+++ /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