pintail.cpp

   1 /*
   2  *  pintail.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "pintail.h"
  11 #include "ignoregaps.h"
  12
  13 //***************************************************************************************************************
  14
  15 Pintail::Pintail(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
  16 //***************************************************************************************************************
  17
  18 Pintail::~Pintail() {
  19         try {
  20                 for (int i = 0; i < querySeqs.size(); i++)              {  delete querySeqs[i];         }
  21                 for (int i = 0; i < templateSeqs.size(); i++)   {  delete templateSeqs[i];      }
  22
  23                 if (processors != 1) {   for (int i = 0; i < bestfit.size(); i++)       {  delete bestfit[i];   }  }
  24         }
  25         catch(exception& e) {
  26                 errorOut(e, "Pintail", "~Pintail");
  27                 exit(1);
  28         }
  29 }
  30 //***************************************************************************************************************
  31 void Pintail::print(ostream& out) {
  32         try {
  33
  34                 for (int i = 0; i < querySeqs.size(); i++) {
  35
  36                         int index = ceil(deviation[i]);
  37 float quan = 2.64 * log10(deviation[i]) + 1.46;
  38 cout << "dist = " << index << endl;
  39 cout << "de = "  << DE[i] << endl;
  40 cout << "mallard quantile = " << quan << endl;
  41 cout << "my quantile = " << quantiles[index][4] << endl;
  42
  43                         //is your DE value higher than the 95%
  44                         string chimera;
  45                         if (DE[i] > quantiles[index][4])                {       chimera = "Yes";        }
  46                         else                                                                    {       chimera = "No";         }
  47
  48                         out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
  49                         if (chimera == "Yes") {
  50                                 mothurOut(querySeqs[i]->getName() + "\tdiv: " + toString(deviation[i]) + "\tstDev: " + toString(DE[i]) + "\tchimera flag: " + chimera); mothurOutEndLine();
  51                         }
  52                         out << "Observed\t";
  53
  54                         for (int j = 0; j < obsDistance[i].size(); j++) {  out << obsDistance[i][j] << '\t';  }
  55                         out << endl;
  56
  57                         out << "Expected\t";
  58
  59                         for (int m = 0; m < expectedDistance[i].size(); m++) {  out << expectedDistance[i][m] << '\t';  }
  60                         out << endl;
  61
  62                 }
  63         }
  64         catch(exception& e) {
  65                 errorOut(e, "Pintail", "print");
  66                 exit(1);
  67         }
  68 }
  69
  70 //***************************************************************************************************************
  71 void Pintail::getChimeras() {
  72         try {
  73
  74                 //read in query sequences and subject sequences
  75                 mothurOut("Reading sequences and template file... "); cout.flush();
  76                 querySeqs = readSeqs(fastafile);
  77                 templateSeqs = readSeqs(templateFile);
  78                 mothurOut("Done."); mothurOutEndLine();
  79
  80                 int numSeqs = querySeqs.size();
  81
  82                 obsDistance.resize(numSeqs);
  83                 expectedDistance.resize(numSeqs);
  84                 seqCoef.resize(numSeqs);
  85                 DE.resize(numSeqs);
  86                 Qav.resize(numSeqs);
  87                 bestfit.resize(numSeqs);
  88                 deviation.resize(numSeqs);
  89                 trimmed.resize(numSeqs);
  90                 windowSizes.resize(numSeqs, window);
  91                 windowSizesTemplate.resize(templateSeqs.size(), window);
  92                 windowsForeachQuery.resize(numSeqs);
  93                 h.resize(numSeqs);
  94                 quantiles.resize(100);  //one for every percent mismatch
  95
  96                 //break up file if needed
  97                 int linesPerProcess = numSeqs / processors ;
  98
  99                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 100                         //find breakup of sequences for all times we will Parallelize
 101                         if (processors == 1) {   lines.push_back(new linePair(0, numSeqs));  }
 102                         else {
 103                                 //fill line pairs
 104                                 for (int i = 0; i < (processors-1); i++) {
 105                                         lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
 106                                 }
 107                                 //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
 108                                 int i = processors - 1;
 109                                 lines.push_back(new linePair((i*linesPerProcess), numSeqs));
 110                         }
 111
 112                         //find breakup of templatefile for quantiles
 113                         if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
 114                         else {
 115                                 for (int i = 0; i < processors; i++) {
 116                                         templateLines.push_back(new linePair());
 117                                         templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
 118                                         templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
 119                                 }
 120                         }
 121                 #else
 122                         lines.push_back(new linePair(0, numSeqs));
 123                         templateLines.push_back(new linePair(0, templateSeqs.size()));
 124                 #endif
 125
 126                 distcalculator = new ignoreGaps();
