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","fasta-map",false,true,true); parameters.push_back(pfasta);
  18                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","name",false,true,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,true); 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 string ShhhSeqsCommand::getOutputPattern(string type) {
  59     try {
  60         string pattern = "";
  61
  62         if (type == "fasta")            {   pattern = "[filename],shhh_seqs.fasta";   }
  63         else if (type == "name")    {   pattern = "[filename],shhh_seqs.names";   }
  64         else if (type == "map")        {   pattern = "[filename],shhh_seqs.map";   }
  65         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  66
  67         return pattern;
  68     }
  69     catch(exception& e) {
  70         m->errorOut(e, "ShhhSeqsCommand", "getOutputPattern");
  71         exit(1);
  72     }
  73 }
  74
  75 //**********************************************************************************************************************
  76
  77 ShhhSeqsCommand::ShhhSeqsCommand(){
  78         try {
  79                 abort = true; calledHelp = true;
  80                 setParameters();
  81                 vector<string> tempOutNames;
  82                 outputTypes["fasta"] = tempOutNames;
  83                 outputTypes["name"] = tempOutNames;
  84                 outputTypes["map"] = tempOutNames;
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
  88                 exit(1);
  89         }
  90 }
  91
  92 //**********************************************************************************************************************
  93 ShhhSeqsCommand::ShhhSeqsCommand(string option) {
  94         try {
  95                 abort = false; calledHelp = false;
  96
  97                 //allow user to run help
  98                 if(option == "help") { help(); abort = true; calledHelp = true; }
  99                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 100
 101                 else {
 102                         vector<string> myArray = setParameters();
 103
 104                         OptionParser parser(option);
 105                         map<string, string> parameters = parser.getParameters();
 106
 107                         ValidParameters validParameter;
 108                         map<string, string>::iterator it;
 109
 110                         //check to make sure all parameters are valid for command
 111                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 112                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["fasta"] = tempOutNames;
 118                         outputTypes["name"] = tempOutNames;
 119                         outputTypes["map"] = tempOutNames;
 120
 121                         //if the user changes the input directory command factory will send this info to us in the output parameter
 122                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 123                         if (inputDir == "not found"){   inputDir = "";          }
 124                         else {
 125                                 string path;
 126                                 it = parameters.find("fasta");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 132                                 }
 133
 134                                 it = parameters.find("name");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 140                                 }
 141
 142                                 it = parameters.find("group");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 148                                 }
 149                         }
 150
 151                         //check for required parameters
 152                         fastafile = validParameter.validFile(parameters, "fasta", true);
 153                         if (fastafile == "not found") {
 154                                 fastafile = m->getFastaFile();
 155                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 156                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 157                         }
 158                         else if (fastafile == "not open") { abort = true; }
 159                         else { m->setFastaFile(fastafile); }
 160
 161                         //if the user changes the output directory command factory will send this info to us in the output parameter
 162                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 163
 164                         //check for optional parameter and set defaults
 165                         // ...at some point should added some additional type checking...
 166                         namefile = validParameter.validFile(parameters, "name", true);
 167                         if (namefile == "not found") {
 168                                 namefile = m->getNameFile();
 169                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 170                                 else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
 171                         }
 172                         else if (namefile == "not open") { namefile =  ""; abort = true; }
 173                         else {  m->setNameFile(namefile); }
 174
 175                         groupfile = validParameter.validFile(parameters, "group", true);
 176                         if (groupfile == "not found") { groupfile =  "";   }
 177                         else if (groupfile == "not open") { abort = true; groupfile =  ""; }
 178                         else {   m->setGroupFile(groupfile);  }
 179
 180                         string temp     = validParameter.validFile(parameters, "sigma", false);         if(temp == "not found"){        temp = "0.01"; }
 181                         m->mothurConvert(temp, sigma);
 182                         sigma = 1/sigma;
 183
 184                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 185                         m->setProcessors(temp);
 186                         m->mothurConvert(temp, processors);
 187
 188                         if (namefile == "") {
 189                                 vector<string> files; files.push_back(fastafile);
 190                                 parser.getNameFile(files);
 191                         }
 192                 }
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "ShhhSeqsCommand", "ShhhSeqsCommand");
 196                 exit(1);
 197         }
 198 }
 199 //**********************************************************************************************************************
 200 int ShhhSeqsCommand::execute() {
 201         try {
 202
 203                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 204
