeqsCommand::RemoveSeqsCommand(){	
@@ -194,12 +219,12 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 			}else { m->setAccnosFile(accnosfile); }	
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
+			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }	
 			else { m->setFastaFile(fastafile); }
 								   
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") {  namefile = "";  }	
 			else { m->setNameFile(namefile); } 
 								   
@@ -237,6 +262,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 			
 			if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
 			
+			if ((fastafile != "") && (namefile == "")) {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}
@@ -253,7 +282,7 @@ int RemoveSeqsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get names you want to keep
-		readAccnos();
+		names = m->readAccnos(accnosfile);
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -321,7 +350,7 @@ int RemoveSeqsCommand::readFasta(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
@@ -370,7 +399,7 @@ int RemoveSeqsCommand::readQual(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -438,8 +467,7 @@ int RemoveSeqsCommand::readList(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
-		
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -450,6 +478,9 @@ int RemoveSeqsCommand::readList(){
 		int removedCount = 0;
 		
 		while(!in.eof()){
+			
+			removedCount = 0;
+			
 			//read in list vector
 			ListVector list(in);
 			
@@ -514,8 +545,7 @@ int RemoveSeqsCommand::readName(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
-
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -597,8 +627,7 @@ int RemoveSeqsCommand::readGroup(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-		
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -644,7 +673,7 @@ int RemoveSeqsCommand::readTax(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -690,7 +719,7 @@ int RemoveSeqsCommand::readAlign(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
@@ -757,29 +786,5 @@ int RemoveSeqsCommand::readAlign(){
 	}
 }
 //**********************************************************************************************************************
-void RemoveSeqsCommand::readAccnos(){
-	try {
-		
-		ifstream in;
-		m->openInputFile(accnosfile, in);
-		string name;
-		
-		while(!in.eof()){
-			in >> name;
-						
-			names.insert(name);
-			
-			m->gobble(in);
-		}
-		in.close();		
-
-	}
-	catch(exception& e) {
-		m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************