--- /dev/null
+/*
+ * shhhseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/8/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "shhhseqscommand.h"
+
+
+
+//**********************************************************************************************************************
+vector<string> ShhhSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(psigma);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ShhhSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
+ helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
+ helpString += "The group parameter allows you to provide a group file. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "The sigma parameter .... The default is 0.01. \n";
+ helpString += "The shhh.seqs command should be in the following format: \n";
+ helpString += "shhh.seqs(fasta=yourFastaFile, name=yourNameFile) \n";
+ helpString += "Example: shhh.seqs(fasta=AD.align, name=AD.names) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+ShhhSeqsCommand::ShhhSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ShhhSeqsCommand::ShhhSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = 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; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not found") {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not found") { groupfile = ""; }
+ else if (groupfile == "not open") { abort = true; groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ string temp = validParameter.validFile(parameters, "sigma", false); if(temp == "not found"){ temp = "0.01"; }
+ m->mothurConvert(temp, sigma);
+ sigma = 1/sigma;
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ShhhSeqsCommand::execute() {
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
+ string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.names";
+ string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.map";
+
+ if (groupfile != "") {
+ //Parse sequences by group
+ SequenceParser parser(groupfile, fastafile, namefile);
+ vector<string> groups = parser.getNamesOfGroups();
+
+ if (m->control_pressed) { return 0; }
+
+ //clears files
+ ofstream out, out1, out2;
+ m->openOutputFile(outputFileName, out); out.close();
+ m->openOutputFile(nameFileName, out1); out1.close();
+ mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.";
+
+ vector<string> mapFileNames;
+ if(processors == 1) { mapFileNames = driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups); }
+ else { mapFileNames = createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups); }
+
+ if (m->control_pressed) { return 0; }
+
+ for (int j = 0; j < mapFileNames.size(); j++) { outputNames.push_back(mapFileNames[j]); outputTypes["map"].push_back(mapFileNames[j]); }
+
+ //deconvolute results by running unique.seqs
+ deconvoluteResults(outputFileName, nameFileName);
+
+ if (m->control_pressed) { return 0; }
+
+ }else{
+ vector<string> sequences;
+ vector<string> uniqueNames;
+ vector<string> redundantNames;
+ vector<int> seqFreq;
+
+ seqNoise noise;
+ correctDist* correct = new correctDist(processors);
+
+ //reads fasta and name file and loads them in order
+ readData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq);
+ if (m->control_pressed) { return 0; }
+
+ //calc distances for cluster
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.dist";
+ correct->execute(distFileName);
+ delete correct;
+
+ if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
+
+ driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, outputFileName, nameFileName, mapFileName);
+ outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
+ }
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+ outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
+
+ 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();
+
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ShhhSeqsCommand::readData(correctDist* correct, seqNoise& noise, vector<string>& seqs, vector<string>& uNames, vector<string>& rNames, vector<int>& freq) {
+ try {
+ map<string, string> nameMap;
+ map<string, string>::iterator it;
+ m->readNames(namefile, nameMap);
+ bool error = false;
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+ correct->addSeq(seq.getName(), seq.getAligned());
+
+ it = nameMap.find(seq.getName());
+ if (it != nameMap.end()) {
+ noise.addSeq(seq.getAligned(), seqs);
+ noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
+ }else {
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your namefile, please correct.");
+ error = true;
+ }
+ }
+ }
+ in.close();
+
+ if (error) { m->control_pressed = true; }
+
+ return seqs.size();
+
+ }catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "readData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ShhhSeqsCommand::loadData(correctDist* correct, seqNoise& noise, vector<string>& seqs, vector<string>& uNames, vector<string>& rNames, vector<int>& freq, map<string, string>& nameMap, vector<Sequence>& sequences) {
