shhhseqscommand.cpp

   1 /*
   2  *  shhhseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/8/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "shhhseqscommand.h"
  11
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> ShhhSeqsCommand::setParameters(){
  16         try {
  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);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "ShhhSeqsCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string ShhhSeqsCommand::getHelpString(){
  36         try {
  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";
  49                 return helpString;
  50
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "ShhhSeqsCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 ShhhSeqsCommand::ShhhSeqsCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63                 vector<string> tempOutNames;
  64                 outputTypes["fasta"] = tempOutNames;
  65                 outputTypes["name"] = tempOutNames;
  66                 outputTypes["map"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
  70                 exit(1);
  71         }
  72 }
  73
  74 //**********************************************************************************************************************
  75 ShhhSeqsCommand::ShhhSeqsCommand(string option) {
  76         try {
  77                 abort = false; calledHelp = false;
  78
  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;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string, string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter;
  90                         map<string, string>::iterator it;
  91
  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;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["fasta"] = tempOutNames;
 100                         outputTypes["name"] = tempOutNames;
 101                         outputTypes["map"] = tempOutNames;
 102
 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 = "";          }
 106                         else {
 107                                 string path;
 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;            }
 114                                 }
 115
 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;             }
 122                                 }
 123
 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;            }
 130                                 }
 131                         }
 132
 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; }
 139                         }
 140                         else if (fastafile == "not open") { abort = true; }
 141                         else { m->setFastaFile(fastafile); }
 142
 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 = ""; }
 145
 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; }
 153                         }
 154                         else if (namefile == "not open") { namefile =  ""; abort = true; }
 155                         else {  m->setNameFile(namefile); }
 156
 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);  }
 161
 162                         string temp     = validParameter.validFile(parameters, "sigma", false);         if(temp == "not found"){        temp = "0.01"; }
 163                         m->mothurConvert(temp, sigma);
 164                         sigma = 1/sigma;
 165
 166                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 167                         m->setProcessors(temp);
 168                         m->mothurConvert(temp, processors);
 169
 170                         if (namefile == "") {
 171                                 vector<string> files; files.push_back(fastafile);
 172                                 parser.getNameFile(files);
 173                         }
 174                 }
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
 178                 exit(1);
 179         }
 180 }
 181 //**********************************************************************************************************************
 182 int ShhhSeqsCommand::execute() {
 183         try {
 184
 185                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 186
 187                 if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it
 188                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
 189                 string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.names";
 190                 string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.map";
 191
 192                 if (groupfile != "") {
 193                         //Parse sequences by group
 194                         SequenceParser parser(groupfile, fastafile, namefile);
 195                         vector<string> groups = parser.getNamesOfGroups();
 196
 197                         if (m->control_pressed) {  return 0; }
 198
 199                         //clears files
 200                         ofstream out, out1, out2;
 201                         m->openOutputFile(outputFileName, out); out.close();
 202                         m->openOutputFile(nameFileName, out1); out1.close();
 203                         mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.";
 204
 205                         vector<string> mapFileNames;
 206                         if(processors == 1)     {       mapFileNames = driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups);       }
 207                         else                            {       mapFileNames = createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups);                        }
 208
 209                         if (m->control_pressed) {    return 0;  }
 210
 211                         for (int j = 0; j < mapFileNames.size(); j++) { outputNames.push_back(mapFileNames[j]); outputTypes["map"].push_back(mapFileNames[j]); }
 212
 213                         //deconvolute results by running unique.seqs
