mods to shhh.seqs and trim.flows to fix eye candy output

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 0977cfb2f0db4d4df43ff731628c82c8d918047f..f7c3e59714f4109398f97fb67d8dcb908a1ae9fd 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -70,8 +70,8 @@ ShhherCommand::ShhherCommand(){
                setParameters();
                
                //initialize outputTypes
-               vector<string> tempOutNames;
-               outputTypes["pn.dist"] = tempOutNames;
+//             vector<string> tempOutNames;
+//             outputTypes["pn.dist"] = tempOutNames;
 
        }
        catch(exception& e) {
@@ -116,7 +116,7 @@ ShhherCommand::ShhherCommand(string option) {
                        
                        //initialize outputTypes
                        vector<string> tempOutNames;
-                       outputTypes["pn.dist"] = tempOutNames;
+//                     outputTypes["pn.dist"] = tempOutNames;
                        //                      outputTypes["fasta"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -160,12 +160,20 @@ ShhherCommand::ShhherCommand(string option) {
                        }
                        else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
                        
-                       if(flowFileName != "not found"){        compositeFASTAFileName = "";    }
+                       if(flowFileName != "not found"){
+                               compositeFASTAFileName = "";    
+                               compositeNamesFileName = "";    
+                       }
                        else{
-                               compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "pn.fasta";
                                ofstream temp;
+
+                               compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
+                               
+                               compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               m->openOutputFile(compositeNamesFileName, temp);
+                               temp.close();
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -308,6 +316,11 @@ int ShhherCommand::execute(){
                                string listFileName = cluster(distFileName, namesFileName);
 
                                getOTUData(listFileName);
+
+                               remove(distFileName.c_str());
+                               remove(namesFileName.c_str());
+                               remove(listFileName.c_str());
+                               
                                initPyroCluster();
 
                                for(int i=1;i<ncpus;i++){
@@ -445,18 +458,17 @@ int ShhherCommand::execute(){
                                m->mothurOut("\nFinalizing...\n");
                                fill();
                                setOTUs();
+                               
                                vector<int> otuCounts(numOTUs, 0);
                                for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
                                calcCentroidsDriver(0, numOTUs);
+                               
                                writeQualities(otuCounts);
                                writeSequences(otuCounts);
                                writeNames(otuCounts);
                                writeClusters(otuCounts);
                                writeGroups();
                                
-                               remove(distFileName.c_str());
-                               remove(namesFileName.c_str());
-                               remove(listFileName.c_str());
                                                                 
                                m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');                 
                        }
@@ -568,6 +580,17 @@ int ShhherCommand::execute(){
                }               
                MPI_Barrier(MPI_COMM_WORLD);
 
+               
+               if(compositeFASTAFileName != ""){
+                       outputNames.push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName);
+               }
+
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
+               
                return 0;
 
        }
@@ -608,7 +631,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                
                m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
                
-               string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
+               string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
                if(pid != 0){   fDistFileName += ".temp." + toString(pid);      }
 
                ofstream distFile(fDistFileName.c_str());
@@ -670,6 +693,10 @@ int ShhherCommand::execute(){
                        string listFileName = cluster(distFileName, namesFileName);
                        getOTUData(listFileName);
                        
+                       remove(distFileName.c_str());
+                       remove(namesFileName.c_str());
+                       remove(listFileName.c_str());
+                       
                        initPyroCluster();
                        
                        double maxDelta = 0;
@@ -715,12 +742,19 @@ int ShhherCommand::execute(){
                        writeClusters(otuCounts);
                        writeGroups();
                        
-                       remove(distFileName.c_str());
-                       remove(namesFileName.c_str());
-                       remove(listFileName.c_str());
-                       
                        m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
                }
+               
+               if(compositeFASTAFileName != ""){
+                       outputNames.push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName);
+               }
+
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
+               
                return 0;
        }
        catch(exception& e) {
@@ -1012,7 +1046,7 @@ void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int st
 
 string ShhherCommand::createDistFile(int processors){
        try{
-               string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
+               string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
                                
                unsigned long int begTime = time(NULL);
                double begClock = clock();
@@ -1100,7 +1134,7 @@ string ShhherCommand::createNamesFile(){
                        duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
                }
                
-               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.names";
+               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
                
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
@@ -1149,7 +1183,7 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
                
                list->setLabel(toString(cutoff));
                
-               string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.list";
+               string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list";
                ofstream listFile;
                m->openOutputFile(listFileName, listFile);
                list->print(listFile);
@@ -1880,7 +1914,7 @@ void ShhherCommand::setOTUs(){
 void ShhherCommand::writeQualities(vector<int> otuCounts){
        
        try {
-               string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.qual";
+               string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
 
                ofstream qualityFile;
                m->openOutputFile(qualityFileName, qualityFile);
@@ -1969,7 +2003,8 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
                        }
                }
                qualityFile.close();
-               
+               outputNames.push_back(qualityFileName);
+
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "writeQualities");
@@ -1982,7 +2017,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
                
