shhhercommand.cpp

   1 /*
   2  *  shhher.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "shhhercommand.h"
  11
  12 #include "readcolumn.h"
  13 #include "readmatrix.hpp"
  14 #include "rabundvector.hpp"
  15 #include "sabundvector.hpp"
  16 #include "listvector.hpp"
  17 #include "cluster.hpp"
  18 #include "sparsematrix.hpp"
  19 #include <cfloat>
  20
  21 //**********************************************************************************************************************
  22
  23 #define NUMBINS 1000
  24 #define HOMOPS 10
  25 #define MIN_COUNT 0.1
  26 #define MIN_WEIGHT 0.1
  27 #define MIN_TAU 0.0001
  28 #define MIN_ITER 10
  29
  30 //**********************************************************************************************************************
  31
  32 vector<string> ShhherCommand::getValidParameters(){
  33         try {
  34                 string Array[] =  {
  35                         "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"
  36                 };
  37
  38                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "ShhherCommand", "getValidParameters");
  43                 exit(1);
  44         }
  45 }
  46
  47 //**********************************************************************************************************************
  48
  49 ShhherCommand::ShhherCommand(){
  50         try {
  51                 abort = true; calledHelp = true;
  52
  53                 //initialize outputTypes
  54                 vector<string> tempOutNames;
  55                 outputTypes["pn.dist"] = tempOutNames;
  56
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
  60                 exit(1);
  61         }
  62 }
  63
  64 //**********************************************************************************************************************
  65
  66 vector<string> ShhherCommand::getRequiredParameters(){
  67         try {
  68                 string Array[] =  {"flow"};
  69                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  70                 return myArray;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "ShhherCommand", "getRequiredParameters");
  74                 exit(1);
  75         }
  76 }
  77
  78 //**********************************************************************************************************************
  79
  80 vector<string> ShhherCommand::getRequiredFiles(){
  81         try {
  82                 vector<string> myArray;
  83                 return myArray;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "ShhherCommand", "getRequiredFiles");
  87                 exit(1);
  88         }
  89 }
  90
  91 //**********************************************************************************************************************
  92
  93 ShhherCommand::ShhherCommand(string option) {
  94         try {
  95
  96 #ifdef USE_MPI
  97                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  98                 MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
  99
 100                 if(pid == 0){
 101 #endif
 102
 103
 104                 abort = false; calledHelp = false;
 105
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; calledHelp = true; }
 109
 110                 else {
 111
 112                         //valid paramters for this command
 113                         string AlignArray[] =  {
 114                                 "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"
 115                         };
 116
 117                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter;
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         //initialize outputTypes
 131                         vector<string> tempOutNames;
 132                         outputTypes["pn.dist"] = tempOutNames;
 133                         //                      outputTypes["fasta"] = tempOutNames;
 134
 135                         //if the user changes the input directory command factory will send this info to us in the output parameter
 136                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 137                         if (inputDir == "not found"){   inputDir = "";          }
 138                         else {
 139                                 string path;
 140                                 it = parameters.find("flow");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 146                                 }
 147
 148                                 it = parameters.find("lookup");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["lookup"] = inputDir + it->second;           }
 154                                 }
 155
 156                                 it = parameters.find("file");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 162                                 }
 163                         }
 164
 165
 166                         //check for required parameters
 167                         flowFileName = validParameter.validFile(parameters, "flow", true);
 168                         flowFilesFileName = validParameter.validFile(parameters, "file", true);
 169                         if (flowFileName == "not found" && flowFilesFileName == "not found") {
 170                                 m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
 171                                 m->mothurOutEndLine();
 172                                 abort = true;
 173                         }
 174                         else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
 175
 176                         if(flowFileName != "not found"){        compositeFASTAFileName = "";    }
 177                         else{
 178                                 compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "pn.fasta";
 179                                 ofstream temp;
 180                                 m->openOutputFile(compositeFASTAFileName, temp);
 181                                 temp.close();
 182                         }
 183
 184                         //if the user changes the output directory command factory will send this info to us in the output parameter
 185                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 186                                 outputDir = "";
 187                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 188                         }
 189
 190
 191                         //check for optional parameter and set defaults
 192                         // ...at some point should added some additional type checking...
 193                         string temp;
 194                         temp = validParameter.validFile(parameters, "lookup", true);
 195                         if (temp == "not found")        {       lookupFileName = "LookUp_Titanium.pat"; }
 196                         else if(temp == "not open")     {       abort = true;                   }
 197                         else                                            {       lookupFileName = temp;  }
 198
 199                         temp = validParameter.validFile(parameters, "processors", false);if (temp == "not found"){      temp = "1";                     }
 200                         convert(temp, processors);
 201
 202                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
 203                         convert(temp, cutoff);
 204
 205                         temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){       temp = "0.000001";      }
 206                         convert(temp, minDelta);
 207
 208                         temp = validParameter.validFile(parameters, "maxiter", false);  if (temp == "not found"){       temp = "1000";          }
 209                         convert(temp, maxIters);
 210
 211                         temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
 212                         convert(temp, sigma);
 213
 214                         globaldata = GlobalData::getInstance();
 215                 }
 216
 217 #ifdef USE_MPI
 218                 }
 219 #endif
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
 224                 exit(1);
 225         }
 226 }
 227
 228 //**********************************************************************************************************************
 229
 230 ShhherCommand::~ShhherCommand(){}
 231
 232 //**********************************************************************************************************************
 233
 234 void ShhherCommand::help(){
 235         try {
 236                 m->mothurOut("The shhher command reads a file containing flowgrams and creates a file of corrected sequences.\n");
 237         }
 238         catch(exception& e) {
 239                 m->errorOut(e, "ShhherCommand", "help");
 240                 exit(1);
 241         }
 242 }
 243
 244 //**********************************************************************************************************************
 245 #ifdef USE_MPI
 246 int ShhherCommand::execute(){
 247         try {
 248                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 249
 250                 int tag = 1976;
 251                 MPI_Status status;
 252
 253                 double begClock = clock();
 254                 unsigned long int begTime = time(NULL);
 255
 256                 if(pid == 0){
 257
 258                         for(int i=1;i<ncpus;i++){
 259                                 MPI_Send(&abort, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 260                         }
 261                         if(abort == 1){ return 0;       }
 262
 263                         processors = ncpus;
 264
 265                         m->mothurOut("\nGetting preliminary data...\n");
 266                         getSingleLookUp();
 267                         getJointLookUp();
 268
 269                         vector<string> flowFileVector;
 270                         if(flowFilesFileName != "not found"){
 271                                 string fName;
 272
 273                                 ifstream flowFilesFile;
 274                                 m->openInputFile(flowFilesFileName, flowFilesFile);
 275                                 while(flowFilesFile){
 276                                         flowFilesFile >> fName;
 277                                         flowFileVector.push_back(fName);
 278                                         m->gobble(flowFilesFile);
 279                                 }
 280                         }
 281                         else{
 282                                 flowFileVector.push_back(flowFileName);
 283                         }
 284                         int numFiles = flowFileVector.size();
 285
 286                         for(int i=1;i<ncpus;i++){
 287                                 MPI_Send(&numFiles, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 288                         }
 289
 290                         for(int i=0;i<numFiles;i++){
 291                                 flowFileName = flowFileVector[i];
 292
 293
 294
 295                                 m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 296                                 m->mothurOut("Reading flowgrams...\n");
 297
 298                                 getFlowData();
 299                                 m->mothurOut("Identifying unique flowgrams...\n");
 300                                 getUniques();
 301
 302                                 m->mothurOut("Calculating distances between flowgrams...\n");
 303                                 char fileName[1024];
 304                                 strcpy(fileName, flowFileName.c_str());
 305
 306                                 for(int i=1;i<ncpus;i++){
 307                                         MPI_Send(&fileName[0], 1024, MPI_CHAR, i, tag, MPI_COMM_WORLD);
 308
