5 * Created by westcott on 11/8/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "shhhseqscommand.h"
14 //**********************************************************************************************************************
15 vector<string> ShhhSeqsCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
18 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
19 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
20 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
21 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
22 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
23 CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(psigma);
25 vector<string> myArray;
26 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
30 m->errorOut(e, "ShhhSeqsCommand", "setParameters");
34 //**********************************************************************************************************************
35 string ShhhSeqsCommand::getHelpString(){
37 string helpString = "";
38 helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
39 helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
40 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";
41 helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
42 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";
43 helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
44 helpString += "The sigma parameter .... The default is 0.01. \n";
45 helpString += "The shhh.seqs command should be in the following format: \n";
46 helpString += "shhh.seqs(fasta=yourFastaFile, name=yourNameFile) \n";
47 helpString += "Example: shhh.seqs(fasta=AD.align, name=AD.names) \n";
48 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
53 m->errorOut(e, "ShhhSeqsCommand", "getHelpString");
57 //**********************************************************************************************************************
59 ShhhSeqsCommand::ShhhSeqsCommand(){
61 abort = true; calledHelp = true;
63 vector<string> tempOutNames;
64 outputTypes["fasta"] = tempOutNames;
65 outputTypes["name"] = tempOutNames;
66 outputTypes["map"] = tempOutNames;
69 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
74 //**********************************************************************************************************************
75 ShhhSeqsCommand::ShhhSeqsCommand(string option) {
77 abort = false; calledHelp = false;
79 //allow user to run help
80 if(option == "help") { help(); abort = true; calledHelp = true; }
81 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
84 vector<string> myArray = setParameters();
86 OptionParser parser(option);
87 map<string, string> parameters = parser.getParameters();
89 ValidParameters validParameter;
90 map<string, string>::iterator it;
92 //check to make sure all parameters are valid for command
93 for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
94 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
97 //initialize outputTypes
98 vector<string> tempOutNames;
99 outputTypes["fasta"] = tempOutNames;
100 outputTypes["name"] = tempOutNames;
101 outputTypes["map"] = tempOutNames;
103 //if the user changes the input directory command factory will send this info to us in the output parameter
104 string inputDir = validParameter.validFile(parameters, "inputdir", false);
105 if (inputDir == "not found"){ inputDir = ""; }
108 it = parameters.find("fasta");
109 //user has given a template file
110 if(it != parameters.end()){
111 path = m->hasPath(it->second);
112 //if the user has not given a path then, add inputdir. else leave path alone.
113 if (path == "") { parameters["fasta"] = inputDir + it->second; }
116 it = parameters.find("name");
117 //user has given a template file
118 if(it != parameters.end()){
119 path = m->hasPath(it->second);
120 //if the user has not given a path then, add inputdir. else leave path alone.
121 if (path == "") { parameters["name"] = inputDir + it->second; }
124 it = parameters.find("group");
125 //user has given a template file
126 if(it != parameters.end()){
127 path = m->hasPath(it->second);
128 //if the user has not given a path then, add inputdir. else leave path alone.
129 if (path == "") { parameters["group"] = inputDir + it->second; }
133 //check for required parameters
134 fastafile = validParameter.validFile(parameters, "fasta", true);
135 if (fastafile == "not found") {
136 fastafile = m->getFastaFile();
137 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
138 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
140 else if (fastafile == "not open") { abort = true; }
141 else { m->setFastaFile(fastafile); }
143 //if the user changes the output directory command factory will send this info to us in the output parameter
144 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
146 //check for optional parameter and set defaults
147 // ...at some point should added some additional type checking...