-               string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
+               string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
                ofstream fastaFile;
                m->openOutputFile(fastaFileName, fastaFile);
                
@@ -2008,7 +2043,9 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
                        }
                }
                fastaFile.close();
-               
+
+               outputNames.push_back(fastaFileName);
+
                if(compositeFASTAFileName != ""){
                        m->appendFiles(fastaFileName, compositeFASTAFileName);
                }
@@ -2023,7 +2060,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
 
 void ShhherCommand::writeNames(vector<int> otuCounts){
        try {
-               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.final.names";
+               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
                
@@ -2039,6 +2076,12 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
                        }
                }
                nameFile.close();
+               outputNames.push_back(nameFileName);
+               
+               
+               if(compositeNamesFileName != ""){
+                       m->appendFiles(nameFileName, compositeNamesFileName);
+               }               
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "writeNames");
@@ -2051,7 +2094,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
 void ShhherCommand::writeGroups(){
        try {
                string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
-               string groupFileName = fileRoot + ".pn.groups";
+               string groupFileName = fileRoot + ".shhh.groups";
                ofstream groupFile;
                m->openOutputFile(groupFileName, groupFile);
                
@@ -2059,6 +2102,8 @@ void ShhherCommand::writeGroups(){
                        groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
                }
                groupFile.close();
+               outputNames.push_back(groupFileName);
+
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "writeGroups");
@@ -2070,7 +2115,7 @@ void ShhherCommand::writeGroups(){
 
 void ShhherCommand::writeClusters(vector<int> otuCounts){
        try {
-               string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.counts";
+               string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);
                
@@ -2111,6 +2156,8 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
                        }
                }
                otuCountsFile.close();
+               outputNames.push_back(otuCountsFileName);
+
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "writeClusters");

diff --git a/shhhercommand.h b/shhhercommand.h
index dba4d68917e9027edc8d8888de82b2e6938e9256..a95815fd154be1027d79cb33861c733be207ef1d 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -33,7 +33,7 @@ private:
        
        int abort;
        
-       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
 
        int processors, maxIters;
        float cutoff, sigma, minDelta;
@@ -66,7 +66,9 @@ private:
        vector<int> mapSeqToUnique;
        vector<int> mapUniqueToSeq;
        vector<int> uniqueLengths;
-       
+
+       vector<string> outputNames;
+
        int numSeqs, numUniques, numOTUs, numFlowCells;
        
        void getSingleLookUp();

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 05ed31ebd880af06984fa87cba97349df3f5e8c4..6ee865516bee6851fadf28f81e70bb249c35562d 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -124,14 +124,6 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                                        if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
                                }
                                
-                               
-//                             it = parameters.find("group");
-//                             //user has given a template file
-//                             if(it != parameters.end()){ 
-//                                     path = m->hasPath(it->second);
-//                                     //if the user has not given a path then, add inputdir. else leave path alone.
-//                                     if (path == "") {       parameters["group"] = inputDir + it->second;            }
-//                             }
                        }
                        
                        
@@ -157,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        
                        string temp;
-                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
+                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, minFlows);  
 
-                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
+                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, maxFlows);  
                        
                        
@@ -283,7 +275,7 @@ int TrimFlowsCommand::execute(){
                                        if (pFile==NULL) perror ("Error opening file");
                                        else{
                                                fseek (pFile, 0, SEEK_END);
-                                               size=ftell (pFile);
+                                               size=ftell(pFile);
                                                fclose (pFile);
                                        }
 
@@ -292,6 +284,8 @@ int TrimFlowsCommand::execute(){
                                        }
                                        else{
                                                output << barcodePrimerComboFileNames[i][j] << endl;
+                                               outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+                                               outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                        }
                                }
                        }
@@ -306,14 +300,14 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                outputTypes["flow.files"].push_back(flowFilesFileName);
-               outputNames.push_back(flowFileName);
+               outputNames.push_back(flowFilesFileName);
                
-               //set fasta file as new current fastafile
-               string current = "";
-               itTypes = outputTypes.find("fasta");
-               if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
-               }
+//             set fasta file as new current fastafile
+//             string current = "";
+//             itTypes = outputTypes.find("fasta");
+//             if (itTypes != outputTypes.end()) {
+//                     if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+//             }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -581,8 +575,6 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                                fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
                                        }
                                        
-                                       outputNames.push_back(fileName);
-                                       outputTypes["flow"].push_back(fileName);
                                        outFlowFileNames[itBar->second][itPrimer->second] = fileName;
                                        
                                        ofstream temp;