 214                         deconvoluteResults(outputFileName, nameFileName);
 215
 216                         if (m->control_pressed) {   return 0;   }
 217
 218                 }else{
 219                         vector<string> sequences;
 220                         vector<string> uniqueNames;
 221                         vector<string> redundantNames;
 222                         vector<int> seqFreq;
 223
 224                         seqNoise noise;
 225                         correctDist* correct = new correctDist(processors);
 226
 227                         //reads fasta and name file and loads them in order
 228                         readData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq);
 229                         if (m->control_pressed) { return 0; }
 230
 231                         //calc distances for cluster
 232                         string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.dist";
 233                         correct->execute(distFileName);
 234                         delete correct;
 235
 236                         if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
 237
 238                         driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, outputFileName, nameFileName, mapFileName);
 239                         outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
 240                 }
 241
 242                 if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        } return 0; }
 243
 244                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 245                 outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
 246
 247                 m->mothurOutEndLine();
 248                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 249                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 250                 m->mothurOutEndLine();
 251
 252                 //set accnos file as new current accnosfile
 253                 string current = "";
 254                 itTypes = outputTypes.find("fasta");
 255                 if (itTypes != outputTypes.end()) {
 256                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 257                 }
 258
 259                 itTypes = outputTypes.find("name");
 260                 if (itTypes != outputTypes.end()) {
 261                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 262                 }
 263
 264
 265                 return 0;
 266         }
 267         catch(exception& e) {
 268                 m->errorOut(e, "ShhhSeqsCommand", "execute");
 269                 exit(1);
 270         }
 271 }
 272 //**********************************************************************************************************************
 273 int ShhhSeqsCommand::readData(correctDist* correct, seqNoise& noise, vector<string>& seqs, vector<string>& uNames, vector<string>& rNames, vector<int>& freq) {
 274         try {
 275                 map<string, string> nameMap;
 276                 map<string, string>::iterator it;
 277                 m->readNames(namefile, nameMap);
 278                 bool error = false;
 279
 280                 ifstream in;
 281                 m->openInputFile(fastafile, in);
 282
 283                 while (!in.eof()) {
 284
 285                         if (m->control_pressed) { in.close(); return 0; }
 286
 287                         Sequence seq(in); m->gobble(in);
 288
 289                         if (seq.getName() != "") {
 290                                 correct->addSeq(seq.getName(), seq.getAligned());
 291
 292                                 it = nameMap.find(seq.getName());
 293                                 if (it != nameMap.end()) {
 294                                         noise.addSeq(seq.getAligned(), seqs);
 295                                         noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
 296                                 }else {
 297                                         m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your namefile, please correct.");
 298                                         error = true;
 299                                 }
 300                         }
 301                 }
 302                 in.close();
 303
 304                 if (error) { m->control_pressed = true; }
 305
 306                 return seqs.size();
 307
 308         }catch(exception& e) {
 309                 m->errorOut(e, "ShhhSeqsCommand", "readData");
 310                 exit(1);
 311         }
 312 }
 313 //**********************************************************************************************************************
 314 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) {
 315         try {
 316                 bool error = false;
 317                 map<string, string>::iterator it;
 318
 319                 for (int i = 0; i < sequences.size(); i++) {
 320
 321                         if (m->control_pressed) { return 0; }
 322
 323                         if (sequences[i].getName() != "") {
 324                                 correct->addSeq(sequences[i].getName(), sequences[i].getAligned());
 325
 326                                 it = nameMap.find(sequences[i].getName());
 327                                 if (it != nameMap.end()) {
 328                                         noise.addSeq(sequences[i].getAligned(), seqs);
 329                                         noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
 330                                 }else {
 331                                         m->mothurOut("[ERROR]: " + sequences[i].getName() + " is in your fasta file and not in your namefile, please correct.");
 332                                         error = true;
 333                                 }
 334                         }
 335                 }