 309                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 310                                         MPI_Send(&numUniques, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 311                                         MPI_Send(&numFlowCells, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 312                                         MPI_Send(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 313                                         MPI_Send(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 314                                         MPI_Send(&mapUniqueToSeq[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 315                                         MPI_Send(&mapSeqToUnique[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 316                                         MPI_Send(&lengths[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 317                                         MPI_Send(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 318                                         MPI_Send(&cutoff, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 319                                 }
 320
 321                                 string distFileName = flowDistMPI(0, int(sqrt(1.0/float(ncpus)) * numUniques));
 322
 323                                 int done;
 324                                 for(int i=1;i<ncpus;i++){
 325                                         MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 326
 327                                         m->appendFiles((distFileName + ".temp." + toString(i)), distFileName);
 328                                         remove((distFileName + ".temp." + toString(i)).c_str());
 329                                 }
 330
 331                                 string namesFileName = createNamesFile();
 332
 333                                 m->mothurOut("\nClustering flowgrams...\n");
 334                                 string listFileName = cluster(distFileName, namesFileName);
 335
 336                                 getOTUData(listFileName);
 337                                 initPyroCluster();
 338
 339                                 for(int i=1;i<ncpus;i++){
 340                                         MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 341                                         MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 342                                         MPI_Send(&uniqueFlowgrams[0], numFlowCells * numUniques, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 343                                         MPI_Send(&sigma, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 344                                 }
 345
 346
 347                                 double maxDelta = 0;
 348                                 int iter = 0;
 349
 350                                 int numOTUsOnCPU = numOTUs / ncpus;
 351                                 int numSeqsOnCPU = numSeqs / ncpus;
 352                                 m->mothurOut("\nDenoising flowgrams...\n");
 353                                 m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 354
 355                                 while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 356
 357                                         double cycClock = clock();
 358                                         unsigned long int cycTime = time(NULL);
 359                                         fill();
 360
 361                                         int total = singleTau.size();
 362                                         for(int i=1;i<ncpus;i++){
 363                                                 MPI_Send(&total, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 364                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 365                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 366
 367                                                 MPI_Send(&singleTau[0], total, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 368                                                 MPI_Send(&seqNumber[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 369                                                 MPI_Send(&seqIndex[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 370                                                 MPI_Send(&nSeqsPerOTU[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 371                                                 MPI_Send(&cumNumSeqs[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 372                                         }
 373
 374                                         calcCentroidsDriver(0, numOTUsOnCPU);
 375
 376                                         for(int i=1;i<ncpus;i++){
 377                                                 int otuStart = i * numOTUs / ncpus;
 378                                                 int otuStop = (i + 1) * numOTUs / ncpus;
 379
 380                                                 vector<int> tempCentroids(numOTUs, 0);
 381                                                 vector<short> tempChange(numOTUs, 0);
 382
 383                                                 MPI_Recv(&tempCentroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 384                                                 MPI_Recv(&tempChange[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD, &status);
 385
 386                                                 for(int j=otuStart;j<otuStop;j++){
 387                                                         centroids[j] = tempCentroids[j];
 388                                                         change[j] = tempChange[j];
 389                                                 }
 390                                         }
 391
 392                                         maxDelta = getNewWeights();
 393                                         double nLL = getLikelihood();
 394                                         checkCentroids();
 395
 396                                         for(int i=1;i<ncpus;i++){
 397                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 398                                                 MPI_Send(&weight[0], numOTUs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 399                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 400                                         }
 401
 402                                         calcNewDistancesParent(0, numSeqsOnCPU);
 403
 404                                         total = singleTau.size();
 405
 406                                         for(int i=1;i<ncpus;i++){
 407                                                 int childTotal;
 408                                                 int seqStart = i * numSeqs / ncpus;
 409                                                 int seqStop = (i + 1) * numSeqs / ncpus;
 410
 411                                                 MPI_Recv(&childTotal, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 412
 413                                                 vector<int> childSeqIndex(childTotal, 0);
 414                                                 vector<double> childSingleTau(childTotal, 0);
 415                                                 vector<double> childDist(numSeqs * numOTUs, 0);
 416                                                 vector<int> otuIndex(childTotal, 0);
 417
 418                                                 MPI_Recv(&childSeqIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 419                                                 MPI_Recv(&childSingleTau[0], childTotal, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 420                                                 MPI_Recv(&childDist[0], numOTUs * numSeqs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 421                                                 MPI_Recv(&otuIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 422
 423                                                 int oldTotal = total;
 424                                                 total += childTotal;
 425                                                 singleTau.resize(total, 0);
 426                                                 seqIndex.resize(total, 0);
 427                                                 seqNumber.resize(total, 0);
 428
 429                                                 int childIndex = 0;
 430
 431                                                 for(int j=oldTotal;j<total;j++){
 432                                                         int otuI = otuIndex[childIndex];
 433                                                         int seqI = childSeqIndex[childIndex];
 434
 435                                                         singleTau[j] = childSingleTau[childIndex];
 436
 437                                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
 438                                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
 439                                                         nSeqsPerOTU[otuI]++;
 440                                                         childIndex++;
 441                                                 }
 442
 443                                                 int index = seqStart * numOTUs;
 444                                                 for(int j=seqStart;j<seqStop;j++){
 445                                                         for(int k=0;k<numOTUs;k++){
 446                                                                 dist[index] = childDist[index];
 447                                                                 index++;
 448                                                         }
 449                                                 }
 450                                         }
 451
 452                                         iter++;
 453
 454                                         m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 455
 456                                         if((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 457                                                 int live = 1;
 458                                                 for(int i=1;i<ncpus;i++){
 459                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 460                                                 }
 461                                         }
 462                                         else{
 463                                                 int live = 0;
 464                                                 for(int i=1;i<ncpus;i++){
 465                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD); //send kill command
 466                                                 }
 467                                         }
 468
 469                                 }
 470
 471                                 m->mothurOut("\nFinalizing...\n");
 472                                 fill();
 473                                 setOTUs();
 474                                 vector<int> otuCounts(numOTUs, 0);
 475                                 for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 476                                 calcCentroidsDriver(0, numOTUs);
 477                                 writeQualities(otuCounts);
 478                                 writeSequences(otuCounts);
 479                                 writeNames(otuCounts);
 480                                 writeClusters(otuCounts);
 481                                 writeGroups();
 482
 483                                 remove(distFileName.c_str());
 484                                 remove(namesFileName.c_str());
 485                                 remove(listFileName.c_str());
 486
 487                                 m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 488                         }
 489                 }
 490                 else{
 491                         int abort = 1;
 492                         bool live = 1;
 493
 494                         MPI_Recv(&abort, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 495                         if(abort){      return 0;       }
 496
 497                         int numFiles;
 498                         MPI_Recv(&numFiles, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 499
 500                         for(int i=0;i<numFiles;i++){
 501                                 //Now into the pyrodist part
 502                                 char fileName[1024];