 127                 decalc = new DeCalculator();
 128
 129                 //if the user does enter a mask then you want to keep all the spots in the alignment
 130                 if (seqMask.length() == 0)      {       decalc->setAlignmentLength(querySeqs[0]->getAligned().length());        }
 131                 else                                            {       decalc->setAlignmentLength(seqMask.length());                                           }
 132
 133                 decalc->setMask(seqMask);
 134
 135                 //find pairs
 136                 if (processors == 1) {
 137                         mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
 138                         bestfit = findPairs(lines[0]->start, lines[0]->end);
 139                         mothurOut("Done."); mothurOutEndLine();
 140                 }else {         createProcessesPairs();         }
 141
 142
 143                 for (int j = 0; j < bestfit.size(); j++) {
 144                                 //chops off beginning and end of sequences so they both start and end with a base
 145                                 ofstream out;
 146                                 string s = querySeqs[j]->getName();
 147
 148                                 openOutputFile(s, out);
 149                                 out << ">" << querySeqs[j]->getName() << endl;
 150                                 out << querySeqs[j]->getAligned() << endl;
 151                                 out.close();
 152
 153                                 string t =querySeqs[j]->getName() + ".ref";
 154                                 openOutputFile(t, out);
 155                                 out << ">" << bestfit[j]->getName() << endl;
 156                                 out << bestfit[j]->getAligned() << endl;
 157                                 out.close();
 158                 }
 159
 160
 161                 //find P
 162                 mothurOut("Getting conservation... "); cout.flush();
 163                 if (consfile == "") {
 164                         mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
 165                         probabilityProfile = decalc->calcFreq(templateSeqs, templateFile);
 166                         mothurOut("Done."); mothurOutEndLine();
 167                 }else                           {   probabilityProfile = readFreq();                      }
 168
 169                 //make P into Q
 170                 for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];  }  //cout << i << '\t' << probabilityProfile[i] << endl;
 171                 mothurOut("Done."); mothurOutEndLine();
 172
 173                 //mask querys
 174                 for (int i = 0; i < querySeqs.size(); i++) {
 175                 //cout << querySeqs[i]->getName() << " before mask = " << querySeqs[i]->getAligned() << endl << endl;
 176                         decalc->runMask(querySeqs[i]);
 177                 //cout << querySeqs[i]->getName() << " after mask = " << querySeqs[i]->getAligned() << endl << endl;
 178                 }
 179
 180                 //mask templates
 181                 for (int i = 0; i < templateSeqs.size(); i++) {
 182                         decalc->runMask(templateSeqs[i]);
 183                 }
 184
 185 //for (int i = 0; i < lines.size(); i++) { cout << "line pair " << i << " = " << lines[i]->start << '\t' << lines[i]->end << endl;  }
 186
 187                 if (processors == 1) {
 188
 189                         for (int j = 0; j < bestfit.size(); j++) {
 190                         //cout << querySeqs[j]->getName() << " after mask = " << querySeqs[j]->getAligned() << endl << endl;
 191                         ///cout << bestfit[j]->getName() << " after mask = " << bestfit[j]->getAligned() << endl << endl;
 192                                 decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
 193                         }
 194
 195                         mothurOut("Finding window breaks... "); cout.flush();
 196                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 197                                 it = trimmed[i].begin();
 198 //cout << querySeqs[i]->getName() << '\t' << "trimmed = " << it->first << '\t' << it->second << endl;
 199                                 vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 200                                 windowsForeachQuery[i] = win;
 201                         }
 202                         mothurOut("Done."); mothurOutEndLine();
 203
 204                 }else {         createProcessesSpots();         }
 205
 206
 207                 if (processors == 1) {
 208
 209                         mothurOut("Calculating observed distance... "); cout.flush();
 210                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 211         //cout << querySeqs[i]->getName() << '\t' << bestfit[i]->getName() << " windows = " << windowsForeachQuery[i].size() << " size = " << windowSizes[i] << endl;
 212                                 vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
 213
 214         for (int j = 0; j < obsi.size(); j++) {
 215                 //cout << obsi[j] << '\t';
 216         }
 217         //cout << endl;
 218                                 obsDistance[i] = obsi;
 219                         }
 220                         mothurOut("Done."); mothurOutEndLine();
 221
 222
 223                         mothurOut("Finding variability... "); cout.flush();
 224                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 225                                 vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
 226
 227                                 Qav[i] = q;
 228 //cout << querySeqs[i]->getName() << endl;
 229 for (int j = 0; j < Qav[i].size(); j++) {
 230         //cout << Qav[i][j] << '\t';
 231 }
 232 //cout << endl << endl;
 233
 234                         }
 235                         mothurOut("Done."); mothurOutEndLine();
 236
 237
 238                         mothurOut("Calculating alpha... "); cout.flush();
