CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
+ CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge);
CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
temp = validParameter.validFile(parameters, "maxiter", false); if (temp == "not found"){ temp = "1000"; }
m->mothurConvert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "large", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, largeSize);
+ if (largeSize != 0) { large = true; }
+ else { large = false; }
+ if (largeSize < 0) { m->mothurOut("The value of the large cannot be negative.\n"); }
+
+#ifdef USE_MPI
+ if (large) { m->mothurOut("The large parameter is not available with the MPI-Enabled version.\n"); large=false; }
+#endif
+
temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found") { temp = "60"; }
m->mothurConvert(temp, sigma);
}
/**************************************************************************************************/
-int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName, int start, int end){
+vector<string> ShhherCommand::parseFlowFiles(string filename){
try {
+ vector<string> files;
+ int count = 0;
- for(int i=start;i<end;i++){
-
- if (m->control_pressed) { break; }
-
- string flowFileName = filenames[i];
-
- m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(filenames.size()) + ")\t<<<<<\n");
- m->mothurOut("Reading flowgrams...\n");
-
- vector<string> seqNameVector;
- vector<int> lengths;
- vector<short> flowDataIntI;
- vector<double> flowDataPrI;
- map<string, int> nameMap;
- vector<short> uniqueFlowgrams;
- vector<int> uniqueCount;
- vector<int> mapSeqToUnique;
- vector<int> mapUniqueToSeq;
- vector<int> uniqueLengths;
- int numFlowCells;
-
- int numSeqs = getFlowData(flowFileName, seqNameVector, lengths, flowDataIntI, nameMap, numFlowCells);
-
- if (m->control_pressed) { break; }
-
- m->mothurOut("Identifying unique flowgrams...\n");
- int numUniques = getUniques(numSeqs, numFlowCells, uniqueFlowgrams, uniqueCount, uniqueLengths, mapSeqToUnique, mapUniqueToSeq, lengths, flowDataPrI, flowDataIntI);
-
- if (m->control_pressed) { break; }
-
- m->mothurOut("Calculating distances between flowgrams...\n");
- string distFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
- unsigned long long begTime = time(NULL);
- double begClock = clock();
+ ifstream in;
+ m->openInputFile(filename, in);
- flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);
-
- m->mothurOutEndLine();
- m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
-
+ int thisNumFLows = 0;
+ in >> thisNumFLows; m->gobble(in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
- string namesFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
- createNamesFile(numSeqs, numUniques, namesFileName, seqNameVector, mapSeqToUnique, mapUniqueToSeq);
-
- if (m->control_pressed) { break; }
-
- m->mothurOut("\nClustering flowgrams...\n");
- string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list";
- cluster(listFileName, distFileName, namesFileName);
-
- if (m->control_pressed) { break; }
+ ofstream out;
+ string outputFileName = filename + toString(count) + ".temp";
+ m->openOutputFile(outputFileName, out);
+ out << thisNumFLows << endl;
+ files.push_back(outputFileName);
- vector<int> otuData;
- vector<int> cumNumSeqs;
- vector<int> nSeqsPerOTU;
- vector<vector<int> > aaP; //tMaster->aanP: each row is a different otu / each col contains the sequence indices
- vector<vector<int> > aaI; //tMaster->aanI: that are in each otu - can't differentiate between aaP and aaI
- vector<int> seqNumber; //tMaster->anP: the sequence id number sorted by OTU
- vector<int> seqIndex; //tMaster->anI; the index that corresponds to seqNumber
+ for (int i = 0; i < largeSize; i++) {
+ if (in.eof()) { break; }
+ string line = m->getline(in);
+ out << line << endl;
+ }
+ out.close();
+ count++;
+ }
+ in.close();
+
+ if (m->control_pressed) { for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); } files.clear(); }
+
+ return files;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "parseFlowFiles");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
-
- int numOTUs = getOTUData(numSeqs, listFileName, otuData, cumNumSeqs, nSeqsPerOTU, aaP, aaI, seqNumber, seqIndex, nameMap);
+int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName, int start, int end){
