X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=b6dc24fe5751867c6b79f71fb50e3b7b74ad75a6;hb=050e1297eaf24fabbbe0e9b76c3a5acfb90eed7d;hp=328cd58f1f32bc265de857de4ede5aa557c2cd94;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 328cd58..b6dc24f 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -457,13 +457,15 @@ 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 +484,7 @@ 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 {
@@ -500,11 +502,17 @@ int ClassifySeqsCommand::execute(){
 			string baseTName = taxonomyFileName;
 			if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy();	}
 			
-			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 +=  "."; 
-		
+            //set rippedTaxName to 
+			string RippedTaxName = "";
+            bool foundDot = false;
+            for (int i = baseTName.length()-1; i >= 0; i--) {
+                cout << baseTName[i] << endl;
+                if (foundDot && (baseTName[i] != '.')) {  RippedTaxName = baseTName[i] + RippedTaxName; }
+                else if (foundDot && (baseTName[i] == '.')) {  break; }
+                else if (!foundDot && (baseTName[i] == '.')) {  foundDot = true; }
+            }
+            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 +623,7 @@ 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 +631,7 @@ 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 +830,7 @@ 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
@@ -881,7 +890,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 			string extension = "";
 			if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 			
-			classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flipThreshold);
+			classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip);
 			pDataArray.push_back(tempclass);
 			
 			//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
@@ -905,16 +914,35 @@ 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 +1030,7 @@ 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