X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=7a8fbc8cdfe6236601dbc0b369f6ef415a5c7c48;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=9096bb671c830a7f5b0b3638ef0ef0a1d0a5f65d;hpb=fc3b1fc4fc1c4e38fde6b0c0ee7896b5fe0b9d57;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 9096bb6..7a8fbc8 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -57,6 +57,27 @@ string FilterSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string FilterSeqsCommand::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 =  "filter.fasta"; }
+            else if (type == "filter") {  outputFileName =  "filter"; }
+            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, "FilterSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -125,7 +146,12 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 			fasta = validParameter.validFile(parameters, "fasta", false);
 			if (fasta == "not found") { 				
 				fasta = m->getFastaFile(); 
-				if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+				if (fasta != "") { 
+                    fastafileNames.push_back(fasta);  
+                    m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+                    string simpleName = m->getSimpleName(fasta);
+                    filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else { 
@@ -273,8 +299,8 @@ int FilterSeqsCommand::execute() {
 		
 		//prevent giantic file name
 		string filterFile;
-		if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
-		else {  filterFile = outputDir + filterFileName + ".filter";  }
+		if (fastafileNames.size() > 3) { filterFile = outputDir + "merge." + getOutputFileNameTag("filter"); }
+		else {  filterFile = outputDir + filterFileName + "." + getOutputFileNameTag("filter");  }
 		
 		m->openOutputFile(filterFile, outFilter);
 		outFilter << filter << endl;
@@ -337,7 +363,7 @@ int FilterSeqsCommand::filterSequences() {
 			
 				for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 				
-				string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+				string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + getOutputFileNameTag("fasta");
 #ifdef USE_MPI	
 				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
@@ -424,16 +450,17 @@ int FilterSeqsCommand::filterSequences() {
             vector<unsigned long long> positions;
             if (savedPositions.size() != 0) { positions = savedPositions[s]; }
             else {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				positions = m->divideFile(fastafileNames[s], processors);
 #else
                 if(processors != 1){
                     int numFastaSeqs = 0;
                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                 }
 #endif
             }
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			//vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 			
 			for (int i = 0; i < (positions.size()-1); i++) {
@@ -590,7 +617,7 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
 				count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -623,7 +650,7 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, strin
 		int num = 0;
 		processIDS.clear();
         
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		
 		
 		//loop through and create all the processes you want
@@ -811,7 +838,7 @@ string FilterSeqsCommand::createFilter() {
 #else
 				
                 vector<unsigned long long> positions;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				positions = m->divideFile(fastafileNames[s], processors);
 				for (int i = 0; i < (positions.size()-1); i++) {
 					lines.push_back(new linePair(positions[i], positions[(i+1)]));
@@ -832,6 +859,7 @@ string FilterSeqsCommand::createFilter() {
 				}else {
                     int numFastaSeqs = 0;
                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                     
                     //figure out how many sequences you have to process
                     int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -969,7 +997,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 					count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -1045,7 +1073,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 		int num = 0;
 		processIDS.clear();
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				
 		//loop through and create all the processes you want
 		while (process != processors) {