 205                 if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it
 206
 207         map<string, string> variables;
 208                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
 209                 string outputFileName = getOutputFileName("fasta",variables);
 210                 string nameFileName = getOutputFileName("name",variables);
 211                 string mapFileName = getOutputFileName("map",variables);
 212
 213                 if (groupfile != "") {
 214                         //Parse sequences by group
 215                         SequenceParser parser(groupfile, fastafile, namefile);
 216                         vector<string> groups = parser.getNamesOfGroups();
 217
 218                         if (m->control_pressed) {  return 0; }
 219
 220                         //clears files
 221                         ofstream out, out1, out2;
 222                         m->openOutputFile(outputFileName, out); out.close();
 223                         m->openOutputFile(nameFileName, out1); out1.close();
 224                         mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.";
 225
 226                         vector<string> mapFileNames;
 227                         if(processors == 1)     {       mapFileNames = driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups);       }
 228                         else                            {       mapFileNames = createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups);                        }
 229
 230                         if (m->control_pressed) {    return 0;  }
 231
 232                         for (int j = 0; j < mapFileNames.size(); j++) { outputNames.push_back(mapFileNames[j]); outputTypes["map"].push_back(mapFileNames[j]); }
 233
 234                         //deconvolute results by running unique.seqs
 235                         deconvoluteResults(outputFileName, nameFileName);
 236
 237                         if (m->control_pressed) {   return 0;   }
 238
 239                 }else{
 240                         vector<string> sequences;
 241                         vector<string> uniqueNames;
 242                         vector<string> redundantNames;
 243                         vector<int> seqFreq;
 244
 245                         seqNoise noise;
 246                         correctDist* correct = new correctDist(processors);
 247
 248                         //reads fasta and name file and loads them in order
 249                         readData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq);
 250                         if (m->control_pressed) { return 0; }
 251
 252                         //calc distances for cluster
 253                         string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.dist";
 254                         correct->execute(distFileName);
 255                         delete correct;
 256
 257                         if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
 258
 259                         driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, outputFileName, nameFileName, mapFileName);
 260                         outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
 261                 }
 262
 263                 if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        } return 0; }
 264
 265                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 266                 outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
 267
 268                 m->mothurOutEndLine();
 269                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 270                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 271                 m->mothurOutEndLine();
 272
 273                 //set accnos file as new current accnosfile
 274                 string current = "";
 275                 itTypes = outputTypes.find("fasta");
 276                 if (itTypes != outputTypes.end()) {
 277                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 278                 }
 279
 280                 itTypes = outputTypes.find("name");
 281                 if (itTypes != outputTypes.end()) {
 282                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 283                 }
 284
 285
 286                 return 0;
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "ShhhSeqsCommand", "execute");
 290                 exit(1);
 291         }
 292 }
 293 //**********************************************************************************************************************
 294 int ShhhSeqsCommand::readData(correctDist* correct, seqNoise& noise, vector<string>& seqs, vector<string>& uNames, vector<string>& rNames, vector<int>& freq) {
 295         try {
 296                 map<string, string> nameMap;
 297                 map<string, string>::iterator it;
 298                 m->readNames(namefile, nameMap);
 299                 bool error = false;
 300
 301                 ifstream in;
 302                 m->openInputFile(fastafile, in);
 303
 304                 while (!in.eof()) {
 305
 306                         if (m->control_pressed) { in.close(); return 0; }
 307
 308                         Sequence seq(in); m->gobble(in);
 309
 310                         if (seq.getName() != "") {
 311                                 correct->addSeq(seq.getName(), seq.getAligned());
 312
 313                                 it = nameMap.find(seq.getName());
 314                                 if (it != nameMap.end()) {
 315                                         noise.addSeq(seq.getAligned(), seqs);
 316                                         noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
 317                                 }else {
 318                                         m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your namefile, please correct.");
 319                                         error = true;
 320                                 }
 321                         }
 322                 }
 323                 in.close();
 324
 325                 if (error) { m->control_pressed = true; }
 326
 327                 return seqs.size();
 328
 329         }catch(exception& e) {
 330                 m->errorOut(e, "ShhhSeqsCommand", "readData");
 331                 exit(1);
 332         }
 333 }
 334 //**********************************************************************************************************************
 335 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) {
 336         try {
 337                 bool error = false;
 338                 map<string, string>::iterator it;
 339
 340                 for (int i = 0; i < sequences.size(); i++) {
 341
 342                         if (m->control_pressed) { return 0; }