148 namefile = validParameter.validFile(parameters, "name", true);
149 if (namefile == "not found") {
150 namefile = m->getNameFile();
151 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
152 else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
154 else if (namefile == "not open") { namefile = ""; abort = true; }
155 else { m->setNameFile(namefile); }
157 groupfile = validParameter.validFile(parameters, "group", true);
158 if (groupfile == "not found") { groupfile = ""; }
159 else if (groupfile == "not open") { abort = true; groupfile = ""; }
160 else { m->setGroupFile(groupfile); }
162 string temp = validParameter.validFile(parameters, "sigma", false); if(temp == "not found"){ temp = "0.01"; }
163 m->mothurConvert(temp, sigma);
165 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
166 m->setProcessors(temp);
167 m->mothurConvert(temp, processors);
170 catch(exception& e) {
171 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
175 //**********************************************************************************************************************
176 int ShhhSeqsCommand::execute() {
179 if (abort == true) { if (calledHelp) { return 0; } return 2; }
181 if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
182 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
183 string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.names";
184 string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.map";
186 if (groupfile != "") {
187 //Parse sequences by group
188 SequenceParser parser(groupfile, fastafile, namefile);
189 vector<string> groups = parser.getNamesOfGroups();
191 if (m->control_pressed) { return 0; }
194 ofstream out, out1, out2;
195 m->openOutputFile(outputFileName, out); out.close();
196 m->openOutputFile(nameFileName, out1); out1.close();
197 mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.";
199 vector<string> mapFileNames;
200 if(processors == 1) { mapFileNames = driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups); }
201 else { mapFileNames = createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups); }
203 if (m->control_pressed) { return 0; }
205 for (int j = 0; j < mapFileNames.size(); j++) { outputNames.push_back(mapFileNames[j]); outputTypes["map"].push_back(mapFileNames[j]); }
207 //deconvolute results by running unique.seqs
208 deconvoluteResults(outputFileName, nameFileName);
210 if (m->control_pressed) { return 0; }
213 vector<string> sequences;
214 vector<string> uniqueNames;
215 vector<string> redundantNames;
219 correctDist* correct = new correctDist(processors);
221 //reads fasta and name file and loads them in order
222 readData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq);
223 if (m->control_pressed) { return 0; }
225 //calc distances for cluster
226 string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.dist";
227 correct->execute(distFileName);
230 if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
232 driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, outputFileName, nameFileName, mapFileName);
233 outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
236 if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
238 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
239 outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
241 m->mothurOutEndLine();
242 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
243 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
244 m->mothurOutEndLine();
246 //set accnos file as new current accnosfile
248 itTypes = outputTypes.find("fasta");
249 if (itTypes != outputTypes.end()) {
250 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
253 itTypes = outputTypes.find("name");
254 if (itTypes != outputTypes.end()) {
255 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
261 catch(exception& e) {
262 m->errorOut(e, "ShhhSeqsCommand", "execute");
266 //**********************************************************************************************************************
267 int ShhhSeqsCommand::readData(correctDist* correct, seqNoise& noise, vector<string>& seqs, vector<string>& uNames, vector<string>& rNames, vector<int>& freq) {
269 map<string, string> nameMap;
270 map<string, string>::iterator it;
271 m->readNames(namefile, nameMap);
275 m->openInputFile(fastafile, in);
279 if (m->control_pressed) { in.close(); return 0; }
281 Sequence seq(in); m->gobble(in);
283 if (seq.getName() != "") {
284 correct->addSeq(seq.getName(), seq.getAligned());
286 it = nameMap.find(seq.getName());
287 if (it != nameMap.end()) {
288 noise.addSeq(seq.getAligned(), seqs);
289 noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
291 m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your namefile, please correct.");
298 if (error) { m->control_pressed = true; }
302 }catch(exception& e) {
303 m->errorOut(e, "ShhhSeqsCommand", "readData");
307 //**********************************************************************************************************************
308 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) {
311 map<string, string>::iterator it;
313 for (int i = 0; i < sequences.size(); i++) {
315 if (m->control_pressed) { return 0; }
317 if (sequences[i].getName() != "") {
318 correct->addSeq(sequences[i].getName(), sequences[i].getAligned());
320 it = nameMap.find(sequences[i].getName());
321 if (it != nameMap.end()) {
322 noise.addSeq(sequences[i].getAligned(), seqs);
323 noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
325 m->mothurOut("[ERROR]: " + sequences[i].getName() + " is in your fasta file and not in your namefile, please correct.");
331 if (error) { m->control_pressed = true; }
335 }catch(exception& e) {
336 m->errorOut(e, "ShhhSeqsCommand", "loadData");
340 /**************************************************************************************************/
341 vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
344 vector<int> processIDS;
346 vector<string> mapfileNames;
349 if (groups.size() < processors) { processors = groups.size(); }
351 //divide the groups between the processors
352 vector<linePair> lines;
353 int numGroupsPerProcessor = groups.size() / processors;
354 for (int i = 0; i < processors; i++) {
355 int startIndex = i * numGroupsPerProcessor;
356 int endIndex = (i+1) * numGroupsPerProcessor;
357 if(i == (processors - 1)){ endIndex = groups.size(); }
358 lines.push_back(linePair(startIndex, endIndex));
361 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
363 //loop through and create all the processes you want
364 while (process != processors) {
368 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
371 mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
373 //pass filenames to parent
375 string tempFile = newMName + toString(getpid()) + ".temp";
376 m->openOutputFile(tempFile, out);
377 out << mapfileNames.size() << endl;
378 for (int i = 0; i < mapfileNames.size(); i++) {
379 out << mapfileNames[i] << endl;
385 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
386 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
392 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
394 //force parent to wait until all the processes are done
395 for (int i=0;i<processIDS.size();i++) {
396 int temp = processIDS[i];
400 //append output files
401 for(int i=0;i<processIDS.size();i++){
403 string tempFile = newMName + toString(processIDS[i]) + ".temp";
404 m->openInputFile(tempFile, in);
406 int tempNum = 0; in >> tempNum; m->gobble(in);
407 for (int j = 0; j < tempNum; j++) {
409 in >> filename; m->gobble(in);
410 mapfileNames.push_back(filename);
413 in.close(); m->mothurRemove(tempFile);
418 //////////////////////////////////////////////////////////////////////////////////////////////////////
419 //Windows version shared memory, so be careful when passing variables through the shhhseqsData struct.