 239                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 240                                 float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
 241 //cout << querySeqs[i]->getName() << "\tcoef = " << alpha << endl;
 242                                 seqCoef[i] = alpha;
 243                         }
 244                         mothurOut("Done."); mothurOutEndLine();
 245
 246
 247                         mothurOut("Calculating expected distance... "); cout.flush();
 248                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 249                                 vector<float> exp = decalc->calcExpected(Qav[i], seqCoef[i]);
 250                                 expectedDistance[i] = exp;
 251                         }
 252                         mothurOut("Done."); mothurOutEndLine();
 253
 254
 255                         mothurOut("Finding deviation... "); cout.flush();
 256                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 257                                 float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
 258                                 DE[i] = de;
 259 //cout << querySeqs[i]->getName() << '\t' << "de value = " << de << endl;
 260                                 it = trimmed[i].begin();
 261                                 float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 262 //cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl;
 263                                 deviation[i] = dist;
 264                         }
 265                         mothurOut("Done."); mothurOutEndLine();
 266
 267                 }
 268                 else {          createProcesses();              }
 269
 270
 271                 //quantiles are used to determine whether the de values found indicate a chimera
 272                 //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
 273                 //combination of sequences in the template
 274                 if (quanfile != "") {  quantiles =  readQuantiles();  }
 275                 else {
 276
 277                         mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
 278                         if (processors == 1) {
 279                                 quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 280                         }else {         createProcessesQuan();          }
 281
 282
 283                         decalc->removeObviousOutliers(quantiles);
 284
 285                         ofstream out4;
 286                         string o = getRootName(templateFile) + "quan";
 287
 288                         openOutputFile(o, out4);
 289
 290                         //adjust quantiles
 291                         for (int i = 0; i < quantiles.size(); i++) {
 292                                 if (quantiles[i].size() == 0) {
 293                                         //in case this is not a distance found in your template files
 294                                         for (int g = 0; g < 6; g++) {
 295                                                 quantiles[i].push_back(0.0);
 296                                         }
 297                                 }else{
 298
 299                                         sort(quantiles[i].begin(), quantiles[i].end());
 300
 301                                         vector<float> temp;
 302                                         //save 10%
 303                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)]);
 304                                         //save 25%
 305                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.25)]);
 306                                         //save 50%
 307                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.5)]);
 308                                         //save 75%
 309                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.75)]);
 310                                         //save 95%
 311                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.95)]);
 312                                         //save 99%
 313                                         temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)]);
 314
 315                                         quantiles[i] = temp;
 316                                 }
 317
 318                                 //output quan value
 319                                 out4 << i+1 << '\t';
 320                                 for (int u = 0; u < quantiles[i].size(); u++) {   out4 << quantiles[i][u] << '\t'; }
 321                                 out4 << endl;
 322
 323                         }
 324
 325                         mothurOut("Done."); mothurOutEndLine();
 326                 }
 327
 328                 //free memory
 329                 for (int i = 0; i < lines.size(); i++)                                  {       delete lines[i];                                }
 330                 for (int i = 0; i < templateLines.size(); i++)                  {       delete templateLines[i];                }
 331
 332                 delete distcalculator;
 333                 delete decalc;
 334         }
 335         catch(exception& e) {
 336                 errorOut(e, "Pintail", "getChimeras");
 337                 exit(1);
 338         }
 339 }
 340
 341 //***************************************************************************************************************
 342
 343 vector<float> Pintail::readFreq() {
 344         try {
 345
 346                 ifstream in;
 347                 openInputFile(consfile, in);
 348
 349                 vector<float> prob;
 350                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 351
 352                 //read in probabilities and store in vector
 353                 int pos; float num;
 354
 355                 while(!in.eof()){
 356
 357                         in >> pos >> num;
 358
 359                         if (h.count(pos) > 0) {
 360                                 float Pi;
 361                                 Pi =  (num - 0.25) / 0.75;
 362
 363                                 //cannot have probability less than 0.
