X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=bcff0fcd820a497da04405bef0ddb42d7d60ded9;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=cf4256851eb583a78b78fd5ab800bbfa5d46f5e8;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf42568..bcff0fc 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -147,7 +147,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			// ...at some point should added some additional type checking...
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not found") { namefile =  "";  }
-			else if (namefile == "not open") { abort = true; }	
+			else if (namefile == "not open") { namefile = ""; abort = true; }	
 			else {  m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
@@ -156,13 +156,16 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else {   m->setGroupFile(groupfile); bygroup = true;  }
 			
 			string temp	= validParameter.validFile(parameters, "diffs", false);		if(temp == "not found"){	temp = "1"; }
-			convert(temp, diffs); 
+			m->mothurConvert(temp, diffs); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
-			
+			m->mothurConvert(temp, processors);
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 				
 	}
@@ -214,17 +217,19 @@ int PreClusterCommand::execute(){
 			m->mothurOutEndLine(); 
 			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(); 
 			
 			m->renameFile(filenames["fasta"][0], newFastaFile);
+            m->renameFile(filenames["name"][0], newNamesFile);
 			
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
@@ -299,7 +304,7 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 			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) {
@@ -309,7 +314,17 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
+                outputNames.clear();
 				num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+                
+                string tempFile = toString(getpid()) + ".outputNames.temp";
+                ofstream outTemp;
+                m->openOutputFile(tempFile, outTemp);
+                
+                outTemp << outputNames.size();
+                for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
+                outTemp.close();
+                
 				exit(0);
 			}else { 
 				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
@@ -326,7 +341,23 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 			int temp = processIDS[i];
 			wait(&temp);
 		}
-		
+        
+        for (int i = 0; i < processIDS.size(); i++) {
+            string tempFile = toString(processIDS[i]) +  ".outputNames.temp";
+            ifstream intemp;
+            m->openInputFile(tempFile, intemp);
+            
+            int num;
+            intemp >> num;
+            for (int k = 0; k < num; k++) {
+                string name = "";
+                intemp >> name; m->gobble(intemp);
+                
+                outputNames.push_back(name); outputTypes["map"].push_back(name);
+            }
+            intemp.close();
+            m->mothurRemove(tempFile);
+        }
 #else
 		
 		//////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -372,6 +403,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 		
 		//append output files
 		for(int i=0;i<processIDS.size();i++){
+			//newFName = m->getFullPathName(".\\" + newFName);
+			//newNName = m->getFullPathName(".\\" + newNName);
+			
 			m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 			m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 			
@@ -508,7 +542,7 @@ int PreClusterCommand::readFASTA(){
 		m->openInputFile(fastafile, inFasta);
 		
 		//string firstCol, secondCol, nameString;
-		length = 0;
+		set<int> lengths;
 		
 		while (!inFasta.eof()) {
 			
@@ -534,17 +568,21 @@ int PreClusterCommand::readFASTA(){
 					else{
 						seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 						alignSeqs.push_back(tempNode);
-						if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+						lengths.insert(seq.getAligned().length());
 					}	
 				}else { //no names file, you are identical to yourself 
 					seqPNode tempNode(1, seq, seq.getName());
 					alignSeqs.push_back(tempNode);
-					if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+					lengths.insert(seq.getAligned().length());
 				}
 			}
 		}
 		inFasta.close();
 		//inNames.close();
+        
+        if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
+        
 		return alignSeqs.size();
 	}
 	
@@ -556,7 +594,7 @@ int PreClusterCommand::readFASTA(){
 /**************************************************************************************************/
 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
 	try {
-		length = 0;
+		set<int> lengths;
 		alignSeqs.clear();
 		map<string, string>::iterator it;
 		bool error = false;
@@ -579,15 +617,18 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
 					
 					seqPNode tempNode(numReps, thisSeqs[i], it->second);
 					alignSeqs.push_back(tempNode);
-					if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+                    lengths.insert(thisSeqs[i].getAligned().length());
 				}	
 			}else { //no names file, you are identical to yourself 
 				seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
 				alignSeqs.push_back(tempNode);
-				if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+				lengths.insert(thisSeqs[i].getAligned().length());
 			}
 		}
 		
+        if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
+        
 		//sanity check
 		if (error) { m->control_pressed = true; }