 503                                 MPI_Recv(&fileName, 1024, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
 504                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 505                                 MPI_Recv(&numUniques, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 506                                 MPI_Recv(&numFlowCells, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 507
 508                                 flowDataIntI.resize(numSeqs * numFlowCells);
 509                                 flowDataPrI.resize(numSeqs * numFlowCells);
 510                                 mapUniqueToSeq.resize(numSeqs);
 511                                 mapSeqToUnique.resize(numSeqs);
 512                                 lengths.resize(numSeqs);
 513                                 jointLookUp.resize(NUMBINS * NUMBINS);
 514
 515                                 MPI_Recv(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 516                                 MPI_Recv(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 517                                 MPI_Recv(&mapUniqueToSeq[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 518                                 MPI_Recv(&mapSeqToUnique[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 519                                 MPI_Recv(&lengths[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 520                                 MPI_Recv(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 521                                 MPI_Recv(&cutoff, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 522
 523                                 flowFileName = string(fileName);
 524                                 int flowDistStart = int(sqrt(float(pid)/float(ncpus)) * numUniques);
 525                                 int flowDistEnd = int(sqrt(float(pid+1)/float(ncpus)) * numUniques);
 526
 527                                 string distanceStringChild = flowDistMPI(flowDistStart, flowDistEnd);
 528
 529                                 int done = 1;
 530                                 MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 531
 532                                 //Now into the pyronoise part
 533                                 MPI_Recv(&numOTUs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 534
 535                                 singleLookUp.resize(HOMOPS * NUMBINS);
 536                                 uniqueFlowgrams.resize(numUniques * numFlowCells);
 537                                 weight.resize(numOTUs);
 538                                 centroids.resize(numOTUs);
 539                                 change.resize(numOTUs);
 540                                 dist.assign(numOTUs * numSeqs, 0);
 541                                 nSeqsPerOTU.resize(numOTUs);
 542                                 cumNumSeqs.resize(numOTUs);
 543
 544                                 MPI_Recv(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 545                                 MPI_Recv(&uniqueFlowgrams[0], uniqueFlowgrams.size(), MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 546                                 MPI_Recv(&sigma, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 547
 548                                 int startOTU = pid * numOTUs / ncpus;
 549                                 int endOTU = (pid + 1) * numOTUs / ncpus;
 550
 551                                 int startSeq = pid * numSeqs / ncpus;
 552                                 int endSeq = (pid + 1) * numSeqs /ncpus;
 553
 554                                 int total;
 555
 556                                 while(live){
 557
 558                                         MPI_Recv(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 559                                         singleTau.assign(total, 0.0000);
 560                                         seqNumber.assign(total, 0);
 561                                         seqIndex.assign(total, 0);
 562
 563                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 564                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 565                                         MPI_Recv(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 566                                         MPI_Recv(&seqNumber[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 567                                         MPI_Recv(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 568                                         MPI_Recv(&nSeqsPerOTU[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 569                                         MPI_Recv(&cumNumSeqs[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 570
 571                                         calcCentroidsDriver(startOTU, endOTU);
 572
 573                                         MPI_Send(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD);
 574                                         MPI_Send(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD);
 575
 576
 577                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 578                                         MPI_Recv(&weight[0], numOTUs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 579                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 580
 581                                         vector<int> otuIndex(total, 0);
 582                                         calcNewDistancesChildMPI(startSeq, endSeq, otuIndex);
 583                                         total = otuIndex.size();
 584
 585                                         MPI_Send(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 586                                         MPI_Send(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 587                                         MPI_Send(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 588                                         MPI_Send(&dist[0], numOTUs * numSeqs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 589                                         MPI_Send(&otuIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 590
 591                                         MPI_Recv(&live, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 592                                 }
 593                         }
 594                 }
 595
 596                 MPI_Barrier(MPI_COMM_WORLD);
 597                 return 0;
 598
 599         }
 600         catch(exception& e) {
 601                 m->errorOut(e, "ShhherCommand", "execute");
 602                 exit(1);
 603         }
 604 }
 605
 606 /**************************************************************************************************/
 607
 608 string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 609         try{
 610                 ostringstream outStream;
 611                 outStream.setf(ios::fixed, ios::floatfield);
 612                 outStream.setf(ios::dec, ios::basefield);
 613                 outStream.setf(ios::showpoint);
 614                 outStream.precision(6);
 615
 616                 int begTime = time(NULL);
 617                 double begClock = clock();
 618
 619                 for(int i=startSeq;i<stopSeq;i++){
 620                         for(int j=0;j<i;j++){
 621                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
 622
 623                                 if(flowDistance < 1e-6){
 624                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
 625                                 }
 626                                 else if(flowDistance <= cutoff){
 627                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
 628                                 }
 629                         }
 630                         if(i % 100 == 0){
 631                                 m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 632                         }
 633                 }
 634
 635                 m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 636
 637                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
 638                 if(pid != 0){   fDistFileName += ".temp." + toString(pid);      }
 639
 640                 ofstream distFile(fDistFileName.c_str());
 641                 distFile << outStream.str();
 642                 distFile.close();
 643
 644                 return fDistFileName;
 645         }
 646         catch(exception& e) {
 647                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
 648                 exit(1);
 649         }
 650 }
 651
 652 #else
 653 //**********************************************************************************************************************
 654
 655 int ShhherCommand::execute(){
 656         try {
 657                 if (abort == true) { return 0; }
 658
 659                 getSingleLookUp();
 660                 getJointLookUp();
 661
 662                 vector<string> flowFileVector;
 663                 if(flowFilesFileName != "not found"){
 664                         string fName;
 665
 666                         ifstream flowFilesFile;
 667                         m->openInputFile(flowFilesFileName, flowFilesFile);
 668                         while(flowFilesFile){
 669                                 flowFilesFile >> fName;
 670                                 flowFileVector.push_back(fName);
 671                                 m->gobble(flowFilesFile);
 672                         }
 673                 }
 674                 else{
 675                         flowFileVector.push_back(flowFileName);
 676                 }
 677                 int numFiles = flowFileVector.size();
 678
 679
 680                 for(int i=0;i<numFiles;i++){
 681                         flowFileName = flowFileVector[i];
 682
 683                         m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 684                         m->mothurOut("Reading flowgrams...\n");
 685                         getFlowData();
 686
 687                         m->mothurOut("Identifying unique flowgrams...\n");
 688                         getUniques();
 689
 690
 691                         m->mothurOut("Calculating distances between flowgrams...\n");
 692                         string distFileName = createDistFile(processors);
 693                         string namesFileName = createNamesFile();
 694
 695                         m->mothurOut("\nClustering flowgrams...\n");
 696                         string listFileName = cluster(distFileName, namesFileName);
 697                         getOTUData(listFileName);
 698
 699                         initPyroCluster();
 700
 701                         double maxDelta = 0;
 702                         int iter = 0;
 703
 704                         double begClock = clock();
 705                         unsigned long int begTime = time(NULL);
 706
 707                         m->mothurOut("\nDenoising flowgrams...\n");
 708                         m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 709
 710                         while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 711
 712                                 double cycClock = clock();
 713                                 unsigned long int cycTime = time(NULL);
 714                                 fill();
 715
 716                                 calcCentroids();
 717
 718                                 maxDelta = getNewWeights();
 719                                 double nLL = getLikelihood();
 720                                 checkCentroids();
 721
 722                                 calcNewDistances();
 723
 724                                 iter++;
 725
 726                                 m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 727
 728                         }
 729
 730                         m->mothurOut("\nFinalizing...\n");
 731                         fill();
 732                         setOTUs();
 733
 734                         vector<int> otuCounts(numOTUs, 0);
 735                         for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 736
 737                         calcCentroidsDriver(0, numOTUs);
 738                         writeQualities(otuCounts);
