X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=636e17536a024f04476fc04ce431bb6524e29839;hb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;hp=097664efc2640af01a0b10cfa3bcd9efcc46d5e3;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 097664e..636e175 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -205,6 +205,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
 						}
 					}
 				}
@@ -279,6 +281,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 							//erase from file list
 							nameFileNames.erase(nameFileNames.begin()+i);
 							i--;
+						}else {
+							m->setNameFile(nameFileNames[i]);
 						}
 					}
 				}
@@ -305,9 +309,10 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 					
 					templatefile = validParameter.validFile(parameters, "reference", true);
 					if (templatefile == "not open") { abort = true; }
-					else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }	
+					else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true;  }	
 				}
-			}
+			}else if (hasName) {  templatefile = "self"; }
+			else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }	
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
@@ -508,6 +513,16 @@ int ChimeraSlayerCommand::execute(){
 					//do your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 					
+					int numNoParents = chimera->getNumNoParents();
+					int temp;
+					for(int i = 1; i < processors; i++) { 
+						MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status);
+						numNoParents += temp;
+					}
+					
+					
+					if (numSeqs == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+					
 					if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 
 				}else{ //you are a child process
@@ -523,6 +538,9 @@ int ChimeraSlayerCommand::execute(){
 					
 						//do your part
 						driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
+						
+						int numNoParents = chimera->getNumNoParents();
+						MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 					
 						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  delete chimera; return 0;  }
 				
@@ -555,6 +573,9 @@ int ChimeraSlayerCommand::execute(){
 				if(processors == 1){
 					numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 					
+					int numNoParents = chimera->getNumNoParents();
+					if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+					
 					if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 					
 				}else{
@@ -591,6 +612,10 @@ int ChimeraSlayerCommand::execute(){
 			#else
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 				
+				int numNoParents = chimera->getNumNoParents();
+				if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+
+				
 				if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 				
 			#endif
@@ -669,7 +694,6 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
 			string candidateAligned = candidateSeq->getAligned();
 			
 			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
-				
 				if (candidateSeq->getAligned().length() != templateSeqsLength) {  
 					m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 				}else{
@@ -715,15 +739,15 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
 						data_results rightResults = chimera->getResults();
 						
 						//if either piece is chimeric then report
-						Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
-						if (trim) { trimmed->printSequence(out3); delete trimmed; }
+						Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
+						if (trim) { trimmed.printSequence(out3);  }
 						
 						delete left; delete right;
 						
 					}else { //already chimeric
 						//print results
-						Sequence* trimmed = chimera->print(out, out2);
-						if (trim) { trimmed->printSequence(out3); delete trimmed; }
+						Sequence trimmed = chimera->print(out, out2);
+						if (trim) { trimmed.printSequence(out3);  }
 					}
 					
 					
@@ -831,10 +855,9 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
 						data_results rightResults = chimera->getResults();
 						
 						//if either piece is chimeric then report
-						Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
+						Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
 						if (trim) {  
-							string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
-							delete trimmed;
+							string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 							
 							//write to accnos file
 							int length = outputString.length();
@@ -849,11 +872,10 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
 						
 					}else { 
 						//print results
-						Sequence* trimmed = chimera->print(outMPI, outAccMPI);
+						Sequence trimmed = chimera->print(outMPI, outAccMPI);
 						
 						if (trim) {  
-							string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
-							delete trimmed;
+							string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 							
 							//write to accnos file
 							int length = outputString.length();
@@ -907,9 +929,8 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
 				ofstream out;
 				string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 				m->openOutputFile(tempFile, out);
-				out << num << endl;
+				out << num << '\t' << chimera->getNumNoParents() << endl;
 				out.close();
-				
 				exit(0);
 			}else { 
 				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
@@ -924,14 +945,17 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
 			wait(&temp);
 		}
 		
+		int numNoParents = 0;
 		for (int i = 0; i < processIDS.size(); i++) {
 			ifstream in;
 			string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 			m->openInputFile(tempFile, in);
-			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+			if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
 			in.close(); remove(tempFile.c_str());
 		}
 		
+		if (num == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+		
 		return num;
 #endif		
 	}