420 //Above fork() will clone, so memory is separate, but that's not the case with windows,
421 //////////////////////////////////////////////////////////////////////////////////////////////////////
423 vector<shhhseqsData*> pDataArray;
424 DWORD dwThreadIdArray[processors-1];
425 HANDLE hThreadArray[processors-1];
427 //Create processor worker threads.
428 for( int i=1; i<processors; i++ ){
429 // Allocate memory for thread data.
430 string extension = toString(i) + ".temp";
432 shhhseqsData* tempShhhseqs = new shhhseqsData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMName, groups, m, lines[i].start, lines[i].end, sigma, i);
433 pDataArray.push_back(tempShhhseqs);
434 processIDS.push_back(i);
436 //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
437 //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
438 hThreadArray[i-1] = CreateThread(NULL, 0, MyShhhSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
442 //using the main process as a worker saves time and memory
443 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
445 //Wait until all threads have terminated.
446 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
448 //Close all thread handles and free memory allocations.
449 for(int i=0; i < pDataArray.size(); i++){
450 for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
451 mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
453 CloseHandle(hThreadArray[i]);
454 delete pDataArray[i];
459 //append output files
460 for(int i=0;i<processIDS.size();i++){
461 m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
462 m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
464 m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
465 m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
471 catch(exception& e) {
472 m->errorOut(e, "ShhhSeqsCommand", "createProcessesGroups");
476 /**************************************************************************************************/
477 vector<string> ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
480 vector<string> mapFileNames;
482 for (int i = start; i < end; i++) {
486 if (m->control_pressed) { return mapFileNames; }
488 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
490 map<string, string> thisNameMap;
491 thisNameMap = parser.getNameMap(groups[i]);
492 vector<Sequence> thisSeqs = parser.getSeqs(groups[i]);
494 vector<string> sequences;
495 vector<string> uniqueNames;
496 vector<string> redundantNames;
500 correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
502 //load this groups info in order
503 loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
504 if (m->control_pressed) { return mapFileNames; }
506 //calc distances for cluster
507 string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + groups[i] + ".shhh.dist";
508 correct->execute(distFileName);
511 if (m->control_pressed) { m->mothurRemove(distFileName); return mapFileNames; }
513 driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
515 if (m->control_pressed) { return mapFileNames; }
517 m->appendFiles(newFFile+groups[i], newFFile); m->mothurRemove(newFFile+groups[i]);
518 m->appendFiles(newNFile+groups[i], newNFile); m->mothurRemove(newNFile+groups[i]);
519 mapFileNames.push_back(newMFile+groups[i]+".map");
521 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + groups[i] + "."); m->mothurOutEndLine();
526 catch(exception& e) {
527 m->errorOut(e, "ShhhSeqsCommand", "driverGroups");
531 //**********************************************************************************************************************
532 int ShhhSeqsCommand::driver(seqNoise& noise,
533 vector<string>& sequences,
534 vector<string>& uniqueNames,
535 vector<string>& redundantNames,
536 vector<int>& seqFreq,
537 string distFileName, string outputFileName, string nameFileName, string mapFileName) {
539 double cutOff = 0.08;
542 double minDelta = 1e-6;
544 double maxDelta = 1e6;
545 int numSeqs = sequences.size();
547 //run cluster command
548 string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
549 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
550 m->mothurOut("Running command: cluster(" + inputString + ")"); m->mothurOutEndLine();
552 Command* clusterCommand = new ClusterCommand(inputString);
553 clusterCommand->execute();
555 map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
556 string listFileName = filenames["list"][0];
557 string rabundFileName = filenames["rabund"][0]; m->mothurRemove(rabundFileName);