+ try {
+
+ for(int i=start;i<end;i++){
if (m->control_pressed) { break; }
- m->mothurRemove(distFileName);
- m->mothurRemove(namesFileName);
- m->mothurRemove(listFileName);
-
- vector<double> dist; //adDist - distance of sequences to centroids
- vector<short> change; //did the centroid sequence change? 0 = no; 1 = yes
- vector<int> centroids; //the representative flowgram for each cluster m
- vector<double> weight;
- vector<double> singleTau; //tMaster->adTau: 1-D Tau vector (1xnumSeqs)
- vector<int> nSeqsBreaks;
- vector<int> nOTUsBreaks;
+ vector<string> theseFlowFileNames; theseFlowFileNames.push_back(filenames[i]);
+ if (large) { theseFlowFileNames = parseFlowFiles(filenames[i]); }
- dist.assign(numSeqs * numOTUs, 0);
- change.assign(numOTUs, 1);
- centroids.assign(numOTUs, -1);
- weight.assign(numOTUs, 0);
- singleTau.assign(numSeqs, 1.0);
-
- nSeqsBreaks.assign(2, 0);
- nOTUsBreaks.assign(2, 0);
+ if (m->control_pressed) { break; }
- nSeqsBreaks[0] = 0;
- nSeqsBreaks[1] = numSeqs;
- nOTUsBreaks[1] = numOTUs;
-
- if (m->control_pressed) { break; }
-
- double maxDelta = 0;
- int iter = 0;
-
- begClock = clock();
- begTime = time(NULL);
+ double begClock = clock();
+ unsigned long long begTime;
- m->mothurOut("\nDenoising flowgrams...\n");
- m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
-
- while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
-
- if (m->control_pressed) { break; }
-
- double cycClock = clock();
- unsigned long long cycTime = time(NULL);
- fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI);
-
- if (m->control_pressed) { break; }
+ for (int g = 0; g < theseFlowFileNames.size(); g++) {
- calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
-
- if (m->control_pressed) { break; }
+ string flowFileName = theseFlowFileNames[g];
+ m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(filenames.size()) + ")\t<<<<<\n");
+ m->mothurOut("Reading flowgrams...\n");
+
+ vector<string> seqNameVector;
+ vector<int> lengths;
+ vector<short> flowDataIntI;
+ vector<double> flowDataPrI;
+ map<string, int> nameMap;
+ vector<short> uniqueFlowgrams;
+ vector<int> uniqueCount;
+ vector<int> mapSeqToUnique;
+ vector<int> mapUniqueToSeq;
+ vector<int> uniqueLengths;
+ int numFlowCells;
- maxDelta = getNewWeights(numOTUs, cumNumSeqs, nSeqsPerOTU, singleTau, seqNumber, weight);
+ int numSeqs = getFlowData(flowFileName, seqNameVector, lengths, flowDataIntI, nameMap, numFlowCells);
if (m->control_pressed) { break; }
- double nLL = getLikelihood(numSeqs, numOTUs, nSeqsPerOTU, seqNumber, cumNumSeqs, seqIndex, dist, weight);
+ m->mothurOut("Identifying unique flowgrams...\n");
+ int numUniques = getUniques(numSeqs, numFlowCells, uniqueFlowgrams, uniqueCount, uniqueLengths, mapSeqToUnique, mapUniqueToSeq, lengths, flowDataPrI, flowDataIntI);
if (m->control_pressed) { break; }
- checkCentroids(numOTUs, centroids, weight);
-
- if (m->control_pressed) { break; }
-
- calcNewDistances(numSeqs, numOTUs, nSeqsPerOTU, dist, weight, change, centroids, aaP, singleTau, aaI, seqNumber, seqIndex, uniqueFlowgrams, flowDataIntI, numFlowCells, lengths);
-
- if (m->control_pressed) { break; }
-
- iter++;
-
- m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
+ m->mothurOut("Calculating distances between flowgrams...\n");
+ string distFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
+ begTime = time(NULL);
+
- }
-
- if (m->control_pressed) { break; }
-
- m->mothurOut("\nFinalizing...\n");
- fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI);
-
- if (m->control_pressed) { break; }
-
- setOTUs(numOTUs, numSeqs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, otuData, singleTau, dist, aaP, aaI);
-
- if (m->control_pressed) { break; }
-
- vector<int> otuCounts(numOTUs, 0);
- for(int i=0;i<numSeqs;i++) { otuCounts[otuData[i]]++; }
-
- calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
-
- if (m->control_pressed) { break; }
+ flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);
+
+ m->mothurOutEndLine();
+ m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
+
+
+ string namesFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+ createNamesFile(numSeqs, numUniques, namesFileName, seqNameVector, mapSeqToUnique, mapUniqueToSeq);
+
+ if (m->control_pressed) { break; }
+