 364                                 if (Pi < 0) { Pi = 0.0; }
 365
 366                                 //do you want this spot
 367                                 prob.push_back(Pi);
 368                         }
 369
 370                         gobble(in);
 371                 }
 372
 373                 in.close();
 374                 return prob;
 375
 376         }
 377         catch(exception& e) {
 378                 errorOut(e, "Pintail", "readFreq");
 379                 exit(1);
 380         }
 381 }
 382
 383 //***************************************************************************************************************
 384
 385 vector< vector<float> > Pintail::readQuantiles() {
 386         try {
 387
 388                 ifstream in;
 389                 openInputFile(quanfile, in);
 390
 391                 vector< vector<float> > quan;
 392
 393                 int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
 394
 395                 while(!in.eof()){
 396
 397                         in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 398
 399                         vector <float> temp;
 400
 401                         temp.push_back(ten);
 402                         temp.push_back(twentyfive);
 403                         temp.push_back(fifty);
 404                         temp.push_back(seventyfive);
 405                         temp.push_back(ninetyfive);
 406                         temp.push_back(ninetynine);
 407
 408                         quan.push_back(temp);
 409
 410                         gobble(in);
 411                 }
 412
 413                 in.close();
 414                 return quan;
 415
 416         }
 417         catch(exception& e) {
 418                 errorOut(e, "Pintail", "readQuantiles");
 419                 exit(1);
 420         }
 421 }
 422 //***************************************************************************************************************
 423 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 424 vector<Sequence*> Pintail::findPairs(int start, int end) {
 425         try {
 426
 427                 vector<Sequence*> seqsMatches;
 428
 429                 for(int i = start; i < end; i++){
 430
 431                         float smallest = 10000.0;
 432                         Sequence query = *(querySeqs[i]);
 433                         Sequence* match;
 434
 435                         for(int j = 0; j < templateSeqs.size(); j++){
 436
 437                                 Sequence temp = *(templateSeqs[j]);
 438
 439                                 distcalculator->calcDist(query, temp);
 440                                 float dist = distcalculator->getDist();
 441
 442                                 if (dist < smallest) {
 443                                         match = templateSeqs[j];
 444                                         smallest = dist;
 445                                 }
 446                         }
 447
 448                         seqsMatches.push_back(match);
 449                 }
 450
 451                 return seqsMatches;
 452
 453         }
 454         catch(exception& e) {
 455                 errorOut(e, "Pintail", "findPairs");
 456                 exit(1);
 457         }
 458 }
 459
 460 /**************************************************************************************************/
 461
 462 void Pintail::createProcessesSpots() {
 463         try {
 464 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 465                 int process = 0;
 466                 vector<int> processIDS;
 467
 468                 //loop through and create all the processes you want
 469                 while (process != processors) {
 470                         int pid = fork();
 471
 472                         if (pid > 0) {
 473                                 processIDS.push_back(pid);
 474                                 process++;
 475                         }else if (pid == 0){
 476
 477                                 for (int j = lines[process]->start; j < lines[process]->end; j++) {
 478
 479                                         //chops off beginning and end of sequences so they both start and end with a base
 480                                         map<int, int> trim;
 481                                         decalc->trimSeqs(querySeqs[j], bestfit[j], trim);
 482                                         trimmed[j] = trim;
 483
 484                                 }
 485
 486                                 mothurOut("Finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 487                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 488                                         it = trimmed[i].begin();
 489                                         windowsForeachQuery[i] = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 490                                 }
 491                                 mothurOut("Done finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 492
 493                                 //write out data to file so parent can read it
 494                                 ofstream out;
 495                                 string s = toString(getpid()) + ".temp";
 496                                 openOutputFile(s, out);
 497
 498                                 //output windowsForeachQuery
 499                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 500                                         out << windowsForeachQuery[i].size() << '\t';
 501                                         for (int j = 0; j < windowsForeachQuery[i].size(); j++) {
 502                                                 out << windowsForeachQuery[i][j] << '\t';
 503                                         }
 504                                         out << endl;
 505                                 }
 506
 507                                 //output windowSizes
 508                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 509                                         out << windowSizes[i] << '\t';
 510                                 }
 511                                 out << endl;
 512
 513                                 //output trimmed values
 514                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 515                                         it = trimmed[i].begin();
 516
 517                                         out << it->first << '\t' << it->second << endl;
 518                                 }
 519                                 out.close();
 520
 521                                 exit(0);
 522                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 523                 }
 524
 525                 //force parent to wait until all the processes are done
 526                 for (int i=0;i<processors;i++) {
 527                         int temp = processIDS[i];
 528                         wait(&temp);
 529                 }
 530
 531                 //get data created by processes
 532                 for (int i=0;i<processors;i++) {
 533                         ifstream in;