 336
 337                 if (error) { m->control_pressed = true; }
 338
 339                 return seqs.size();
 340
 341         }catch(exception& e) {
 342                 m->errorOut(e, "ShhhSeqsCommand", "loadData");
 343                 exit(1);
 344         }
 345 }
 346 /**************************************************************************************************/
 347 vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
 348         try {
 349
 350                 vector<int> processIDS;
 351                 int process = 1;
 352                 vector<string> mapfileNames;
 353
 354                 //sanity check
 355                 if (groups.size() < processors) { processors = groups.size(); }
 356
 357                 //divide the groups between the processors
 358                 vector<linePair> lines;
 359                 int numGroupsPerProcessor = groups.size() / processors;
 360                 for (int i = 0; i < processors; i++) {
 361                         int startIndex =  i * numGroupsPerProcessor;
 362                         int endIndex = (i+1) * numGroupsPerProcessor;
 363                         if(i == (processors - 1)){      endIndex = groups.size();       }
 364                         lines.push_back(linePair(startIndex, endIndex));
 365                 }
 366
 367 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 368
 369                 //loop through and create all the processes you want
 370                 while (process != processors) {
 371                         int pid = fork();
 372
 373                         if (pid > 0) {
 374                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 375                                 process++;
 376                         }else if (pid == 0){
 377                                 mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
 378
 379                                 //pass filenames to parent
 380                                 ofstream out;
 381                                 string tempFile = newMName + toString(getpid()) + ".temp";
 382                                 m->openOutputFile(tempFile, out);
 383                                 out << mapfileNames.size() << endl;
 384                                 for (int i = 0; i < mapfileNames.size(); i++) {
 385                                         out << mapfileNames[i] << endl;
 386                                 }
 387                                 out.close();
 388
 389                                 exit(0);
 390                         }else {
 391                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 392                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 393                                 exit(0);
 394                         }
 395                 }
 396
 397                 //do my part
 398                 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
 399
 400                 //force parent to wait until all the processes are done
 401                 for (int i=0;i<processIDS.size();i++) {
 402                         int temp = processIDS[i];
 403                         wait(&temp);
 404                 }
 405
 406                 //append output files
 407                 for(int i=0;i<processIDS.size();i++){
 408                         ifstream in;
 409                         string tempFile =  newMName + toString(processIDS[i]) + ".temp";
 410                         m->openInputFile(tempFile, in);
 411                         if (!in.eof()) {
 412                                 int tempNum = 0; in >> tempNum;  m->gobble(in);
 413                                 for (int j = 0; j < tempNum; j++) {
 414                                         string filename;
 415                                         in >> filename; m->gobble(in);
 416                                         mapfileNames.push_back(filename);
 417                                 }
 418                         }
 419                         in.close(); m->mothurRemove(tempFile);
 420
 421                 }
 422 #else
 423
 424                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 425                 //Windows version shared memory, so be careful when passing variables through the shhhseqsData struct.
 426                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 427                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 428
 429                 vector<shhhseqsData*> pDataArray;
 430                 DWORD   dwThreadIdArray[processors-1];
 431                 HANDLE  hThreadArray[processors-1];
 432
 433                 //Create processor worker threads.
 434                 for( int i=1; i<processors; i++ ){
 435                         // Allocate memory for thread data.
 436                         string extension = toString(i) + ".temp";
 437
 438                         shhhseqsData* tempShhhseqs = new shhhseqsData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMName, groups, m, lines[i].start, lines[i].end, sigma, i);
 439                         pDataArray.push_back(tempShhhseqs);
 440                         processIDS.push_back(i);
 441
 442                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 443                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 444                         hThreadArray[i-1] = CreateThread(NULL, 0, MyShhhSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 445                 }
 446
 447
 448                 //using the main process as a worker saves time and memory
 449                 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
 450
 451                 //Wait until all threads have terminated.
 452                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 453
 454                 //Close all thread handles and free memory allocations.