+ m->mothurOut("\nClustering flowgrams...\n");
+ string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list";
+ cluster(listFileName, distFileName, namesFileName);
+
+ if (m->control_pressed) { break; }
+
+ vector<int> otuData;
+ vector<int> cumNumSeqs;
+ vector<int> nSeqsPerOTU;
+ vector<vector<int> > aaP; //tMaster->aanP: each row is a different otu / each col contains the sequence indices
+ vector<vector<int> > aaI; //tMaster->aanI: that are in each otu - can't differentiate between aaP and aaI
+ vector<int> seqNumber; //tMaster->anP: the sequence id number sorted by OTU
+ vector<int> seqIndex; //tMaster->anI; the index that corresponds to seqNumber
+
+
+ int numOTUs = getOTUData(numSeqs, listFileName, otuData, cumNumSeqs, nSeqsPerOTU, aaP, aaI, seqNumber, seqIndex, nameMap);
+
+ if (m->control_pressed) { break; }
+
+ m->mothurRemove(distFileName);
+ m->mothurRemove(namesFileName);
+ m->mothurRemove(listFileName);
+
+ vector<double> dist; //adDist - distance of sequences to centroids
+ vector<short> change; //did the centroid sequence change? 0 = no; 1 = yes
+ vector<int> centroids; //the representative flowgram for each cluster m
+ vector<double> weight;
+ vector<double> singleTau; //tMaster->adTau: 1-D Tau vector (1xnumSeqs)
+ vector<int> nSeqsBreaks;
+ vector<int> nOTUsBreaks;
+
+ dist.assign(numSeqs * numOTUs, 0);
+ change.assign(numOTUs, 1);
+ centroids.assign(numOTUs, -1);
+ weight.assign(numOTUs, 0);
+ singleTau.assign(numSeqs, 1.0);
+
+ nSeqsBreaks.assign(2, 0);
+ nOTUsBreaks.assign(2, 0);
+
+ nSeqsBreaks[0] = 0;
+ nSeqsBreaks[1] = numSeqs;
+ nOTUsBreaks[1] = numOTUs;
+
+ if (m->control_pressed) { break; }
+
+ double maxDelta = 0;
+ int iter = 0;
+
+ begClock = clock();
+ begTime = time(NULL);
+
+ m->mothurOut("\nDenoising flowgrams...\n");
+ m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
+
+ while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
+
+ if (m->control_pressed) { break; }
+
+ double cycClock = clock();
+ unsigned long long cycTime = time(NULL);
+ fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI);
+
+ if (m->control_pressed) { break; }
+
+ calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
+
+ if (m->control_pressed) { break; }
+
+ maxDelta = getNewWeights(numOTUs, cumNumSeqs, nSeqsPerOTU, singleTau, seqNumber, weight);
+
+ if (m->control_pressed) { break; }
+
+ double nLL = getLikelihood(numSeqs, numOTUs, nSeqsPerOTU, seqNumber, cumNumSeqs, seqIndex, dist, weight);
+
+ if (m->control_pressed) { break; }
+
+ checkCentroids(numOTUs, centroids, weight);
+
+ if (m->control_pressed) { break; }
+
+ calcNewDistances(numSeqs, numOTUs, nSeqsPerOTU, dist, weight, change, centroids, aaP, singleTau, aaI, seqNumber, seqIndex, uniqueFlowgrams, flowDataIntI, numFlowCells, lengths);
+
+ if (m->control_pressed) { break; }
+
+ iter++;
+
+ m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
+
+ }
+
+ if (m->control_pressed) { break; }
+
+ m->mothurOut("\nFinalizing...\n");
+ fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI);
+
+ if (m->control_pressed) { break; }
+
+ setOTUs(numOTUs, numSeqs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, otuData, singleTau, dist, aaP, aaI);
+
+ if (m->control_pressed) { break; }
+
+ vector<int> otuCounts(numOTUs, 0);
+ for(int i=0;i<numSeqs;i++) { otuCounts[otuData[i]]++; }
+
+ calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
+
+ if (m->control_pressed) { break; }
+
+ if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; }
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); }
+ string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual";
+ string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta";
+ string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.names";
+ string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.counts";
+ string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string groupFileName = fileRoot + "shhh.groups";
+
+
+ writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
+ writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, fastaFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; }
+ writeNames(thisCompositeNamesFileName, numOTUs, nameFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU); if (m->control_pressed) { break; }