 343
 344                         if (sequences[i].getName() != "") {
 345                                 correct->addSeq(sequences[i].getName(), sequences[i].getAligned());
 346
 347                                 it = nameMap.find(sequences[i].getName());
 348                                 if (it != nameMap.end()) {
 349                                         noise.addSeq(sequences[i].getAligned(), seqs);
 350                                         noise.addRedundantName(it->first, it->second, uNames, rNames, freq);
 351                                 }else {
 352                                         m->mothurOut("[ERROR]: " + sequences[i].getName() + " is in your fasta file and not in your namefile, please correct.");
 353                                         error = true;
 354                                 }
 355                         }
 356                 }
 357
 358                 if (error) { m->control_pressed = true; }
 359
 360                 return seqs.size();
 361
 362         }catch(exception& e) {
 363                 m->errorOut(e, "ShhhSeqsCommand", "loadData");
 364                 exit(1);
 365         }
 366 }
 367 /**************************************************************************************************/
 368 vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
 369         try {
 370
 371                 vector<int> processIDS;
 372                 int process = 1;
 373                 vector<string> mapfileNames;
 374
 375                 //sanity check
 376                 if (groups.size() < processors) { processors = groups.size(); }
 377
 378                 //divide the groups between the processors
 379                 vector<linePair> lines;
 380                 int numGroupsPerProcessor = groups.size() / processors;
 381                 for (int i = 0; i < processors; i++) {
 382                         int startIndex =  i * numGroupsPerProcessor;
 383                         int endIndex = (i+1) * numGroupsPerProcessor;
 384                         if(i == (processors - 1)){      endIndex = groups.size();       }
 385                         lines.push_back(linePair(startIndex, endIndex));
 386                 }
 387
 388 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 389
 390                 //loop through and create all the processes you want
 391                 while (process != processors) {
 392                         int pid = fork();
 393
 394                         if (pid > 0) {
 395                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 396                                 process++;
 397                         }else if (pid == 0){
 398                                 mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
 399
 400                                 //pass filenames to parent
 401                                 ofstream out;
 402                                 string tempFile = newMName + toString(getpid()) + ".temp";
 403                                 m->openOutputFile(tempFile, out);
 404                                 out << mapfileNames.size() << endl;
 405                                 for (int i = 0; i < mapfileNames.size(); i++) {
 406                                         out << mapfileNames[i] << endl;
 407                                 }
 408                                 out.close();
 409
 410                                 exit(0);
 411                         }else {
 412                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 413                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 414                                 exit(0);
 415                         }
 416                 }
 417
 418                 //do my part
 419                 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
 420
 421                 //force parent to wait until all the processes are done
 422                 for (int i=0;i<processIDS.size();i++) {
 423                         int temp = processIDS[i];
 424                         wait(&temp);
 425                 }
 426
 427                 //append output files
 428                 for(int i=0;i<processIDS.size();i++){
 429                         ifstream in;
 430                         string tempFile =  newMName + toString(processIDS[i]) + ".temp";
 431                         m->openInputFile(tempFile, in);
 432                         if (!in.eof()) {
 433                                 int tempNum = 0; in >> tempNum;  m->gobble(in);
 434                                 for (int j = 0; j < tempNum; j++) {
 435                                         string filename;
 436                                         in >> filename; m->gobble(in);
 437                                         mapfileNames.push_back(filename);
 438                                 }
 439                         }
 440                         in.close(); m->mothurRemove(tempFile);
 441
 442                 }
 443 #else
 444
 445                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 446                 //Windows version shared memory, so be careful when passing variables through the shhhseqsData struct.
 447                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 448                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 449
 450                 vector<shhhseqsData*> pDataArray;
 451                 DWORD   dwThreadIdArray[processors-1];
 452                 HANDLE  hThreadArray[processors-1];
 453
 454                 //Create processor worker threads.
 455                 for( int i=1; i<processors; i++ ){
 456                         // Allocate memory for thread data.
 457                         string extension = toString(i) + ".temp";
 458
 459                         shhhseqsData* tempShhhseqs = new shhhseqsData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMName, groups, m, lines[i].start, lines[i].end, sigma, i);
 460                         pDataArray.push_back(tempShhhseqs);
 461                         processIDS.push_back(i);
 462
 463                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 464                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 465                         hThreadArray[i-1] = CreateThread(NULL, 0, MyShhhSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 466                 }
 467
 468
 469                 //using the main process as a worker saves time and memory
 470                 mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
 471
 472                 //Wait until all threads have terminated.
 473                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 474
 475                 //Close all thread handles and free memory allocations.