 739                         writeSequences(otuCounts);
 740                         writeNames(otuCounts);
 741                         writeClusters(otuCounts);
 742                         writeGroups();
 743
 744                         remove(distFileName.c_str());
 745                         remove(namesFileName.c_str());
 746                         remove(listFileName.c_str());
 747
 748                         m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 749                 }
 750                 return 0;
 751         }
 752         catch(exception& e) {
 753                 m->errorOut(e, "ShhherCommand", "execute");
 754                 exit(1);
 755         }
 756 }
 757 #endif
 758 /**************************************************************************************************/
 759
 760 void ShhherCommand::getFlowData(){
 761         try{
 762                 ifstream flowFile;
 763                 m->openInputFile(flowFileName, flowFile);
 764
 765                 string seqName;
 766                 seqNameVector.clear();
 767                 lengths.clear();
 768                 flowDataIntI.clear();
 769                 nameMap.clear();
 770
 771
 772                 int currentNumFlowCells;
 773
 774                 float intensity;
 775
 776                 flowFile >> numFlowCells;
 777                 int index = 0;//pcluster
 778                 while(!flowFile.eof()){
 779                         flowFile >> seqName >> currentNumFlowCells;
 780                         lengths.push_back(currentNumFlowCells);
 781
 782                         seqNameVector.push_back(seqName);
 783                         nameMap[seqName] = index++;//pcluster
 784
 785                         for(int i=0;i<numFlowCells;i++){
 786                                 flowFile >> intensity;
 787                                 if(intensity > 9.99)    {       intensity = 9.99;       }
 788                                 int intI = int(100 * intensity + 0.0001);
 789                                 flowDataIntI.push_back(intI);
 790                         }
 791                         m->gobble(flowFile);
 792                 }
 793                 flowFile.close();
 794
 795                 numSeqs = seqNameVector.size();
 796
 797                 for(int i=0;i<numSeqs;i++){
 798                         int iNumFlowCells = i * numFlowCells;
 799                         for(int j=lengths[i];j<numFlowCells;j++){
 800                                 flowDataIntI[iNumFlowCells + j] = 0;
 801                         }
 802                 }
 803
 804         }
 805         catch(exception& e) {
 806                 m->errorOut(e, "ShhherCommand", "getFlowData");
 807                 exit(1);
 808         }
 809 }
 810
 811 /**************************************************************************************************/
 812
 813 void ShhherCommand::getSingleLookUp(){
 814         try{
 815                 //      these are the -log probabilities that a signal corresponds to a particular homopolymer length
 816                 singleLookUp.assign(HOMOPS * NUMBINS, 0);
 817
 818                 int index = 0;
 819                 ifstream lookUpFile;
 820                 m->openInputFile(lookupFileName, lookUpFile);
 821
 822                 for(int i=0;i<HOMOPS;i++){
 823                         float logFracFreq;
 824                         lookUpFile >> logFracFreq;
 825
 826                         for(int j=0;j<NUMBINS;j++)      {
 827                                 lookUpFile >> singleLookUp[index];
 828                                 index++;
 829                         }
 830                 }
 831                 lookUpFile.close();
 832         }
 833         catch(exception& e) {
 834                 m->errorOut(e, "ShhherCommand", "getSingleLookUp");
 835                 exit(1);
 836         }
 837 }
 838
 839 /**************************************************************************************************/
 840
 841 void ShhherCommand::getJointLookUp(){
 842         try{
 843
 844                 //      the most likely joint probability (-log) that two intenities have the same polymer length
 845                 jointLookUp.resize(NUMBINS * NUMBINS, 0);
 846
 847                 for(int i=0;i<NUMBINS;i++){
 848                         for(int j=0;j<NUMBINS;j++){
 849
 850                                 double minSum = 100000000;
 851
 852                                 for(int k=0;k<HOMOPS;k++){
 853                                         double sum = singleLookUp[k * NUMBINS + i] + singleLookUp[k * NUMBINS + j];
 854
 855                                         if(sum < minSum)        {       minSum = sum;           }
 856                                 }
 857                                 jointLookUp[i * NUMBINS + j] = minSum;
 858                         }
 859                 }
 860         }
 861         catch(exception& e) {
 862                 m->errorOut(e, "ShhherCommand", "getJointLookUp");
 863                 exit(1);
 864         }
 865 }
 866
 867 /**************************************************************************************************/
 868
 869 double ShhherCommand::getProbIntensity(int intIntensity){
 870         try{
 871
 872                 double minNegLogProb = 100000000;
 873
 874
 875                 for(int i=0;i<HOMOPS;i++){//loop signal strength
 876                         float negLogProb = singleLookUp[i * NUMBINS + intIntensity];
 877                         if(negLogProb < minNegLogProb)  {       minNegLogProb = negLogProb; }
 878                 }
 879
 880                 return minNegLogProb;
 881         }
 882         catch(exception& e) {
 883                 m->errorOut(e, "ShhherCommand", "getProbIntensity");
 884                 exit(1);
 885         }
 886 }
 887
 888 /**************************************************************************************************/
 889
 890 void ShhherCommand::getUniques(){
 891         try{
 892
 893
 894                 numUniques = 0;
 895                 uniqueFlowgrams.assign(numFlowCells * numSeqs, -1);
 896                 uniqueCount.assign(numSeqs, 0);                                                 //      anWeights
 897                 uniqueLengths.assign(numSeqs, 0);
 898                 mapSeqToUnique.assign(numSeqs, -1);
 899                 mapUniqueToSeq.assign(numSeqs, -1);
 900
 901                 vector<short> uniqueFlowDataIntI(numFlowCells * numSeqs, -1);
 902
 903                 for(int i=0;i<numSeqs;i++){
 904                         int index = 0;
 905
 906                         vector<short> current(numFlowCells);
 907                         for(int j=0;j<numFlowCells;j++){
 908                                 current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));
 909                         }
 910
 911                         for(int j=0;j<numUniques;j++){
 912                                 int offset = j * numFlowCells;
 913                                 bool toEnd = 1;
 914
 915                                 int shorterLength;
 916                                 if(lengths[i] < uniqueLengths[j])       {       shorterLength = lengths[i];                     }
 917                                 else                                                            {       shorterLength = uniqueLengths[j];       }
 918
 919                                 for(int k=0;k<shorterLength;k++){
 920                                         if(current[k] != uniqueFlowgrams[offset + k]){
 921                                                 toEnd = 0;
 922                                                 break;
 923                                         }
 924                                 }
 925
 926                                 if(toEnd){
 927                                         mapSeqToUnique[i] = j;
 928                                         uniqueCount[j]++;
 929                                         index = j;
 930                                         if(lengths[i] > uniqueLengths[j])       {       uniqueLengths[j] = lengths[i];  }
 931                                         break;
 932                                 }
 933                                 index++;
 934                         }
 935
 936                         if(index == numUniques){
 937                                 uniqueLengths[numUniques] = lengths[i];
 938                                 uniqueCount[numUniques] = 1;
 939                                 mapSeqToUnique[i] = numUniques;//anMap
 940                                 mapUniqueToSeq[numUniques] = i;//anF
 941
 942                                 for(int k=0;k<numFlowCells;k++){
 943                                         uniqueFlowgrams[numUniques * numFlowCells + k] = current[k];
 944                                         uniqueFlowDataIntI[numUniques * numFlowCells + k] = flowDataIntI[i * numFlowCells + k];
 945                                 }
 946
 947                                 numUniques++;
 948                         }
 949                 }
 950                 uniqueFlowDataIntI.resize(numFlowCells * numUniques);
 951                 uniqueLengths.resize(numUniques);
 952
 953                 flowDataPrI.resize(numSeqs * numFlowCells, 0);
 954                 for(int i=0;i<flowDataPrI.size();i++)   {       flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);             }
 955         }
 956         catch(exception& e) {
 957                 m->errorOut(e, "ShhherCommand", "getUniques");
 958                 exit(1);
 959         }
 960 }
 961
 962 /**************************************************************************************************/
 963
 964 float ShhherCommand::calcPairwiseDist(int seqA, int seqB){
 965         try{
 966                 int minLength = lengths[mapSeqToUnique[seqA]];
 967                 if(lengths[seqB] < minLength){  minLength = lengths[mapSeqToUnique[seqB]];      }
 968
 969                 int ANumFlowCells = seqA * numFlowCells;
 970                 int BNumFlowCells = seqB * numFlowCells;
 971
 972                 float dist = 0;
 973
 974                 for(int i=0;i<minLength;i++){
 975                         int flowAIntI = flowDataIntI[ANumFlowCells + i];
 976                         float flowAPrI = flowDataPrI[ANumFlowCells + i];
 977
 978                         int flowBIntI = flowDataIntI[BNumFlowCells + i];
 979                         float flowBPrI = flowDataPrI[BNumFlowCells + i];
 980                         dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI;
 981                 }
 982
 983                 dist /= (float) minLength;
 984                 return dist;
 985         }
 986         catch(exception& e) {
 987                 m->errorOut(e, "ShhherCommand", "calcPairwiseDist");
 988                 exit(1);
 989         }
 990 }
 991
 992 /**************************************************************************************************/
 993
 994 void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int stopSeq){
 995         try{
 996
 997                 ostringstream outStream;
 998                 outStream.setf(ios::fixed, ios::floatfield);
 999                 outStream.setf(ios::dec, ios::basefield);
1000                 outStream.setf(ios::showpoint);
1001                 outStream.precision(6);
1002
1003                 int begTime = time(NULL);
1004                 double begClock = clock();
1005
1006                 for(int i=startSeq;i<stopSeq;i++){
1007                         for(int j=0;j<i;j++){
1008                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
1009
1010                                 if(flowDistance < 1e-6){
1011                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
1012                                 }
1013                                 else if(flowDistance <= cutoff){
1014                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
1015                                 }
1016                         }
1017                         if(i % 100 == 0){
1018                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