+ writeClusters(otuCountsFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI); if (m->control_pressed) { break; }
+ writeGroups(groupFileName, fileRoot, numSeqs, seqNameVector); if (m->control_pressed) { break; }
+
+ if (large) {
+ if (g > 0) {
+ m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.qual"));
+ m->mothurRemove(qualityFileName);
+ m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.fasta"));
+ m->mothurRemove(fastaFileName);
+ m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.names"));
+ m->mothurRemove(nameFileName);
+ m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.counts"));
+ m->mothurRemove(otuCountsFileName);
+ m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.groups"));
+ m->mothurRemove(groupFileName);
+ m->mothurRemove(theseFlowFileNames[g]);
+ }
+ }
+ }
- writeQualities(numOTUs, numFlowCells, flowFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
- writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, flowFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; }
- writeNames(thisCompositeNamesFileName, numOTUs, flowFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU); if (m->control_pressed) { break; }
- writeClusters(flowFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI); if (m->control_pressed) { break; }
- writeGroups(flowFileName, numSeqs, seqNameVector); if (m->control_pressed) { break; }
-
m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
}
}
/**************************************************************************************************/
-void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<int>& nSeqsPerOTU, vector<int>& seqNumber,
+void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string qualityFileName, vector<int> otuCounts, vector<int>& nSeqsPerOTU, vector<int>& seqNumber,
vector<double>& singleTau, vector<short>& flowDataIntI, vector<short>& uniqueFlowgrams, vector<int>& cumNumSeqs,
vector<int>& mapUniqueToSeq, vector<string>& seqNameVector, vector<int>& centroids, vector<vector<int> >& aaI){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
- string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.qual";
ofstream qualityFile;
m->openOutputFile(qualityFileName, qualityFile);
/**************************************************************************************************/
-void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
+void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string fastaFileName, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
- string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.fasta";
+
ofstream fastaFile;
m->openOutputFile(fastaFileName, fastaFile);
}
}
- fastaFile << newSeq.substr(4) << endl;
+ if (newSeq.length() >= 4) { fastaFile << newSeq.substr(4) << endl; }
+ else { fastaFile << "NNNN" << endl; }
}
}
fastaFile.close();
/**************************************************************************************************/
-void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string filename, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
+void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string nameFileName, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
- string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.names";
+
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
/**************************************************************************************************/
-void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& seqNameVector){
+void ShhherCommand::writeGroups(string groupFileName, string fileRoot, int numSeqs, vector<string>& seqNameVector){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
- string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
- string groupFileName = fileRoot + "shhh.groups";
- ofstream groupFile;
+ ofstream groupFile;
m->openOutputFile(groupFileName, groupFile);
for(int i=0;i<numSeqs;i++){
/**************************************************************************************************/
-void ShhherCommand::writeClusters(string filename, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
+void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
- string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.counts";
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);
projects / mothur.git / blobdiff