 476                 for(int i=0; i < pDataArray.size(); i++){
 477                         for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
 478                                 mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
 479                         }
 480                         CloseHandle(hThreadArray[i]);
 481                         delete pDataArray[i];
 482                 }
 483
 484 #endif
 485
 486                 //append output files
 487                 for(int i=0;i<processIDS.size();i++){
 488                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 489                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 490
 491                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 492                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 493                 }
 494
 495                 return mapfileNames;
 496
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "ShhhSeqsCommand", "createProcessesGroups");
 500                 exit(1);
 501         }
 502 }
 503 /**************************************************************************************************/
 504 vector<string> ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
 505         try {
 506
 507                 vector<string> mapFileNames;
 508
 509                 for (int i = start; i < end; i++) {
 510
 511                         start = time(NULL);
 512
 513                         if (m->control_pressed) {  return mapFileNames; }
 514
 515                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 516
 517                         map<string, string> thisNameMap;
 518                         thisNameMap = parser.getNameMap(groups[i]);
 519                         vector<Sequence> thisSeqs = parser.getSeqs(groups[i]);
 520
 521                         vector<string> sequences;
 522                         vector<string> uniqueNames;
 523                         vector<string> redundantNames;
 524                         vector<int> seqFreq;
 525
 526                         seqNoise noise;
 527                         correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
 528
 529                         //load this groups info in order
 530                         loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
 531                         if (m->control_pressed) { return mapFileNames; }
 532
 533                         //calc distances for cluster
 534                         string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + groups[i] + ".shhh.dist";
 535                         correct->execute(distFileName);
 536                         delete correct;
 537
 538                         if (m->control_pressed) { m->mothurRemove(distFileName); return mapFileNames; }
 539
 540                         driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
 541
 542                         if (m->control_pressed) { return mapFileNames; }
 543
 544                         m->appendFiles(newFFile+groups[i], newFFile); m->mothurRemove(newFFile+groups[i]);
 545                         m->appendFiles(newNFile+groups[i], newNFile); m->mothurRemove(newNFile+groups[i]);
 546                         mapFileNames.push_back(newMFile+groups[i]+".map");
 547
 548                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + groups[i] + "."); m->mothurOutEndLine();
 549                 }
 550
 551                 return mapFileNames;
 552         }
 553         catch(exception& e) {
 554                 m->errorOut(e, "ShhhSeqsCommand", "driverGroups");
 555                 exit(1);
 556         }
 557 }
 558 //**********************************************************************************************************************
 559 int ShhhSeqsCommand::driver(seqNoise& noise,
 560                                                         vector<string>& sequences,
 561                                                         vector<string>& uniqueNames,
 562                                                         vector<string>& redundantNames,
 563                                                         vector<int>& seqFreq,
 564                                                         string distFileName, string outputFileName, string nameFileName, string mapFileName) {
 565         try {
 566                 double cutOff = 0.08;
 567                 int minIter = 10;
 568                 int maxIter = 1000;
 569                 double minDelta = 1e-6;
 570                 int numIters = 0;
 571                 double maxDelta = 1e6;
 572                 int numSeqs = sequences.size();
 573
 574                 //run cluster command
 575                 string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
 576                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 577                 m->mothurOut("Running command: cluster(" + inputString + ")"); m->mothurOutEndLine();
 578
 579                 Command* clusterCommand = new ClusterCommand(inputString);
 580                 clusterCommand->execute();
 581
 582                 map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
 583                 string listFileName = filenames["list"][0];
 584                 string rabundFileName = filenames["rabund"][0]; m->mothurRemove(rabundFileName);
 585                 string sabundFileName = filenames["sabund"][0]; m->mothurRemove(sabundFileName);
 586
 587                 delete clusterCommand;
 588                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 589
 590                 if (m->control_pressed) { m->mothurRemove(distFileName); m->mothurRemove(listFileName); return 0; }
 591
 592                 vector<double> distances(numSeqs * numSeqs);
 593                 noise.getDistanceData(distFileName, distances);
 594                 m->mothurRemove(distFileName);
 595                 if (m->control_pressed) { m->mothurRemove(listFileName); return 0; }
 596
 597                 vector<int> otuData(numSeqs);
 598                 vector<int> otuFreq;
 599                 vector<vector<int> > otuBySeqLookUp;
 600                 noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
 601                 m->mothurRemove(listFileName);
 602                 if (m->control_pressed) { return 0; }
 603
 604                 int numOTUs = otuFreq.size();
 605
 606                 vector<double> weights(numOTUs, 0);
 607                 vector<int> change(numOTUs, 1);
 608                 vector<int> centroids(numOTUs, -1);
 609                 vector<int> cumCount(numOTUs, 0);
 610
 611                 vector<double> tau(numSeqs, 1);
 612                 vector<int> anP(numSeqs, 0);