558 string sabundFileName = filenames["sabund"][0]; m->mothurRemove(sabundFileName);
560 delete clusterCommand;
561 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
563 if (m->control_pressed) { m->mothurRemove(distFileName); m->mothurRemove(listFileName); return 0; }
565 vector<double> distances(numSeqs * numSeqs);
566 noise.getDistanceData(distFileName, distances);
567 m->mothurRemove(distFileName);
568 if (m->control_pressed) { m->mothurRemove(listFileName); return 0; }
570 vector<int> otuData(numSeqs);
572 vector<vector<int> > otuBySeqLookUp;
573 noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
574 m->mothurRemove(listFileName);
575 if (m->control_pressed) { return 0; }
577 int numOTUs = otuFreq.size();
579 vector<double> weights(numOTUs, 0);
580 vector<int> change(numOTUs, 1);
581 vector<int> centroids(numOTUs, -1);
582 vector<int> cumCount(numOTUs, 0);
584 vector<double> tau(numSeqs, 1);
585 vector<int> anP(numSeqs, 0);
586 vector<int> anI(numSeqs, 0);
587 vector<int> anN(numSeqs, 0);
588 vector<vector<int> > aanI = otuBySeqLookUp;
590 while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
592 if (m->control_pressed) { return 0; }
594 noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
595 maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau); if (m->control_pressed) { return 0; }
597 noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
598 noise.checkCentroids(weights, centroids); if (m->control_pressed) { return 0; }
600 otuFreq.assign(numOTUs, 0);
604 for(int i=0;i<numSeqs;i++){
605 if (m->control_pressed) { return 0; }
608 double norm = 0.0000;
609 double minWeight = 0.1;
610 vector<double> currentTau(numOTUs);
612 for(int j=0;j<numOTUs;j++){
613 if (m->control_pressed) { return 0; }
614 if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
615 offset = distances[i * numSeqs+centroids[j]];
619 for(int j=0;j<numOTUs;j++){
620 if (m->control_pressed) { return 0; }
621 if(weights[j] > minWeight){
622 currentTau[j] = exp(sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
623 norm += currentTau[j];
626 currentTau[j] = 0.0000;
630 for(int j=0;j<numOTUs;j++){
631 if (m->control_pressed) { return 0; }
632 currentTau[j] /= norm;
635 for(int j=0;j<numOTUs;j++){
636 if (m->control_pressed) { return 0; }
638 if(currentTau[j] > 1.0e-4){
639 int oldTotal = total;
642 tau.resize(oldTotal+1);
643 tau[oldTotal] = currentTau[j];
644 otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
645 aanI[j][otuFreq[j]] = i;
658 noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
660 vector<double> percentage(numSeqs);
661 noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI); if (m->control_pressed) { return 0; }
662 noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau); if (m->control_pressed) { return 0; }
664 change.assign(numOTUs, 1);
665 noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
668 vector<int> finalTau(numOTUs, 0);
669 for(int i=0;i<numSeqs;i++){
670 if (m->control_pressed) { return 0; }
671 finalTau[otuData[i]] += int(seqFreq[i]);
674 noise.writeOutput(outputFileName, nameFileName, mapFileName, finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
678 }catch(exception& e) {
679 m->errorOut(e, "ShhhSeqsCommand", "driver");
683 //**********************************************************************************************************************
684 int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
686 m->mothurOutEndLine(); m->mothurOut("Deconvoluting results:"); m->mothurOutEndLine(); m->mothurOutEndLine();
688 //use unique.seqs to create new name and fastafile
689 string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
690 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
691 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
693 Command* uniqueCommand = new DeconvoluteCommand(inputString);
694 uniqueCommand->execute();
696 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
698 delete uniqueCommand;
700 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
702 string newnameFile = filenames["name"][0];
703 string newfastaFile = filenames["fasta"][0];
705 m->mothurRemove(fastaFile); rename(newfastaFile.c_str(), fastaFile.c_str());
706 if (nameFile != newnameFile) { m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str()); }
710 catch(exception& e) {
711 m->errorOut(e, "ShhhSeqsCommand", "deconvoluteResults");
715 //**********************************************************************************************************************