X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraperseuscommand.cpp;h=e3691e8b942c2f34da91cec14691e717d5c16c1a;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=8eaf536040a5703bbd7d9f4b93329f79cf6c6830;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 8eaf536..e3691e8 100644
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -58,6 +58,27 @@ string ChimeraPerseusCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraPerseusCommand::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 == "chimera") {  outputFileName =  "perseus.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "perseus.accnos"; }
+            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, "ChimeraPerseusCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraPerseusCommand::ChimeraPerseusCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -376,8 +397,9 @@ int ChimeraPerseusCommand::execute(){
 			
 			int start = time(NULL);	
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it				
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "perseus.chimera";
-			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "perseus.accnos";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+
 			//string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
 			
 			//you provided a groupfile
@@ -466,14 +488,15 @@ string ChimeraPerseusCommand::getNamesFile(string& inputFile){
 		string inputString = "fasta=" + inputFile;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-		
+		m->mothurCalling = true;
+        
 		Command* uniqueCommand = new DeconvoluteCommand(inputString);
 		uniqueCommand->execute();
 		
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 		
 		delete uniqueCommand;
-		
+		m->mothurCalling = false;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		
 		nameFile = filenames["name"][0];
@@ -533,6 +556,7 @@ vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, str
 		
 		vector<seqData> sequences;
 		bool error = false;
+        alignLength = 0;
 		
 		for (int i = 0; i < thisGroupsSeqs.size(); i++) {
 		
@@ -543,6 +567,7 @@ vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, str
 			else {
 				int num = m->getNumNames(it->second);
 				sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
+                if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
 			}
 		}
 		
@@ -570,7 +595,8 @@ vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
 		bool error = false;
 		ifstream in;
 		m->openInputFile(inputFile, in);
-		
+		alignLength = 0;
+        
 		while (!in.eof()) {
 			
 			if (m->control_pressed) { in.close(); return sequences; }
@@ -581,6 +607,7 @@ vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
 			if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
 			else {
 				sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
+                if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
 			}
 		}
 		in.close();
@@ -625,7 +652,7 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
 		}
 		
 		int numSeqs = sequences.size();
-		int alignLength = sequences[0].sequence.size();
+		//int alignLength = sequences[0].sequence.size();
 		
 		ofstream chimeraFile;
 		ofstream accnosFile;
@@ -641,7 +668,7 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
 		
 		for(int i=0;i<numSeqs;i++){	
 			if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
-			
+    
 			vector<bool> restricted = chimeras;
 			
 			vector<vector<int> > leftDiffs(numSeqs);
@@ -662,7 +689,9 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
 			
 			string dummyA, dummyB;
 			
-			if(comparisons >= 2){	
+            if (sequences[i].sequence.size() < 3) { 
+                chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
+            }else if(comparisons >= 2){	
 				minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
 				if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
@@ -762,7 +791,7 @@ int ChimeraPerseusCommand::createProcessesGroups(SequenceParser& parser, string
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-#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) {