 455                 for(int i=0; i < pDataArray.size(); i++){
 456                         for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
 457                                 mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
 458                         }
 459                         CloseHandle(hThreadArray[i]);
 460                         delete pDataArray[i];
 461                 }
 462
 463 #endif
 464
 465                 //append output files
 466                 for(int i=0;i<processIDS.size();i++){
 467                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 468                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 469
 470                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 471                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 472                 }
 473
 474                 return mapfileNames;
 475
 476         }
 477         catch(exception& e) {
 478                 m->errorOut(e, "ShhhSeqsCommand", "createProcessesGroups");
 479                 exit(1);
 480         }
 481 }
 482 /**************************************************************************************************/
 483 vector<string> ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
 484         try {
 485
 486                 vector<string> mapFileNames;
 487
 488                 for (int i = start; i < end; i++) {
 489
 490                         start = time(NULL);
 491
 492                         if (m->control_pressed) {  return mapFileNames; }
 493
 494                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 495
 496                         map<string, string> thisNameMap;
 497                         thisNameMap = parser.getNameMap(groups[i]);
 498                         vector<Sequence> thisSeqs = parser.getSeqs(groups[i]);
 499
 500                         vector<string> sequences;
 501                         vector<string> uniqueNames;
 502                         vector<string> redundantNames;
 503                         vector<int> seqFreq;
 504
 505                         seqNoise noise;
 506                         correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
 507
 508                         //load this groups info in order
 509                         loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
 510                         if (m->control_pressed) { return mapFileNames; }
 511
 512                         //calc distances for cluster
 513                         string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + groups[i] + ".shhh.dist";
 514                         correct->execute(distFileName);
 515                         delete correct;
 516
 517                         if (m->control_pressed) { m->mothurRemove(distFileName); return mapFileNames; }
 518
 519                         driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
 520
 521                         if (m->control_pressed) { return mapFileNames; }
 522
 523                         m->appendFiles(newFFile+groups[i], newFFile); m->mothurRemove(newFFile+groups[i]);
 524                         m->appendFiles(newNFile+groups[i], newNFile); m->mothurRemove(newNFile+groups[i]);
 525                         mapFileNames.push_back(newMFile+groups[i]+".map");
 526
 527                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + groups[i] + "."); m->mothurOutEndLine();
 528                 }
 529
 530                 return mapFileNames;
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "ShhhSeqsCommand", "driverGroups");
 534                 exit(1);
 535         }
 536 }
 537 //**********************************************************************************************************************
 538 int ShhhSeqsCommand::driver(seqNoise& noise,
 539                                                         vector<string>& sequences,
 540                                                         vector<string>& uniqueNames,
 541                                                         vector<string>& redundantNames,
 542                                                         vector<int>& seqFreq,
 543                                                         string distFileName, string outputFileName, string nameFileName, string mapFileName) {
 544         try {
 545                 double cutOff = 0.08;
 546                 int minIter = 10;
 547                 int maxIter = 1000;
 548                 double minDelta = 1e-6;
 549                 int numIters = 0;
 550                 double maxDelta = 1e6;
 551                 int numSeqs = sequences.size();
 552
 553                 //run cluster command
 554                 string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
 555                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 556                 m->mothurOut("Running command: cluster(" + inputString + ")"); m->mothurOutEndLine();
 557
 558                 Command* clusterCommand = new ClusterCommand(inputString);
 559                 clusterCommand->execute();
 560
 561                 map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
 562                 string listFileName = filenames["list"][0];
 563                 string rabundFileName = filenames["rabund"][0]; m->mothurRemove(rabundFileName);
 564                 string sabundFileName = filenames["sabund"][0]; m->mothurRemove(sabundFileName);
 565
 566                 delete clusterCommand;
 567                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 568
 569                 if (m->control_pressed) { m->mothurRemove(distFileName); m->mothurRemove(listFileName); return 0; }
 570
 571                 vector<double> distances(numSeqs * numSeqs);
 572                 noise.getDistanceData(distFileName, distances);
 573                 m->mothurRemove(distFileName);
 574                 if (m->control_pressed) { m->mothurRemove(listFileName); return 0; }
 575
 576                 vector<int> otuData(numSeqs);
 577                 vector<int> otuFreq;
 578                 vector<vector<int> > otuBySeqLookUp;
 579                 noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
 580                 m->mothurRemove(listFileName);
 581                 if (m->control_pressed) { return 0; }
 582
 583                 int numOTUs = otuFreq.size();
 584
 585                 vector<double> weights(numOTUs, 0);
 586                 vector<int> change(numOTUs, 1);
 587                 vector<int> centroids(numOTUs, -1);
 588                 vector<int> cumCount(numOTUs, 0);
 589
 590                 vector<double> tau(numSeqs, 1);
 591                 vector<int> anP(numSeqs, 0);