1019                                 m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1020                                 m->mothurOutEndLine();
1021                         }
1022                 }
1023                 m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
1024                 m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1025                 m->mothurOutEndLine();
1026
1027                 ofstream distFile(distFileName.c_str());
1028                 distFile << outStream.str();
1029                 distFile.close();
1030         }
1031         catch(exception& e) {
1032                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
1033                 exit(1);
1034         }
1035 }
1036
1037 /**************************************************************************************************/
1038
1039 string ShhherCommand::createDistFile(int processors){
1040         try{
1041                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
1042
1043                 unsigned long int begTime = time(NULL);
1044                 double begClock = clock();
1045
1046                 vector<int> start;
1047                 vector<int> end;
1048
1049 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1050                 if(processors == 1)     {       flowDistParentFork(fDistFileName, 0, numUniques);               }
1051                 else{ //you have multiple processors
1052
1053                         if (numSeqs < processors){      processors = 1; }
1054
1055                         vector<int> start(processors, 0);
1056                         vector<int> end(processors, 0);
1057
1058                         for (int i = 0; i < processors; i++) {
1059                                 start[i] = int(sqrt(float(i)/float(processors)) * numUniques);
1060                                 end[i] = int(sqrt(float(i+1)/float(processors)) * numUniques);
1061                         }
1062
1063                         int process = 1;
1064                         vector<int> processIDs;
1065
1066                         //loop through and create all the processes you want
1067                         while (process != processors) {
1068                                 int pid = fork();
1069
1070                                 if (pid > 0) {
1071                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1072                                         process++;
1073                                 }else if (pid == 0){
1074                                         flowDistParentFork(fDistFileName + toString(getpid()) + ".temp", start[process], end[process]);
1075                                         exit(0);
1076                                 }else {
1077                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1078                                         perror(" : ");
1079                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1080                                         exit(0);
1081                                 }
1082                         }
1083
1084                         //parent does its part
1085                         flowDistParentFork(fDistFileName, start[0], end[0]);
1086
1087                         //force parent to wait until all the processes are done
1088                         for (int i=0;i<processIDs.size();i++) {
1089                                 int temp = processIDs[i];
1090                                 wait(&temp);
1091                         }
1092
1093                         //append and remove temp files
1094                         for (int i=0;i<processIDs.size();i++) {
1095                                 m->appendFiles((fDistFileName + toString(processIDs[i]) + ".temp"), fDistFileName);
1096                                 remove((fDistFileName + toString(processIDs[i]) + ".temp").c_str());
1097                         }
1098
1099                 }
1100
1101 #else
1102                 flowDistParentFork(fDistFileName, 0, numUniques);
1103 #endif
1104
1105                 m->mothurOutEndLine();
1106
1107                 m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
1108
1109
1110                 return fDistFileName;
1111         }
1112         catch(exception& e) {
1113                 m->errorOut(e, "ShhherCommand", "createDistFile");
1114                 exit(1);
1115         }
1116
1117 }
1118
1119 /**************************************************************************************************/
1120
1121 string ShhherCommand::createNamesFile(){
1122         try{
1123
1124                 vector<string> duplicateNames(numUniques, "");
1125                 for(int i=0;i<numSeqs;i++){
1126                         duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
1127                 }
1128
1129                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.names";
1130
1131                 ofstream nameFile;
1132                 m->openOutputFile(nameFileName, nameFile);
1133
1134                 for(int i=0;i<numUniques;i++){
1135 //                      nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1136                         nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1137                 }
1138
1139                 nameFile.close();
1140                 return  nameFileName;
1141         }
1142         catch(exception& e) {
1143                 m->errorOut(e, "ShhherCommand", "createNamesFile");
1144                 exit(1);
1145         }
1146 }
1147
1148 //**********************************************************************************************************************
1149
1150 string ShhherCommand::cluster(string distFileName, string namesFileName){
1151         try {
1152
1153
1154                 globaldata->setNameFile(namesFileName);
1155                 globaldata->setColumnFile(distFileName);
1156                 globaldata->setFormat("column");
1157
1158                 ReadMatrix* read = new ReadColumnMatrix(distFileName);
1159                 read->setCutoff(cutoff);
1160
1161                 NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
1162                 clusterNameMap->readMap();
1163                 read->read(clusterNameMap);
1164
1165                 ListVector* list = read->getListVector();
1166                 SparseMatrix* matrix = read->getMatrix();
1167
1168                 delete read;
1169                 delete clusterNameMap;
1170
1171                 RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
1172
1173                 Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest");
1174                 string tag = cluster->getTag();
1175
1176                 double clusterCutoff = cutoff;
1177                 while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){
1178                         cluster->update(clusterCutoff);
1179                 }
1180
1181                 list->setLabel(toString(cutoff));
1182
1183                 string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.list";
1184                 ofstream listFile;
1185                 m->openOutputFile(listFileName, listFile);
1186                 list->print(listFile);
1187                 listFile.close();
1188
1189                 delete matrix;  delete cluster; delete rabund; delete list;
1190
1191                 return listFileName;
1192         }
1193         catch(exception& e) {
1194                 m->errorOut(e, "ShhherCommand", "cluster");
1195                 exit(1);
1196         }
1197 }
1198
1199 /**************************************************************************************************/
1200
1201 void ShhherCommand::getOTUData(string listFileName){
1202         try {
1203
1204                 ifstream listFile;
1205                 m->openInputFile(listFileName, listFile);
1206                 string label;
1207
1208                 listFile >> label >> numOTUs;
1209
1210                 otuData.assign(numSeqs, 0);
1211                 cumNumSeqs.assign(numOTUs, 0);
1212                 nSeqsPerOTU.assign(numOTUs, 0);
1213                 aaP.resize(numOTUs);
1214
1215                 seqNumber.clear();
1216                 aaI.clear();
1217                 seqIndex.clear();
1218
1219                 string singleOTU = "";
1220
1221                 for(int i=0;i<numOTUs;i++){
1222
1223                         listFile >> singleOTU;
1224
1225                         istringstream otuString(singleOTU);
1226
1227                         while(otuString){
1228
1229                                 string seqName = "";
1230
1231                                 for(int j=0;j<singleOTU.length();j++){
1232                                         char letter = otuString.get();
1233
1234                                         if(letter != ','){
1235                                                 seqName += letter;
1236                                         }
1237                                         else{
1238                                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1239                                                 int index = nmIt->second;
1240
1241                                                 nameMap.erase(nmIt);
1242
1243                                                 otuData[index] = i;
1244                                                 nSeqsPerOTU[i]++;
1245                                                 aaP[i].push_back(index);
1246                                                 seqName = "";
1247                                         }
1248                                 }
1249
1250                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1251
1252                                 int index = nmIt->second;
1253                                 nameMap.erase(nmIt);
1254
1255                                 otuData[index] = i;
1256                                 nSeqsPerOTU[i]++;
1257                                 aaP[i].push_back(index);
1258
1259                                 otuString.get();
1260                         }
1261
1262                         sort(aaP[i].begin(), aaP[i].end());
1263                         for(int j=0;j<nSeqsPerOTU[i];j++){
1264                                 seqNumber.push_back(aaP[i][j]);
1265                         }
1266                         for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
1267                                 aaP[i].push_back(0);
1268                         }
1269                 }
1270
1271                 for(int i=1;i<numOTUs;i++){
1272                         cumNumSeqs[i] = cumNumSeqs[i-1] + nSeqsPerOTU[i-1];
1273                 }
1274                 aaI = aaP;
1275                 seqIndex = seqNumber;
1276
1277                 listFile.close();
1278         }
1279         catch(exception& e) {
1280                 m->errorOut(e, "ShhherCommand", "getOTUData");
1281                 exit(1);
1282         }
1283 }
1284
1285 /**************************************************************************************************/
1286
1287 void ShhherCommand::initPyroCluster(){
1288         try{
1289                 dist.assign(numSeqs * numOTUs, 0);
1290                 change.assign(numOTUs, 1);
1291                 centroids.assign(numOTUs, -1);
1292                 weight.assign(numOTUs, 0);
1293                 singleTau.assign(numSeqs, 1.0);
1294
1295                 nSeqsBreaks.assign(processors+1, 0);
1296                 nOTUsBreaks.assign(processors+1, 0);
1297
1298                 nSeqsBreaks[0] = 0;
1299                 for(int i=0;i<processors;i++){
1300                         nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
1301                         nOTUsBreaks[i+1] = nOTUsBreaks[i] + (int)((double) numOTUs / (double) processors);
1302                 }
1303                 nSeqsBreaks[processors] = numSeqs;
1304                 nOTUsBreaks[processors] = numOTUs;
1305         }
1306         catch(exception& e) {
1307                 m->errorOut(e, "ShhherCommand", "initPyroCluster");
1308                 exit(1);
1309         }
1310 }
1311
1312 /**************************************************************************************************/
1313
1314 void ShhherCommand::fill(){
1315         try {
1316                 int index = 0;
1317                 for(int i=0;i<numOTUs;i++){
1318                         cumNumSeqs[i] = index;
1319                         for(int j=0;j<nSeqsPerOTU[i];j++){
1320                                 seqNumber[index] = aaP[i][j];
1321                                 seqIndex[index] = aaI[i][j];
1322
1323                                 index++;
1324                         }
1325                 }
1326         }
1327         catch(exception& e) {
1328                 m->errorOut(e, "ShhherCommand", "fill");
1329                 exit(1);
1330         }
1331 }
1332
1333 /**************************************************************************************************/
1334
1335 void ShhherCommand::calcCentroids(){
1336         try{
1337
1338 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1339
1340                 if(processors == 1)     {
1341                         calcCentroidsDriver(0, numOTUs);
1342                 }
1343                 else{ //you have multiple processors
1344                         if (numOTUs < processors){      processors = 1; }
1345
1346                         int process = 1;
1347                         vector<int> processIDs;
1348
1349                         //loop through and create all the processes you want
1350                         while (process != processors) {
1351                                 int pid = vfork();
1352
1353                                 if (pid > 0) {
1354                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1355                                         process++;
1356                                 }else if (pid == 0){
1357                                         calcCentroidsDriver(nOTUsBreaks[process], nOTUsBreaks[process+1]);
1358                                         exit(0);
1359                                 }else {
1360                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1361                                         perror(" : ");
1362                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1363                                         exit(0);
1364                                 }
1365                         }
1366
1367                         //parent does its part
1368                         calcCentroidsDriver(nOTUsBreaks[0], nOTUsBreaks[1]);
1369
1370                         //force parent to wait until all the processes are done
1371                         for (int i=0;i<processIDs.size();i++) {
1372                                 int temp = processIDs[i];
1373                                 wait(&temp);
1374                         }
1375                 }
1376
1377 #else
1378                 calcCentroidsDriver(0, numOTUs);
1379 #endif
1380         }
1381         catch(exception& e) {
1382                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1383                 exit(1);
1384         }
1385 }
1386
1387 /**************************************************************************************************/
1388
1389 void ShhherCommand::calcCentroidsDriver(int start, int finish){
1390
1391         //this function gets the most likely homopolymer length at a flow position for a group of sequences
1392         //within an otu
1393
1394         try{
1395
1396                 for(int i=start;i<finish;i++){
1397
1398                         double count = 0;
1399                         int position = 0;
1400                         int minFlowGram = 100000000;
1401                         double minFlowValue = 1e8;
1402                         change[i] = 0; //FALSE
1403
1404                         for(int j=0;j<nSeqsPerOTU[i];j++){
1405                                 count += singleTau[seqNumber[cumNumSeqs[i] + j]];
1406                         }
1407
1408                         if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
1409                                 vector<double> adF(nSeqsPerOTU[i]);
1410                                 vector<int> anL(nSeqsPerOTU[i]);
1411
1412                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1413                                         int index = cumNumSeqs[i] + j;
1414                                         int nI = seqIndex[index];
1415                                         int nIU = mapSeqToUnique[nI];
1416
1417                                         int k;
1418                                         for(k=0;k<position;k++){
1419                                                 if(nIU == anL[k]){
1420                                                         break;
1421                                                 }
1422                                         }
1423                                         if(k == position){
1424                                                 anL[position] = nIU;
1425                                                 adF[position] = 0.0000;
1426                                                 position++;
1427                                         }
1428                                 }
1429
1430                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1431                                         int index = cumNumSeqs[i] + j;
1432                                         int nI = seqIndex[index];
1433
1434                                         double tauValue = singleTau[seqNumber[index]];
1435
1436                                         for(int k=0;k<position;k++){
1437                                                 double dist = getDistToCentroid(anL[k], nI, lengths[nI]);
1438                                                 adF[k] += dist * tauValue;
1439                                         }
1440                                 }
1441
1442                                 for(int j=0;j<position;j++){
1443                                         if(adF[j] < minFlowValue){
1444                                                 minFlowGram = j;
1445                                                 minFlowValue = adF[j];
1446                                         }
1447                                 }
1448
1449                                 if(centroids[i] != anL[minFlowGram]){
1450                                         change[i] = 1;
1451                                         centroids[i] = anL[minFlowGram];
1452                                 }
1453                         }
1454                         else if(centroids[i] != -1){
1455                                 change[i] = 1;
1456                                 centroids[i] = -1;
1457                         }
1458                 }
1459         }
1460         catch(exception& e) {
1461                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1462                 exit(1);
1463         }
1464 }
1465
1466 /**************************************************************************************************/
1467
1468 double ShhherCommand::getDistToCentroid(int cent, int flow, int length){
1469         try{
1470
1471                 int flowAValue = cent * numFlowCells;
1472                 int flowBValue = flow * numFlowCells;
1473
1474                 double dist = 0;
1475
1476                 for(int i=0;i<length;i++){
1477                         dist += singleLookUp[uniqueFlowgrams[flowAValue] * NUMBINS + flowDataIntI[flowBValue]];
1478                         flowAValue++;
1479                         flowBValue++;
1480                 }
1481
1482                 return dist / (double)length;
1483         }
1484         catch(exception& e) {
1485                 m->errorOut(e, "ShhherCommand", "getDistToCentroid");
1486                 exit(1);
1487         }
1488 }
1489
1490 /**************************************************************************************************/
1491
1492 double ShhherCommand::getNewWeights(){
1493         try{
1494
1495                 double maxChange = 0;
1496
1497                 for(int i=0;i<numOTUs;i++){
1498
1499                         double difference = weight[i];
1500                         weight[i] = 0;
1501
1502                         for(int j=0;j<nSeqsPerOTU[i];j++){
1503                                 int index = cumNumSeqs[i] + j;
1504                                 double tauValue = singleTau[seqNumber[index]];
1505                                 weight[i] += tauValue;
1506                         }
1507
1508                         difference = fabs(weight[i] - difference);
1509                         if(difference > maxChange){     maxChange = difference; }
1510                 }
1511                 return maxChange;
1512         }
1513         catch(exception& e) {
1514                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1515                 exit(1);
1516         }
1517 }
1518
1519 /**************************************************************************************************/
1520
1521 double ShhherCommand::getLikelihood(){
1522
1523         try{
1524
1525                 vector<long double> P(numSeqs, 0);
1526                 int effNumOTUs = 0;
1527
1528                 for(int i=0;i<numOTUs;i++){
1529                         if(weight[i] > MIN_WEIGHT){
1530                                 effNumOTUs++;
1531                         }
1532                 }
1533
1534                 string hold;
1535                 for(int i=0;i<numOTUs;i++){
1536                         for(int j=0;j<nSeqsPerOTU[i];j++){
1537                                 int index = cumNumSeqs[i] + j;
1538                                 int nI = seqIndex[index];
1539                                 double singleDist = dist[seqNumber[index]];
1540
1541                                 P[nI] += weight[i] * exp(-singleDist * sigma);
1542                         }
1543                 }
1544                 double nLL = 0.00;
1545                 for(int i=0;i<numSeqs;i++){
1546                         if(P[i] == 0){  P[i] = DBL_EPSILON;     }
1547
1548                         nLL += -log(P[i]);
1549                 }
1550
1551                 nLL = nLL -(double)numSeqs * log(sigma);
1552
1553                 return nLL;
1554         }
1555         catch(exception& e) {
1556                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1557                 exit(1);
1558         }
1559 }
1560
1561 /**************************************************************************************************/
1562
1563 void ShhherCommand::checkCentroids(){
1564         try{
1565                 vector<int> unique(numOTUs, 1);
1566
1567                 for(int i=0;i<numOTUs;i++){
1568                         if(centroids[i] == -1 || weight[i] < MIN_WEIGHT){
1569                                 unique[i] = -1;
1570                         }
1571                 }
1572
1573                 for(int i=0;i<numOTUs;i++){
1574                         if(unique[i] == 1){
1575                                 for(int j=i+1;j<numOTUs;j++){
1576                                         if(unique[j] == 1){
1577
1578                                                 if(centroids[j] == centroids[i]){
1579                                                         unique[j] = 0;
1580                                                         centroids[j] = -1;
1581
1582                                                         weight[i] += weight[j];
1583                                                         weight[j] = 0.0;
1584                                                 }
1585                                         }
1586                                 }
1587                         }
1588                 }
1589         }
1590         catch(exception& e) {
1591                 m->errorOut(e, "ShhherCommand", "checkCentroids");
1592                 exit(1);
1593         }
1594 }
1595
1596 /**************************************************************************************************/
1597
1598 void ShhherCommand::calcNewDistances(){
1599         try{
1600
1601 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1602
1603                 if(processors == 1)     {
1604                         calcNewDistancesParent(0, numSeqs);
1605                 }
1606                 else{ //you have multiple processors
1607                         if (numSeqs < processors){      processors = 1; }
1608
1609                         vector<vector<int> > child_otuIndex(processors);
1610                         vector<vector<int> > child_seqIndex(processors);
1611                         vector<vector<double> > child_singleTau(processors);
1612                         vector<int> totals(processors);
1613
1614                         int process = 1;
1615                         vector<int> processIDs;
1616
1617                         //loop through and create all the processes you want
1618                         while (process != processors) {
1619                                 int pid = vfork();
1620
1621                                 if (pid > 0) {
1622                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1623                                         process++;
1624                                 }else if (pid == 0){
1625                                         calcNewDistancesChild(nSeqsBreaks[process], nSeqsBreaks[process+1], child_otuIndex[process], child_seqIndex[process], child_singleTau[process]);
1626                                         totals[process] = child_otuIndex[process].size();
1627
1628                                         exit(0);
1629                                 }else {
1630                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1631                                         perror(" : ");
1632                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1633                                         exit(0);
1634                                 }
1635                         }
1636
1637                         //parent does its part
1638                         calcNewDistancesParent(nSeqsBreaks[0], nSeqsBreaks[1]);
1639                         int total = seqIndex.size();
1640
1641                         //force parent to wait until all the processes are done
1642                         for (int i=0;i<processIDs.size();i++) {
1643                                 int temp = processIDs[i];
1644                                 wait(&temp);
1645                         }
1646
1647                         for(int i=1;i<processors;i++){
1648                                 int oldTotal = total;
1649                                 total += totals[i];
1650
1651                                 singleTau.resize(total, 0);
1652                                 seqIndex.resize(total, 0);
1653                                 seqNumber.resize(total, 0);
1654
1655                                 int childIndex = 0;
1656
1657                                 for(int j=oldTotal;j<total;j++){
1658                                         int otuI = child_otuIndex[i][childIndex];
1659                                         int seqI = child_seqIndex[i][childIndex];
1660
1661                                         singleTau[j] = child_singleTau[i][childIndex];
1662                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
1663                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
1664                                         nSeqsPerOTU[otuI]++;
1665
1666                                         childIndex++;
1667                                 }
1668                         }
1669                 }
1670 #else
1671                 calcNewDistancesParent(0, numSeqs);
1672 #endif
1673         }
1674         catch(exception& e) {
1675                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
1676                 exit(1);
1677         }
1678 }
1679
1680 /**************************************************************************************************/
1681 #ifdef USE_MPI
1682 void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector<int>& otuIndex){
1683
1684         try{
1685                 vector<double> newTau(numOTUs,0);
1686                 vector<double> norms(numSeqs, 0);
1687                 otuIndex.clear();
1688                 seqIndex.clear();
1689                 singleTau.clear();
1690
1691
1692
1693                 for(int i=startSeq;i<stopSeq;i++){
1694                         double offset = 1e8;
1695                         int indexOffset = i * numOTUs;
1696
1697                         for(int j=0;j<numOTUs;j++){
1698
1699                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1700                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1701                                 }
1702                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1703                                         offset = dist[indexOffset + j];
1704                                 }
1705                         }
1706
1707                         for(int j=0;j<numOTUs;j++){
1708                                 if(weight[j] > MIN_WEIGHT){
1709                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1710                                         norms[i] += newTau[j];
1711                                 }
1712                                 else{
1713                                         newTau[j] = 0.0;
1714                                 }
1715                         }
1716
1717                         for(int j=0;j<numOTUs;j++){
1718
1719                                 newTau[j] /= norms[i];
1720
1721                                 if(newTau[j] > MIN_TAU){
1722                                         otuIndex.push_back(j);
1723                                         seqIndex.push_back(i);
1724                                         singleTau.push_back(newTau[j]);
1725                                 }
1726                         }
1727
1728                 }
1729         }
1730         catch(exception& e) {
1731                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChildMPI");
1732                 exit(1);
1733         }
1734 }
1735 #endif
1736 /**************************************************************************************************/
1737
1738 void ShhherCommand::calcNewDistancesChild(int startSeq, int stopSeq, vector<int>& child_otuIndex, vector<int>& child_seqIndex, vector<double>& child_singleTau){
1739
1740         try{
1741                 vector<double> newTau(numOTUs,0);
1742                 vector<double> norms(numSeqs, 0);
1743                 child_otuIndex.resize(0);
1744                 child_seqIndex.resize(0);
1745                 child_singleTau.resize(0);
1746
1747                 for(int i=startSeq;i<stopSeq;i++){
1748                         double offset = 1e8;
1749                         int indexOffset = i * numOTUs;
1750
1751
1752                         for(int j=0;j<numOTUs;j++){
1753                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1754                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1755                                 }
1756
1757                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1758                                         offset = dist[indexOffset + j];
1759                                 }
1760                         }
1761
1762                         for(int j=0;j<numOTUs;j++){
1763                                 if(weight[j] > MIN_WEIGHT){
1764                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1765                                         norms[i] += newTau[j];
1766                                 }
1767                                 else{
1768                                         newTau[j] = 0.0;
1769                                 }
1770                         }
1771
1772                         for(int j=0;j<numOTUs;j++){
1773                                 newTau[j] /= norms[i];
1774
1775                                 if(newTau[j] > MIN_TAU){
1776                                         child_otuIndex.push_back(j);
1777                                         child_seqIndex.push_back(i);
1778                                         child_singleTau.push_back(newTau[j]);
1779                                 }
1780                         }
1781                 }
1782         }
1783         catch(exception& e) {
1784                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChild");
1785                 exit(1);
1786         }
1787 }
1788
1789 /**************************************************************************************************/
1790
1791 void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){
1792
1793         try{
1794
1795                 int total = 0;
1796                 vector<double> newTau(numOTUs,0);
1797                 vector<double> norms(numSeqs, 0);
1798                 nSeqsPerOTU.assign(numOTUs, 0);
1799
1800                 for(int i=startSeq;i<stopSeq;i++){
1801                         int indexOffset = i * numOTUs;
1802
1803                         double offset = 1e8;
1804
1805                         for(int j=0;j<numOTUs;j++){
1806                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1807                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1808                                 }
1809
1810                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1811                                         offset = dist[indexOffset + j];
1812                                 }
1813                         }
1814
1815                         for(int j=0;j<numOTUs;j++){
1816                                 if(weight[j] > MIN_WEIGHT){
1817                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1818                                         norms[i] += newTau[j];
1819                                 }
1820                                 else{
1821                                         newTau[j] = 0.0;
1822                                 }
1823                         }
1824
1825                         for(int j=0;j<numOTUs;j++){
1826                                 newTau[j] /= norms[i];
1827                         }
1828
1829                         for(int j=0;j<numOTUs;j++){
1830                                 if(newTau[j] > MIN_TAU){
1831
1832                                         int oldTotal = total;
1833
1834                                         total++;
1835
1836                                         singleTau.resize(total, 0);
1837                                         seqNumber.resize(total, 0);
1838                                         seqIndex.resize(total, 0);
1839
1840                                         singleTau[oldTotal] = newTau[j];
1841
1842                                         aaP[j][nSeqsPerOTU[j]] = oldTotal;
1843                                         aaI[j][nSeqsPerOTU[j]] = i;
1844                                         nSeqsPerOTU[j]++;
1845                                 }
1846                         }
1847                 }
1848         }
1849         catch(exception& e) {
1850                 m->errorOut(e, "ShhherCommand", "calcNewDistancesParent");
1851                 exit(1);
1852         }
1853 }
1854
1855 /**************************************************************************************************/
1856
1857 void ShhherCommand::setOTUs(){
1858
1859         try {
1860                 vector<double> bigTauMatrix(numOTUs * numSeqs, 0.0000);
1861
1862                 for(int i=0;i<numOTUs;i++){
1863                         for(int j=0;j<nSeqsPerOTU[i];j++){
1864                                 int index = cumNumSeqs[i] + j;
1865                                 double tauValue = singleTau[seqNumber[index]];
1866                                 int sIndex = seqIndex[index];
1867                                 bigTauMatrix[sIndex * numOTUs + i] = tauValue;
1868                         }
1869                 }
1870
1871                 for(int i=0;i<numSeqs;i++){
1872                         double maxTau = -1.0000;
1873                         int maxOTU = -1;
1874                         for(int j=0;j<numOTUs;j++){
1875                                 if(bigTauMatrix[i * numOTUs + j] > maxTau){
1876                                         maxTau = bigTauMatrix[i * numOTUs + j];
1877                                         maxOTU = j;
1878                                 }
1879                         }
1880
1881                         otuData[i] = maxOTU;
1882                 }
1883
1884                 nSeqsPerOTU.assign(numOTUs, 0);
1885
1886                 for(int i=0;i<numSeqs;i++){
1887                         int index = otuData[i];
1888
1889                         singleTau[i] = 1.0000;
1890                         dist[i] = 0.0000;
1891
1892                         aaP[index][nSeqsPerOTU[index]] = i;
1893                         aaI[index][nSeqsPerOTU[index]] = i;
1894
1895                         nSeqsPerOTU[index]++;
1896                 }
1897                 fill();
1898         }
1899         catch(exception& e) {
1900                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
1901                 exit(1);
1902         }
1903 }
1904
1905 /**************************************************************************************************/
1906
1907 void ShhherCommand::writeQualities(vector<int> otuCounts){
1908
1909         try {
1910                 string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.qual";
1911
1912                 ofstream qualityFile;
1913                 m->openOutputFile(qualityFileName, qualityFile);
1914
1915                 qualityFile.setf(ios::fixed, ios::floatfield);
1916                 qualityFile.setf(ios::showpoint);
1917                 qualityFile << setprecision(6);
1918
1919                 vector<vector<int> > qualities(numOTUs);
1920                 vector<double> pr(HOMOPS, 0);
1921
1922
1923                 for(int i=0;i<numOTUs;i++){
1924                         int index = 0;
1925                         int base = 0;
1926
1927                         if(nSeqsPerOTU[i] > 0){
1928                                 qualities[i].assign(1024, -1);
1929
1930                                 while(index < numFlowCells){
1931                                         double maxPrValue = 1e8;
1932                                         short maxPrIndex = -1;
1933                                         double count = 0.0000;
1934
1935                                         pr.assign(HOMOPS, 0);
1936
1937                                         for(int j=0;j<nSeqsPerOTU[i];j++){
1938                                                 int lIndex = cumNumSeqs[i] + j;
1939                                                 double tauValue = singleTau[seqNumber[lIndex]];
1940                                                 int sequenceIndex = aaI[i][j];
1941                                                 short intensity = flowDataIntI[sequenceIndex * numFlowCells + index];
1942
1943                                                 count += tauValue;
1944
1945                                                 for(int s=0;s<HOMOPS;s++){
1946                                                         pr[s] += tauValue * singleLookUp[s * NUMBINS + intensity];
1947                                                 }
1948                                         }
1949
1950                                         maxPrIndex = uniqueFlowgrams[centroids[i] * numFlowCells + index];
1951                                         maxPrValue = pr[maxPrIndex];
1952
1953                                         if(count > MIN_COUNT){
1954                                                 double U = 0.0000;
1955                                                 double norm = 0.0000;
1956
1957                                                 for(int s=0;s<HOMOPS;s++){
1958                                                         norm += exp(-(pr[s] - maxPrValue));
1959                                                 }
1960
1961                                                 for(int s=1;s<=maxPrIndex;s++){
1962                                                         int value = 0;
1963                                                         double temp = 0.0000;
1964
1965                                                         U += exp(-(pr[s-1]-maxPrValue))/norm;
1966
1967                                                         if(U>0.00){
1968                                                                 temp = log10(U);
1969                                                         }
1970                                                         else{
1971                                                                 temp = -10.1;
1972                                                         }
1973                                                         temp = floor(-10 * temp);
1974                                                         value = (int)floor(temp);
1975                                                         if(value > 100){        value = 100;    }
1976
1977                                                         qualities[i][base] = (int)value;
1978                                                         base++;
1979                                                 }
1980                                         }
1981
1982                                         index++;
1983                                 }
1984                         }
1985
1986
1987                         if(otuCounts[i] > 0){
1988                                 qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
1989
1990                                 int j=4;        //need to get past the first four bases
1991                                 while(qualities[i][j] != -1){
1992                                         qualityFile << qualities[i][j] << ' ';
1993                                         j++;
1994                                 }
1995                                 qualityFile << endl;
1996                         }
1997                 }
1998                 qualityFile.close();
1999
2000         }
2001         catch(exception& e) {
2002                 m->errorOut(e, "ShhherCommand", "writeQualities");
2003                 exit(1);
2004         }
2005 }
2006
2007 /**************************************************************************************************/
2008
2009 void ShhherCommand::writeSequences(vector<int> otuCounts){
2010         try {
2011                 string bases = "TACG";
2012
2013                 string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
2014                 ofstream fastaFile;
2015                 m->openOutputFile(fastaFileName, fastaFile);
2016
2017                 vector<string> names(numOTUs, "");
2018
2019                 for(int i=0;i<numOTUs;i++){
2020                         int index = centroids[i];
2021
2022                         if(otuCounts[i] > 0){
2023                                 fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
2024
2025                                 for(int j=8;j<numFlowCells;j++){
2026
2027                                         char base = bases[j % 4];
2028                                         for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
2029                                                 fastaFile << base;
2030                                         }
2031                                 }
2032                                 fastaFile << endl;
2033                         }
2034                 }
2035                 fastaFile.close();
2036
2037                 if(compositeFASTAFileName != ""){
2038                         m->appendFiles(fastaFileName, compositeFASTAFileName);
2039                 }
2040         }
2041         catch(exception& e) {
2042                 m->errorOut(e, "ShhherCommand", "writeSequences");
2043                 exit(1);
2044         }
2045 }
2046
2047 /**************************************************************************************************/
2048
2049 void ShhherCommand::writeNames(vector<int> otuCounts){
2050         try {
2051                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.final.names";
2052                 ofstream nameFile;
2053                 m->openOutputFile(nameFileName, nameFile);
2054
2055                 for(int i=0;i<numOTUs;i++){
2056                         if(otuCounts[i] > 0){
2057                                 nameFile << seqNameVector[aaI[i][0]] << '\t' << seqNameVector[aaI[i][0]];
2058
2059                                 for(int j=1;j<nSeqsPerOTU[i];j++){
2060                                         nameFile << ',' << seqNameVector[aaI[i][j]];
2061                                 }
2062
2063                                 nameFile << endl;
2064                         }
2065                 }
2066                 nameFile.close();
2067         }
2068         catch(exception& e) {
2069                 m->errorOut(e, "ShhherCommand", "writeNames");
2070                 exit(1);
2071         }
2072 }
2073
2074 /**************************************************************************************************/
2075
2076 void ShhherCommand::writeGroups(){
2077         try {
2078                 string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
2079                 string groupFileName = fileRoot + ".pn.groups";
2080                 ofstream groupFile;
2081                 m->openOutputFile(groupFileName, groupFile);
2082
2083                 for(int i=0;i<numSeqs;i++){
2084                         groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
2085                 }
2086                 groupFile.close();
2087         }
2088         catch(exception& e) {
2089                 m->errorOut(e, "ShhherCommand", "writeGroups");
2090                 exit(1);
2091         }
2092 }
2093
2094 /**************************************************************************************************/
2095
2096 void ShhherCommand::writeClusters(vector<int> otuCounts){
2097         try {
2098                 string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.counts";
2099                 ofstream otuCountsFile;
2100                 m->openOutputFile(otuCountsFileName, otuCountsFile);
2101
2102                 string bases = "TACG";
2103
2104                 for(int i=0;i<numOTUs;i++){
2105                         //output the translated version of the centroid sequence for the otu
2106                         if(otuCounts[i] > 0){
2107                                 int index = centroids[i];
2108
2109                                 otuCountsFile << "ideal\t";
2110                                 for(int j=8;j<numFlowCells;j++){
2111                                         char base = bases[j % 4];
2112                                         for(int s=0;s<uniqueFlowgrams[index * numFlowCells + j];s++){
2113                                                 otuCountsFile << base;
2114                                         }
2115                                 }
2116                                 otuCountsFile << endl;
2117
2118                                 for(int j=0;j<nSeqsPerOTU[i];j++){
2119                                         int sequence = aaI[i][j];
2120                                         otuCountsFile << seqNameVector[sequence] << '\t';
2121
2122                                         for(int k=8;k<lengths[sequence];k++){
2123                                                 char base = bases[k % 4];
2124                                                 int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
2125
2126                                                 for(int s=0;s<freq;s++){
2127                                                         otuCountsFile << base;
2128                                                 }
2129                                         }
2130                                         otuCountsFile << endl;
2131                                 }
2132                                 otuCountsFile << endl;
2133                         }
2134                 }
2135                 otuCountsFile.close();
2136         }
2137         catch(exception& e) {
2138                 m->errorOut(e, "ShhherCommand", "writeClusters");
2139                 exit(1);
2140         }
2141 }
2142
2143 //**********************************************************************************************************************