X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=4e244905ff6b755fd064617368506b9160770048;hb=ffc44592ff7ae94f14f9e21f87198e33d323cd1d;hp=794b961dcc29ecdc79bf063d116887b4cf8c30ac;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 794b961..4e24490 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -457,13 +457,16 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 				search = "kmer";
 			}
 			
-			if (namefileNames.size() == 0){
-				vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]); 
-				parser.getNameFile(files);
-			}
+            if (!abort) {
+                if (namefileNames.size() == 0){
+                    if (fastaFileNames.size() != 0) {
+                        vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]); 
+                        parser.getNameFile(files);
+                    }
+                }
+            }
 			
 		}
-		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
@@ -482,7 +485,7 @@ ClassifySeqsCommand::~ClassifySeqsCommand(){
 int ClassifySeqsCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		
+        
 		if(method == "bayesian"){	classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);		}
 		else if(method == "knn"){	classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());				}
 		else {
@@ -503,8 +506,8 @@ int ClassifySeqsCommand::execute(){
 			string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
 			RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 			if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
-			RippedTaxName +=  "."; 
-		
+			if (RippedTaxName != "") { RippedTaxName +=  "."; }
+           
 			if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 			string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 			string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";
@@ -615,7 +618,7 @@ int ClassifySeqsCommand::execute(){
 #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)]));	}
 #else
@@ -623,6 +626,7 @@ int ClassifySeqsCommand::execute(){
 				lines.push_back(new linePair(0, 1000));
 			}else {
 				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;
@@ -821,7 +825,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		int num = 0;
 		processIDS.clear();
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		//loop through and create all the processes you want
@@ -905,16 +909,35 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		}
 		
 	#endif	
-		
+        vector<string> nonBlankAccnosFiles;
+		if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
+		else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
+        
 		for(int i=0;i<processIDS.size();i++){
 			appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 			appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
-			appendTaxFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
+            if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
+				nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
+			}else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
+
 			m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
 			m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
-			m->mothurRemove((m->getFullPathName(accnos) + toString(processIDS[i]) + ".temp"));
 		}
 		
+        //append accnos files
+		if (nonBlankAccnosFiles.size() != 0) { 
+			rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
+			
+			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+				appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+				m->mothurRemove(nonBlankAccnosFiles[h]);
+			}
+		}else { //recreate the accnosfile if needed
+			ofstream out;
+			m->openOutputFile(accnos, out);
+			out.close();
+		}
+
 		return num;
 		
 	}
@@ -1002,7 +1025,7 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else