+ try {
+ bool error = false;
+ map<string, string>::iterator it;
+
+ for (int i = 0; i < sequences.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ if (sequences[i].getName() != "") {
+ correct->addSeq(sequences[i].getName(), sequences[i].getAligned());
+
+ it = nameMap.find(sequences[i].getName());
+ if (it != nameMap.end()) {
+ noise.addSeq(sequences[i].getAligned(), seqs);
+ noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
+ }else {
+ m->mothurOut("[ERROR]: " + sequences[i].getName() + " is in your fasta file and not in your namefile, please correct.");
+ error = true;
+ }
+ }
+ }
+
+ if (error) { m->control_pressed = true; }
+
+ return seqs.size();
+
+ }catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "loadData");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
+ try {
+
+ vector<int> processIDS;
+ int process = 1;
+ vector<string> mapfileNames;
+
+ //sanity check
+ if (groups.size() < processors) { processors = groups.size(); }
+
+ //divide the groups between the processors
+ vector<linePair> lines;
+ int numGroupsPerProcessor = groups.size() / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numGroupsPerProcessor;
+ int endIndex = (i+1) * numGroupsPerProcessor;
+ if(i == (processors - 1)){ endIndex = groups.size(); }
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ 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){
+ mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
+
+ //pass filenames to parent
+ ofstream out;
+ string tempFile = newMName + toString(getpid()) + ".temp";
+ m->openOutputFile(tempFile, out);
+ out << mapfileNames.size() << endl;
+ for (int i = 0; i < mapfileNames.size(); i++) {
+ out << mapfileNames[i] << endl;
+ }
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ ifstream in;
+ string tempFile = newMName + toString(processIDS[i]) + ".temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) {
+ int tempNum = 0; in >> tempNum; m->gobble(in);
+ for (int j = 0; j < tempNum; j++) {
+ string filename;
+ in >> filename; m->gobble(in);
+ mapfileNames.push_back(filename);
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
+
+ }
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the shhhseqsData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<shhhseqsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ shhhseqsData* tempShhhseqs = new shhhseqsData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMName, groups, m, lines[i].start, lines[i].end, sigma, i);
+ pDataArray.push_back(tempShhhseqs);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyShhhSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
+ mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
+ m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
+ m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
+ }
+
+ return mapfileNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "createProcessesGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<string> ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
+ try {
+
+ vector<string> mapFileNames;
+
+ for (int i = start; i < end; i++) {
+
+ start = time(NULL);
+
+ if (m->control_pressed) { return mapFileNames; }
+
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
+
+ map<string, string> thisNameMap;
+ thisNameMap = parser.getNameMap(groups[i]);
+ vector<Sequence> thisSeqs = parser.getSeqs(groups[i]);
+
+ vector<string> sequences;
+ vector<string> uniqueNames;
+ vector<string> redundantNames;
+ vector<int> seqFreq;
+
+ seqNoise noise;
+ correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
+
+ //load this groups info in order
+ loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
+ if (m->control_pressed) { return mapFileNames; }
+
+ //calc distances for cluster
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + groups[i] + ".shhh.dist";
+ correct->execute(distFileName);
+ delete correct;
+
+ if (m->control_pressed) { m->mothurRemove(distFileName); return mapFileNames; }
+
+ driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
+
+ if (m->control_pressed) { return mapFileNames; }
+
+ m->appendFiles(newFFile+groups[i], newFFile); m->mothurRemove(newFFile+groups[i]);
+ m->appendFiles(newNFile+groups[i], newNFile); m->mothurRemove(newNFile+groups[i]);
+ mapFileNames.push_back(newMFile+groups[i]+".map");
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + groups[i] + "."); m->mothurOutEndLine();
+ }
+
+ return mapFileNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "driverGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ShhhSeqsCommand::driver(seqNoise& noise,
+ vector<string>& sequences,
+ vector<string>& uniqueNames,
+ vector<string>& redundantNames,