 592                 vector<int> anI(numSeqs, 0);
 593                 vector<int> anN(numSeqs, 0);
 594                 vector<vector<int> > aanI = otuBySeqLookUp;
 595
 596                 while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
 597
 598                         if (m->control_pressed) { return 0; }
 599
 600                         noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
 601                         maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau);  if (m->control_pressed) { return 0; }
 602
 603                         noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
 604                         noise.checkCentroids(weights, centroids); if (m->control_pressed) { return 0; }
 605
 606                         otuFreq.assign(numOTUs, 0);
 607
 608                         int total = 0;
 609
 610                         for(int i=0;i<numSeqs;i++){
 611                                 if (m->control_pressed) { return 0; }
 612
 613                                 double offset = 1e6;
 614                                 double norm = 0.0000;
 615                                 double minWeight = 0.1;
 616                                 vector<double> currentTau(numOTUs);
 617
 618                                 for(int j=0;j<numOTUs;j++){
 619                                         if (m->control_pressed) { return 0; }
 620                                         if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
 621                                                 offset = distances[i * numSeqs+centroids[j]];
 622                                         }
 623                                 }
 624
 625                                 for(int j=0;j<numOTUs;j++){
 626                                         if (m->control_pressed) { return 0; }
 627                                         if(weights[j] > minWeight){
 628                                                 currentTau[j] = exp(sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
 629                                                 norm += currentTau[j];
 630                                         }
 631                                         else{
 632                                                 currentTau[j] = 0.0000;
 633                                         }
 634                                 }
 635
 636                                 for(int j=0;j<numOTUs;j++){
 637                                         if (m->control_pressed) { return 0; }
 638                                         currentTau[j] /= norm;
 639                                 }
 640
 641                                 for(int j=0;j<numOTUs;j++){
 642                                         if (m->control_pressed) { return 0; }
 643
 644                                         if(currentTau[j] > 1.0e-4){
 645                                                 int oldTotal = total;
 646                                                 total++;
 647
 648                                                 tau.resize(oldTotal+1);
 649                                                 tau[oldTotal] = currentTau[j];
 650                                                 otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
 651                                                 aanI[j][otuFreq[j]] = i;
 652                                                 otuFreq[j]++;
 653
 654                                         }
 655                                 }
 656
 657                                 anP.resize(total);
 658                                 anI.resize(total);
 659                         }
 660
 661                         numIters++;
 662                 }
 663
 664                 noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount);  if (m->control_pressed) { return 0; }
 665
 666                 vector<double> percentage(numSeqs);
 667                 noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI);  if (m->control_pressed) { return 0; }
 668                 noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau);  if (m->control_pressed) { return 0; }
 669
 670                 change.assign(numOTUs, 1);
 671                 noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
 672
 673
 674                 vector<int> finalTau(numOTUs, 0);
 675                 for(int i=0;i<numSeqs;i++){
 676                         if (m->control_pressed) { return 0; }
 677                         finalTau[otuData[i]] += int(seqFreq[i]);
 678                 }
 679
 680                 noise.writeOutput(outputFileName, nameFileName, mapFileName, finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
 681
 682                 return 0;
 683
 684         }catch(exception& e) {
 685                 m->errorOut(e, "ShhhSeqsCommand", "driver");
 686                 exit(1);
 687         }
 688 }
 689 //**********************************************************************************************************************
 690 int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
 691         try {
 692                 m->mothurOutEndLine(); m->mothurOut("Deconvoluting results:"); m->mothurOutEndLine(); m->mothurOutEndLine();
 693
 694                 //use unique.seqs to create new name and fastafile
 695                 string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
 696                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 697                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 698                 m->mothurCalling = true;
 699
 700                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
 701                 uniqueCommand->execute();
 702
 703                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 704
 705                 delete uniqueCommand;
 706                 m->mothurCalling = false;
 707                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 708
 709                 string newnameFile = filenames["name"][0];
 710                 string newfastaFile = filenames["fasta"][0];
 711
 712                 m->mothurRemove(fastaFile); rename(newfastaFile.c_str(), fastaFile.c_str());
 713                 if (nameFile != newnameFile) { m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str()); }
 714
 715                 return 0;
 716         }
 717         catch(exception& e) {
 718                 m->errorOut(e, "ShhhSeqsCommand", "deconvoluteResults");
 719                 exit(1);
 720         }
 721 }
 722 //**********************************************************************************************************************
 723
 724
 725