 613                 vector<int> anI(numSeqs, 0);
 614                 vector<int> anN(numSeqs, 0);
 615                 vector<vector<int> > aanI = otuBySeqLookUp;
 616
 617                 while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
 618
 619                         if (m->control_pressed) { return 0; }
 620
 621                         noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (m->control_pressed) { return 0; }
 622                         maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau);  if (m->control_pressed) { return 0; }
 623
 624                         noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
 625                         noise.checkCentroids(weights, centroids); if (m->control_pressed) { return 0; }
 626
 627                         otuFreq.assign(numOTUs, 0);
 628
 629                         int total = 0;
 630
 631                         for(int i=0;i<numSeqs;i++){
 632                                 if (m->control_pressed) { return 0; }
 633
 634                                 double offset = 1e6;
 635                                 double norm = 0.0000;
 636                                 double minWeight = 0.1;
 637                                 vector<double> currentTau(numOTUs);
 638
 639                                 for(int j=0;j<numOTUs;j++){
 640                                         if (m->control_pressed) { return 0; }
 641                                         if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
 642                                                 offset = distances[i * numSeqs+centroids[j]];
 643                                         }
 644                                 }
 645
 646                                 for(int j=0;j<numOTUs;j++){
 647                                         if (m->control_pressed) { return 0; }
 648                                         if(weights[j] > minWeight){
 649                                                 currentTau[j] = exp(sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
 650                                                 norm += currentTau[j];
 651                                         }
 652                                         else{
 653                                                 currentTau[j] = 0.0000;
 654                                         }
 655                                 }
 656
 657                                 for(int j=0;j<numOTUs;j++){
 658                                         if (m->control_pressed) { return 0; }
 659                                         currentTau[j] /= norm;
 660                                 }
 661
 662                                 for(int j=0;j<numOTUs;j++){
 663                                         if (m->control_pressed) { return 0; }
 664
 665                                         if(currentTau[j] > 1.0e-4){
 666                                                 int oldTotal = total;
 667                                                 total++;
 668
 669                                                 tau.resize(oldTotal+1);
 670                                                 tau[oldTotal] = currentTau[j];
 671                                                 otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
 672                                                 aanI[j][otuFreq[j]] = i;
 673                                                 otuFreq[j]++;
 674
 675                                         }
 676                                 }
 677
 678                                 anP.resize(total);
 679                                 anI.resize(total);
 680                         }
 681
 682                         numIters++;
 683                 }
 684
 685                 noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount);  if (m->control_pressed) { return 0; }
 686
 687                 vector<double> percentage(numSeqs);
 688                 noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI);  if (m->control_pressed) { return 0; }
 689                 noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau);  if (m->control_pressed) { return 0; }
 690
 691                 change.assign(numOTUs, 1);
 692                 noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (m->control_pressed) { return 0; }
 693
 694
 695                 vector<int> finalTau(numOTUs, 0);
 696                 for(int i=0;i<numSeqs;i++){
 697                         if (m->control_pressed) { return 0; }
 698                         finalTau[otuData[i]] += int(seqFreq[i]);
 699                 }
 700
 701                 noise.writeOutput(outputFileName, nameFileName, mapFileName, finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
 702
 703                 return 0;
 704
 705         }catch(exception& e) {
 706                 m->errorOut(e, "ShhhSeqsCommand", "driver");
 707                 exit(1);
 708         }
 709 }
 710 //**********************************************************************************************************************
 711 int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
 712         try {
 713                 m->mothurOutEndLine(); m->mothurOut("Deconvoluting results:"); m->mothurOutEndLine(); m->mothurOutEndLine();
 714
 715                 //use unique.seqs to create new name and fastafile
 716                 string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
 717                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 718                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 719                 m->mothurCalling = true;
 720
 721                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
 722                 uniqueCommand->execute();
 723
 724                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 725
 726                 delete uniqueCommand;
 727                 m->mothurCalling = false;
 728                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 729
 730                 string newnameFile = filenames["name"][0];
 731                 string newfastaFile = filenames["fasta"][0];
 732
 733                 m->mothurRemove(fastaFile); rename(newfastaFile.c_str(), fastaFile.c_str());
 734                 if (nameFile != newnameFile) { m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str()); }
 735
 736                 return 0;
 737         }
 738         catch(exception& e) {
 739                 m->errorOut(e, "ShhhSeqsCommand", "deconvoluteResults");
 740                 exit(1);
 741         }
 742 }
 743 //**********************************************************************************************************************
 744
 745
 746