+ vector<int>& seqFreq,
+ string distFileName, string outputFileName, string nameFileName, string mapFileName) {
+ try {
+ double cutOff = 0.08;
+ int minIter = 10;
+ int maxIter = 1000;
+ double minDelta = 1e-6;
+ int numIters = 0;
+ double maxDelta = 1e6;
+ int numSeqs = sequences.size();
+
+ //run cluster command
+ string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: cluster(" + inputString + ")"); m->mothurOutEndLine();
+
+ Command* clusterCommand = new ClusterCommand(inputString);
+ clusterCommand->execute();
+
+ map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
+ string listFileName = filenames["list"][0];
+ string rabundFileName = filenames["rabund"][0]; m->mothurRemove(rabundFileName);
+ string sabundFileName = filenames["sabund"][0]; m->mothurRemove(sabundFileName);
+
+ delete clusterCommand;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ if (m->control_pressed) { m->mothurRemove(distFileName); m->mothurRemove(listFileName); return 0; }
+
+ vector<double> distances(numSeqs * numSeqs);
+ noise.getDistanceData(distFileName, distances);
+ m->mothurRemove(distFileName);
+ if (m->control_pressed) { m->mothurRemove(listFileName); return 0; }
+
+ vector<int> otuData(numSeqs);
+ vector<int> otuFreq;
+ vector<vector<int> > otuBySeqLookUp;
+ noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
+ m->mothurRemove(listFileName);
+ if (m->control_pressed) { return 0; }
+
+ int numOTUs = otuFreq.size();
+
+ vector<double> weights(numOTUs, 0);
+ vector<int> change(numOTUs, 1);
+ vector<int> centroids(numOTUs, -1);
+ vector<int> cumCount(numOTUs, 0);
+
+ vector<double> tau(numSeqs, 1);
+ vector<int> anP(numSeqs, 0);
+ vector<int> anI(numSeqs, 0);
+ vector<int> anN(numSeqs, 0);
+ vector<vector<int> > aanI = otuBySeqLookUp;
+
+ while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
+
+ if (m->control_pressed) { return 0; }
+
+ noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
+ maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau); if (m->control_pressed) { return 0; }
+
+ noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
+ noise.checkCentroids(weights, centroids); if (m->control_pressed) { return 0; }
+
+ otuFreq.assign(numOTUs, 0);
+
+ int total = 0;
+
+ for(int i=0;i<numSeqs;i++){
+ if (m->control_pressed) { return 0; }
+
+ double offset = 1e6;
+ double norm = 0.0000;
+ double minWeight = 0.1;
+ vector<double> currentTau(numOTUs);
+
+ for(int j=0;j<numOTUs;j++){
+ if (m->control_pressed) { return 0; }
+ if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
+ offset = distances[i * numSeqs+centroids[j]];
+ }
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (m->control_pressed) { return 0; }
+ if(weights[j] > minWeight){
+ currentTau[j] = exp(sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
+ norm += currentTau[j];
+ }
+ else{
+ currentTau[j] = 0.0000;
+ }
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (m->control_pressed) { return 0; }
+ currentTau[j] /= norm;
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (m->control_pressed) { return 0; }
+
+ if(currentTau[j] > 1.0e-4){
+ int oldTotal = total;
+ total++;
+
+ tau.resize(oldTotal+1);
+ tau[oldTotal] = currentTau[j];
+ otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
+ aanI[j][otuFreq[j]] = i;
+ otuFreq[j]++;
+
+ }
+ }
+
+ anP.resize(total);
+ anI.resize(total);
+ }
+
+ numIters++;
+ }
+
+ noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
+
+ vector<double> percentage(numSeqs);
+ noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI); if (m->control_pressed) { return 0; }
+ noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau); if (m->control_pressed) { return 0; }
+
+ change.assign(numOTUs, 1);
+ noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
+
+
+ vector<int> finalTau(numOTUs, 0);
+ for(int i=0;i<numSeqs;i++){
+ if (m->control_pressed) { return 0; }
+ finalTau[otuData[i]] += int(seqFreq[i]);
+ }
+
+ noise.writeOutput(outputFileName, nameFileName, mapFileName, finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
+
+ return 0;
+
+ }catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
+ try {
+ m->mothurOutEndLine(); m->mothurOut("Deconvoluting results:"); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ //use unique.seqs to create new name and fastafile
+ string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
+ 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();
+
+ string newnameFile = filenames["name"][0];
+ string newfastaFile = filenames["fasta"][0];
+
+ m->mothurRemove(fastaFile); rename(newfastaFile.c_str(), fastaFile.c_str());
+ if (nameFile != newnameFile) { m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str()); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "deconvoluteResults");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff