bayesian.cpp

   1 /*
   2  *  bayesian.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/3/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "bayesian.h"
  11 #include "kmer.hpp"
  12 #include "phylosummary.h"
  13 #include "referencedb.h"
  14 /**************************************************************************************************/
  15 Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid, bool f, bool sh) :
  16 Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
  17         try {
  18                 ReferenceDB* rdb = ReferenceDB::getInstance();
  19
  20                 threadID = tid;
  21                 flip = f;
  22         shortcuts = sh;
  23                 string baseName = tempFile;
  24
  25                 if (baseName == "saved") { baseName = rdb->getSavedReference(); }
  26
  27                 string baseTName = tfile;
  28                 if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
  29
  30                 /************calculate the probablity that each word will be in a specific taxonomy*************/
  31                 string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
  32                 string tempfileroot = m->getRootName(m->getSimpleName(baseName));
  33                 string phyloTreeName = tfileroot + "tree.train";
  34                 string phyloTreeSumName = tfileroot + "tree.sum";
  35                 string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
  36                 string probFileName2 = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.numNonZero";
  37
  38                 ofstream out;
  39                 ofstream out2;
  40
  41                 ifstream phyloTreeTest(phyloTreeName.c_str());
  42                 ifstream probFileTest2(probFileName2.c_str());
  43                 ifstream probFileTest(probFileName.c_str());
  44                 ifstream probFileTest3(phyloTreeSumName.c_str());
  45
  46                 int start = time(NULL);
  47
  48                 //if they are there make sure they were created after this release date
  49                 bool FilesGood = false;
  50                 if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
  51                         FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
  52                 }
  53
  54                 //if you want to save, but you dont need to calculate then just read
  55                 if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood && (tempFile != "saved")) {
  56                         ifstream saveIn;
  57                         m->openInputFile(tempFile, saveIn);
  58
  59                         while (!saveIn.eof()) {
  60                                 Sequence temp(saveIn);
  61                                 m->gobble(saveIn);
  62
  63                                 rdb->referenceSeqs.push_back(temp);
  64                         }
  65                         saveIn.close();
  66                 }
  67
  68                 if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
  69                         if (tempFile == "saved") { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");     m->mothurOutEndLine(); }
  70
  71                         m->mothurOut("Reading template taxonomy...     "); cout.flush();
  72
  73                         phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
  74
  75                         m->mothurOut("DONE."); m->mothurOutEndLine();
  76
  77                         genusNodes = phyloTree->getGenusNodes();
  78                         genusTotals = phyloTree->getGenusTotals();
  79
  80                         if (tfile == "saved") {
  81                                 m->mothurOutEndLine();  m->mothurOut("Using probabilties from " + rdb->getSavedTaxonomy() + " that are saved in memory...    ");        cout.flush();;
  82                                 wordGenusProb = rdb->wordGenusProb;
  83                                 WordPairDiffArr = rdb->WordPairDiffArr;
  84                         }else {
  85                                 m->mothurOut("Reading template probabilities...     "); cout.flush();
  86                                 readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
  87                         }
  88
  89                         //save probabilities
  90                         if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
  91                 }else{
  92
  93                         //create search database and names vector
  94                         generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
  95
  96                         //prevents errors caused by creating shortcut files if you had an error in the sanity check.
  97                         if (m->control_pressed) {  m->mothurRemove(phyloTreeName);  m->mothurRemove(probFileName); m->mothurRemove(probFileName2); }
  98                         else{
  99                                 genusNodes = phyloTree->getGenusNodes();
 100                                 genusTotals = phyloTree->getGenusTotals();
 101
 102                                 m->mothurOut("Calculating template taxonomy tree...     "); cout.flush();
 103
 104                                 phyloTree->printTreeNodes(phyloTreeName);
 105
 106                                 m->mothurOut("DONE."); m->mothurOutEndLine();
 107
 108                                 m->mothurOut("Calculating template probabilities...     "); cout.flush();
 109
 110                                 numKmers = database->getMaxKmer() + 1;
 111
 112                                 //initialze probabilities
 113                                 wordGenusProb.resize(numKmers);
 114                                 WordPairDiffArr.resize(numKmers);
 115
 116                                 for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 117                 ofstream out;
 118                                 ofstream out2;
 119
 120                                 #ifdef USE_MPI
 121                                         int pid;
 122                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 123
 124                                         if (pid == 0) {
 125                                 #endif
 126
 127
 128                 if (shortcuts) {
 129                     m->openOutputFile(probFileName, out);
 130
 131                     //output mothur version
 132                     out << "#" << m->getVersion() << endl;
 133
 134                     out << numKmers << endl;
 135
 136                     m->openOutputFile(probFileName2, out2);
 137
 138                     //output mothur version
 139                     out2 << "#" << m->getVersion() << endl;
 140                 }
 141
 142                                 #ifdef USE_MPI
 143                                         }
 144                                 #endif
 145
 146                                 //for each word
 147                                 for (int i = 0; i < numKmers; i++) {
 148                     //m->mothurOut("[DEBUG]: kmer = " + toString(i) + "\n");
 149
 150                                         if (m->control_pressed) {  break; }
 151
 152                                         #ifdef USE_MPI
 153                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 154
 155                                                 if (pid == 0) {
 156                                         #endif
 157
 158                     if (shortcuts) {  out << i << '\t'; }
 159
 160                                         #ifdef USE_MPI
 161                                                 }
 162                                         #endif
 163
 164                                         vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
 165
 166                                         //for each sequence with that word
 167                     vector<int> count; count.resize(genusNodes.size(), 0);
 168                                         for (int j = 0; j < seqsWithWordi.size(); j++) {
 169                                                 int temp = phyloTree->getGenusIndex(names[seqsWithWordi[j]]);
 170                                                 count[temp]++;  //increment count of seq in this genus who have this word
 171                                         }
 172
 173                                         //probabilityInTemplate = (# of seqs with that word in template + 0.50) / (total number of seqs in template + 1);
 174                                         float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
 175                                         diffPair tempProb(log(probabilityInTemplate), 0.0);
 176                                         WordPairDiffArr[i] = tempProb;
 177
 178                                         int numNotZero = 0;
 179                                         for (int k = 0; k < genusNodes.size(); k++) {
 180                                                 //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
 181
 182
 183                                                 wordGenusProb[i][k] = log((count[k] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
 184
 185                                                 if (count[k] != 0) {
 186                                                         #ifdef USE_MPI
 187                                                                 int pid;
 188                                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 189
 190                                                                 if (pid == 0) {
 191                                                         #endif
 192
 193                             if (shortcuts) { out << k << '\t' << wordGenusProb[i][k] << '\t' ; }
 194
 195                                                         #ifdef USE_MPI
 196                                                                 }
 197                                                         #endif
 198
 199                                                         numNotZero++;
 200                                                 }
 201                                         }
 202
 203                                         #ifdef USE_MPI
 204                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 205
 206                                                 if (pid == 0) {
 207                                         #endif
 208
 209                             if (shortcuts) {
 210                                 out << endl;
 211                                 out2 << probabilityInTemplate << '\t' << numNotZero << '\t' << log(probabilityInTemplate) << endl;
 212                             }
 213
 214                                         #ifdef USE_MPI
 215                                                 }
 216                                         #endif
 217                                 }
 218
 219                                 #ifdef USE_MPI
 220                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 221
 222                                         if (pid == 0) {
 223                                 #endif
 224
 225                         if (shortcuts) {
 226                             out.close();
 227                             out2.close();
 228                         }
 229                                 #ifdef USE_MPI
 230                                         }
 231                                 #endif
 232
 233                                 //read in new phylotree with less info. - its faster
 234                                 ifstream phyloTreeTest(phyloTreeName.c_str());
 235                                 delete phyloTree;
 236
 237                                 phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
 238
 239                                 //save probabilities
 240                                 if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
 241                         }
 242                 }
 243
 244         if (m->debug) { m->mothurOut("[DEBUG]: about to generateWordPairDiffArr\n"); }
 245                 generateWordPairDiffArr();
 246         if (m->debug) { m->mothurOut("[DEBUG]: done generateWordPairDiffArr\n"); }
 247
 248                 //save probabilities
 249                 if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
 250
 251                 m->mothurOut("DONE."); m->mothurOutEndLine();
 252                 m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "Bayesian", "Bayesian");
 256                 exit(1);
 257         }
 258 }
 259 /**************************************************************************************************/
 260 Bayesian::~Bayesian() {
 261         try {
 262         if (phyloTree != NULL) { delete phyloTree; }
 263         if (database != NULL) {  delete database; }
 264         }
 265         catch(exception& e) {
 266                 m->errorOut(e, "Bayesian", "~Bayesian");
 267                 exit(1);
 268         }
 269 }
 270
 271 /**************************************************************************************************/
 272 string Bayesian::getTaxonomy(Sequence* seq) {
 273         try {
 274                 string tax = "";
 275                 Kmer kmer(kmerSize);
 276                 flipped = false;
 277
 278                 //get words contained in query
 279                 //getKmerString returns a string where the index in the string is hte kmer number
 280                 //and the character at that index can be converted to be the number of times that kmer was seen
 281                 string queryKmerString = kmer.getKmerString(seq->getUnaligned());
 282
 283                 vector<int> queryKmers;
 284                 for (int i = 0; i < queryKmerString.length()-1; i++) {  // the -1 is to ignore any kmer with an N in it
 285                         if (queryKmerString[i] != '!') { //this kmer is in the query
 286                                 queryKmers.push_back(i);
 287                         }
 288                 }
 289
 290                 //if user wants to test reverse compliment and its reversed use that instead
 291                 if (flip) {
 292                         if (isReversed(queryKmers)) {
 293                                 flipped = true;
 294                                 seq->reverseComplement();
 295                                 queryKmerString = kmer.getKmerString(seq->getUnaligned());
 296                                 queryKmers.clear();
 297                                 for (int i = 0; i < queryKmerString.length()-1; i++) {  // the -1 is to ignore any kmer with an N in it
 298                                         if (queryKmerString[i] != '!') { //this kmer is in the query
 299                                                 queryKmers.push_back(i);
 300                                         }
 301                                 }
 302                         }
 303                 }
 304
 305                 if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + " is bad. It has no kmers of length " + toString(kmerSize) + "."); m->mothurOutEndLine(); simpleTax = "unknown;";  return "unknown;"; }
 306
 307
 308                 int index = getMostProbableTaxonomy(queryKmers);
 309
 310                 if (m->control_pressed) { return tax; }
 311
 312                 //bootstrap - to set confidenceScore
 313                 int numToSelect = queryKmers.size() / 8;
 314
 315         if (m->debug) {  m->mothurOut(seq->getName() + "\t"); }
 316
 317                 tax = bootstrapResults(queryKmers, index, numToSelect);
 318
 319         if (m->debug) {  m->mothurOut("\n"); }
 320
 321                 return tax;
 322         }
 323         catch(exception& e) {
 324                 m->errorOut(e, "Bayesian", "getTaxonomy");
 325                 exit(1);
 326         }
 327 }
 328 /**************************************************************************************************/
 329 string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 330         try {
 331
 332                 map<int, int> confidenceScores;
 333
 334                 //initialize confidences to 0
 335                 int seqIndex = tax;
 336                 TaxNode seq = phyloTree->get(tax);
 337                 confidenceScores[tax] = 0;
 338
 339                 while (seq.level != 0) { //while you are not at the root
 340                         seqIndex = seq.parent;
 341                         confidenceScores[seqIndex] = 0;
 342                         seq = phyloTree->get(seq.parent);
 343                 }
 344
 345                 map<int, int>::iterator itBoot;
 346                 map<int, int>::iterator itBoot2;
 347                 map<int, int>::iterator itConvert;
 348
 349                 for (int i = 0; i < iters; i++) {
 350                         if (m->control_pressed) { return "control"; }
 351
 352                         vector<int> temp;
 353                         for (int j = 0; j < numToSelect; j++) {
 354                                 int index = int(rand() % kmers.size());
 355
 356                                 //add word to temp
 357                                 temp.push_back(kmers[index]);
 358                         }
 359
 360                         //get taxonomy
 361                         int newTax = getMostProbableTaxonomy(temp);
 362                         //int newTax = 1;
 363                         TaxNode taxonomyTemp = phyloTree->get(newTax);
 364
 365                         //add to confidence results
 366                         while (taxonomyTemp.level != 0) { //while you are not at the root
 367                                 itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
 368
 369                                 if (itBoot2 != confidenceScores.end()) { //this is a classification we need a confidence for
 370                                         (itBoot2->second)++;
 371                                 }
 372
 373                                 newTax = taxonomyTemp.parent;
 374                                 taxonomyTemp = phyloTree->get(newTax);
 375                         }
 376
 377                 }
 378
 379                 string confidenceTax = "";
 380                 simpleTax = "";
 381
 382                 int seqTaxIndex = tax;
 383                 TaxNode seqTax = phyloTree->get(tax);
 384
 385
 386                 while (seqTax.level != 0) { //while you are not at the root
 387
 388                                 itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
 389
 390                                 int confidence = 0;
 391                                 if (itBoot2 != confidenceScores.end()) { //already in confidence scores
 392                                         confidence = itBoot2->second;
 393                                 }
 394
 395                 if (m->debug) { m->mothurOut(seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");"); }
 396
 397                                 if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
 398                                         confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
 399                                         simpleTax = seqTax.name + ";" + simpleTax;
 400                                 }
 401
 402                                 seqTaxIndex = seqTax.parent;
 403                                 seqTax = phyloTree->get(seqTax.parent);
 404                 }
 405
 406                 if (confidenceTax == "") { confidenceTax = "unknown;"; simpleTax = "unknown;";  }
 407
 408                 return confidenceTax;
 409
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "Bayesian", "bootstrapResults");
 413                 exit(1);
 414         }
 415 }
 416 /**************************************************************************************************/
 417 int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
 418         try {
 419                 int indexofGenus = 0;
 420
 421                 double maxProbability = -1000000.0;
 422                 //find taxonomy with highest probability that this sequence is from it
 423
 424
 425 //              cout << genusNodes.size() << endl;
 426
 427
 428                 for (int k = 0; k < genusNodes.size(); k++) {
 429                         //for each taxonomy calc its probability
 430
 431                         double prob = 0.0000;
 432                         for (int i = 0; i < queryKmer.size(); i++) {
 433                                 prob += wordGenusProb[queryKmer[i]][k];
 434                         }
 435
 436 //                      cout << phyloTree->get(genusNodes[k]).name << '\t' << prob << endl;
 437
 438                         //is this the taxonomy with the greatest probability?
 439                         if (prob > maxProbability) {
 440                                 indexofGenus = genusNodes[k];
 441                                 maxProbability = prob;
 442                         }
 443                 }
 444
 445
 446                 return indexofGenus;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "Bayesian", "getMostProbableTaxonomy");
 450                 exit(1);
 451         }
 452 }
 453 //********************************************************************************************************************
 454 //if it is more probable that the reverse compliment kmers are in the template, then we assume the sequence is reversed.
 455 bool Bayesian::isReversed(vector<int>& queryKmers){
 456         try{
 457                 bool reversed = false;
 458                 float prob = 0;
 459                 float reverseProb = 0;
 460
 461         for (int i = 0; i < queryKmers.size(); i++){
 462             int kmer = queryKmers[i];
 463             if (kmer >= 0){
 464                 prob += WordPairDiffArr[kmer].prob;
 465                                 reverseProb += WordPairDiffArr[kmer].reverseProb;
 466             }
 467         }
 468
 469         if (reverseProb > prob){ reversed = true; }
 470
 471                 return reversed;
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "Bayesian", "isReversed");
 475                 exit(1);
 476         }
 477 }
 478 //********************************************************************************************************************
 479 int Bayesian::generateWordPairDiffArr(){
 480         try{
 481                 Kmer kmer(kmerSize);
 482                 for (int i = 0; i < WordPairDiffArr.size(); i++) {
 483                         int reversedWord = kmer.getReverseKmerNumber(i);
 484                         WordPairDiffArr[i].reverseProb = WordPairDiffArr[reversedWord].prob;
 485                 }
 486
 487                 return 0;
 488         }catch(exception& e) {
 489                 m->errorOut(e, "Bayesian", "generateWordPairDiffArr");
 490                 exit(1);
 491         }
 492 }
 493 /*************************************************************************************************
 494 map<string, int> Bayesian::parseTaxMap(string newTax) {
 495         try{
 496
 497                 map<string, int> parsed;
 498
 499                 newTax = newTax.substr(0, newTax.length()-1);  //get rid of last ';'
 500
 501                 //parse taxonomy
 502                 string individual;
 503                 while (newTax.find_first_of(';') != -1) {
 504                         individual = newTax.substr(0,newTax.find_first_of(';'));
 505                         newTax = newTax.substr(newTax.find_first_of(';')+1, newTax.length());
 506                         parsed[individual] = 1;
 507                 }
 508
 509                 //get last one
 510                 parsed[newTax] = 1;
 511
 512                 return parsed;
 513
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "Bayesian", "parseTax");
 517                 exit(1);
 518         }
 519 }
 520 **************************************************************************************************/
 521 void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string inNumName) {
 522         try{
 523
 524                 #ifdef USE_MPI
 525
 526                         int pid, num, num2, processors;
 527                         vector<unsigned long long> positions;
 528                         vector<unsigned long long> positions2;
 529
 530                         MPI_Status status;
 531                         MPI_File inMPI;
 532                         MPI_File inMPI2;
 533                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 534                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 535                         int tag = 2001;
 536
 537                         char inFileName[1024];
 538                         strcpy(inFileName, inNumName.c_str());
 539
 540                         char inFileName2[1024];
 541                         strcpy(inFileName2, inName.c_str());
 542
 543                         MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 544                         MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2);  //comm, filename, mode, info, filepointer
 545
 546                         if (pid == 0) {
 547                                 positions = m->setFilePosEachLine(inNumName, num);
 548                                 positions2 = m->setFilePosEachLine(inName, num2);
 549
 550                                 for(int i = 1; i < processors; i++) {
 551                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 552                                         MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 553
 554                                         MPI_Send(&num2, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 555                                         MPI_Send(&positions2[0], (num2+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 556                                 }
 557
 558                         }else{
 559                                 MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 560                                 positions.resize(num+1);
 561                                 MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 562
 563                                 MPI_Recv(&num2, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 564                                 positions2.resize(num2+1);
 565                                 MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 566                         }
 567
 568                         //read version
 569                         int length = positions2[1] - positions2[0];
 570                         char* buf5 = new char[length];
 571
 572                         MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
 573                         delete buf5;
 574
 575                         //read numKmers
 576                         length = positions2[2] - positions2[1];
 577                         char* buf = new char[length];
 578
 579                         MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
 580
 581                         string tempBuf = buf;
 582                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 583                         delete buf;
 584
 585                         istringstream iss (tempBuf,istringstream::in);
 586                         iss >> numKmers;
 587
 588                         //initialze probabilities
 589                         wordGenusProb.resize(numKmers);
 590
 591                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 592
 593                         int kmer, name;
 594                         vector<int> numbers; numbers.resize(numKmers);
 595                         float prob;
 596                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 597                         WordPairDiffArr.resize(numKmers);
 598
 599                         //read version
 600                         length = positions[1] - positions[0];
 601                         char* buf6 = new char[length];
 602
 603                         MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
 604                         delete buf6;
 605
 606                         //read file
 607                         for(int i=1;i<num;i++){
 608                                 //read next sequence
 609                                 length = positions[i+1] - positions[i];
 610                                 char* buf4 = new char[length];
 611
 612                                 MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
 613
 614                                 tempBuf = buf4;
 615                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 616                                 delete buf4;
 617
 618                                 istringstream iss (tempBuf,istringstream::in);
 619                                 float probTemp;
 620                                 iss >> zeroCountProb[i] >> numbers[i] >> probTemp;
 621                                 WordPairDiffArr[i].prob = probTemp;
 622
 623                         }
 624
 625                         MPI_File_close(&inMPI);
 626
 627                         for(int i=2;i<num2;i++){
 628                                 //read next sequence
 629                                 length = positions2[i+1] - positions2[i];
 630                                 char* buf4 = new char[length];
 631
 632                                 MPI_File_read_at(inMPI2, positions2[i], buf4, length, MPI_CHAR, &status);
 633
 634                                 tempBuf = buf4;
 635                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 636                                 delete buf4;
 637
 638                                 istringstream iss (tempBuf,istringstream::in);
 639
 640                                 iss >> kmer;
 641
 642                                 //set them all to zero value
 643                                 for (int i = 0; i < genusNodes.size(); i++) {
 644                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 645                                 }
 646
 647                                 //get probs for nonzero values
 648                                 for (int i = 0; i < numbers[kmer]; i++) {
 649                                         iss >> name >> prob;
 650                                         wordGenusProb[kmer][name] = prob;
 651                                 }
 652
 653                         }
 654                         MPI_File_close(&inMPI2);
 655                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 656                 #else
 657                         //read version
 658                         string line = m->getline(in); m->gobble(in);
 659
 660                         in >> numKmers; m->gobble(in);
 661                         //cout << threadID << '\t' << line << '\t' << numKmers << &in << '\t' << &inNum << '\t' << genusNodes.size() << endl;
 662                         //initialze probabilities
 663                         wordGenusProb.resize(numKmers);
 664
 665                         for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
 666
 667                         int kmer, name, count;  count = 0;
 668                         vector<int> num; num.resize(numKmers);
 669                         float prob;
 670                         vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
 671                         WordPairDiffArr.resize(numKmers);
 672
 673                         //read version
 674                         string line2 = m->getline(inNum); m->gobble(inNum);
 675                         float probTemp;
 676                 //cout << threadID << '\t' << line2 << '\t' << this << endl;
 677                         while (inNum) {
 678                                 inNum >> zeroCountProb[count] >> num[count] >> probTemp;
 679                                 WordPairDiffArr[count].prob = probTemp;
 680                                 count++;
 681                                 m->gobble(inNum);
 682                                 //cout << threadID << '\t' << count << endl;
 683                         }
 684                         inNum.close();
 685                 //cout << threadID << '\t' << "here1 " << &wordGenusProb << '\t' << &num << endl; //
 686                 //cout << threadID << '\t' << &genusTotals << '\t' << endl;
 687                 //cout << threadID << '\t' << genusNodes.size() << endl;
 688                         while(in) {
 689                                 in >> kmer;
 690                         //cout << threadID << '\t' << kmer << endl;
 691                                 //set them all to zero value
 692                                 for (int i = 0; i < genusNodes.size(); i++) {
 693                                         wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
 694                                 }
 695                         //cout << threadID << '\t' << num[kmer] << "here" << endl;
 696                                 //get probs for nonzero values
 697                                 for (int i = 0; i < num[kmer]; i++) {
 698                                         in >> name >> prob;
 699                                         wordGenusProb[kmer][name] = prob;
 700                                 }
 701
 702                                 m->gobble(in);
 703                         }
 704                         in.close();
 705                 //cout << threadID << '\t' << "here" << endl;
 706                 #endif
 707         }
 708         catch(exception& e) {
 709                 m->errorOut(e, "Bayesian", "readProbFile");
 710                 exit(1);
 711         }
 712 }
 713 /**************************************************************************************************/
 714 bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
 715         try {
 716
 717                 bool good = true;
 718
 719                 vector<string> lines;
 720                 lines.push_back(m->getline(file1));
 721                 lines.push_back(m->getline(file2));
 722                 lines.push_back(m->getline(file3));
 723                 lines.push_back(m->getline(file4));
 724
 725                 //before we added this check
 726                 if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) {  good = false;  }
 727                 else {
 728                         //rip off #
 729                         for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1);  }
 730
 731                         //get mothurs current version
 732                         string version = m->getVersion();
 733
 734                         vector<string> versionVector;
 735                         m->splitAtChar(version, versionVector, '.');
 736
 737                         //check each files version
 738                         for (int i = 0; i < lines.size(); i++) {
 739                                 vector<string> linesVector;
 740                                 m->splitAtChar(lines[i], linesVector, '.');
 741
 742                                 if (versionVector.size() != linesVector.size()) { good = false; break; }
 743                                 else {
 744                                         for (int j = 0; j < versionVector.size(); j++) {
 745                                                 int num1, num2;
 746                                                 convert(versionVector[j], num1);
 747                                                 convert(linesVector[j], num2);
 748
 749                                                 //if mothurs version is newer than this files version, then we want to remake it
 750                                                 if (num1 > num2) {  good = false; break;  }
 751                                         }
 752                                 }
 753
 754                                 if (!good) { break; }
 755                         }
 756                 }
 757
 758                 if (!good) {  file1.close(); file2.close(); file3.close(); file4.close();  }
 759                 else { file1.seekg(0);  file2.seekg(0);  file3.seekg(0);  file4.seekg(0);  }
 760
 761                 return good;
 762         }
 763         catch(exception& e) {
 764                 m->errorOut(e, "Bayesian", "checkReleaseDate");
 765                 exit(1);
 766         }
 767 }
 768 /**************************************************************************************************/
 769
 770
 771
 772
 773
 774