 534                         string s = toString(processIDS[i]) + ".temp";
 535                         openInputFile(s, in);
 536
 537                         int size = lines[i]->end - lines[i]->start;
 538
 539                         int count = lines[i]->start;
 540                         for (int m = 0; m < size; m++) {
 541                                 int num;
 542                                 in >> num;
 543
 544                                 vector<int> win;  int w;
 545                                 for (int j = 0; j < num; j++) {
 546                                         in >> w;
 547                                         win.push_back(w);
 548                                 }
 549
 550                                 windowsForeachQuery[count] = win;
 551                                 count++;
 552                                 gobble(in);
 553                         }
 554
 555                         gobble(in);
 556                         count = lines[i]->start;
 557                         for (int m = 0; m < size; m++) {
 558                                 int num;
 559                                 in >> num;
 560
 561                                 windowSizes[count] = num;
 562                                 count++;
 563                         }
 564
 565                         gobble(in);
 566
 567                         count = lines[i]->start;
 568                         for (int m = 0; m < size; m++) {
 569                                 int front, back;
 570                                 in >> front >> back;
 571
 572                                 map<int, int> t;
 573
 574                                 t[front] = back;
 575
 576                                 trimmed[count] = t;
 577                                 count++;
 578
 579                                 gobble(in);
 580                         }
 581
 582
 583                         in.close();
 584                         remove(s.c_str());
 585                 }
 586
 587
 588 #else
 589                 for (int j = 0; j < bestfit.size(); j++) {
 590                         //chops off beginning and end of sequences so they both start and end with a base
 591                         decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
 592                 }
 593
 594                 for (int i = lines[0]->start; i < lines[0]->end; i++) {
 595                                 it = trimmed[i].begin();
 596                                 map<int, int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 597                                 windows[i] = win;
 598                 }
 599
 600 #endif
 601         }
 602         catch(exception& e) {
 603                 errorOut(e, "Pintail", "createProcessesSpots");
 604                 exit(1);
 605         }
 606 }
 607 /**************************************************************************************************/
 608
 609 void Pintail::createProcessesPairs() {
 610         try {
 611 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 612                 int process = 0;
 613                 vector<int> processIDS;
 614
 615                 //loop through and create all the processes you want
 616                 while (process != processors) {
 617                         int pid = fork();
 618
 619                         if (pid > 0) {
 620                                 processIDS.push_back(pid);
 621                                 process++;
 622                         }else if (pid == 0){
 623
 624                                 mothurOut("Finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 625                                 bestfit = findPairs(lines[process]->start, lines[process]->end);
 626                                 mothurOut("Done finding pairs for sequences " +  toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 627
 628                                 //write out data to file so parent can read it
 629                                 ofstream out;
 630                                 string s = toString(getpid()) + ".temp";
 631                                 openOutputFile(s, out);
 632
 633                                 //output range and size
 634                                 out << bestfit.size() << endl;
 635
 636                                 //output pairs
 637                                 for (int i = 0; i < bestfit.size(); i++) {
 638                                         out << ">" << bestfit[i]->getName() << endl << bestfit[i]->getAligned() << endl;
 639                                 }
 640                                 out.close();
 641
 642                                 exit(0);
 643                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 644                 }
 645
 646                 //force parent to wait until all the processes are done
 647                 for (int i=0;i<processors;i++) {
 648                         int temp = processIDS[i];
 649                         wait(&temp);
 650                 }
 651
 652                 //get data created by processes
 653                 for (int i=0;i<processors;i++) {
 654                         ifstream in;
 655                         string s = toString(processIDS[i]) + ".temp";
 656                         openInputFile(s, in);
 657
 658                         int size;
 659                         in >> size;  gobble(in);
 660
 661                         //get pairs
 662                         int count = lines[i]->start;
 663                         for (int m = 0; m < size; m++) {
 664                                 Sequence* temp = new Sequence(in);
 665                                 bestfit[count] = temp;
 666
 667                                 count++;
 668                                 gobble(in);
 669                         }
 670
 671                         in.close();
 672                         remove(s.c_str());
 673                 }
 674
 675
 676 #else
 677                 bestfit = findPairs(lines[0]->start, lines[0]->end);
 678 #endif
 679         }
 680         catch(exception& e) {
 681                 errorOut(e, "Pintail", "createProcessesPairs");
 682                 exit(1);
 683         }
 684 }
 685 /**************************************************************************************************/
 686
 687 void Pintail::createProcesses() {
 688         try {
 689 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 690                 int process = 0;
 691                 vector<int> processIDS;
 692
 693                 //loop through and create all the processes you want
 694                 while (process != processors) {
 695                         int pid = fork();
 696
 697                         if (pid > 0) {
 698                                 processIDS.push_back(pid);
 699                                 process++;
 700                         }else if (pid == 0){
 701
 702                                 mothurOut("Calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 703                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 704
 705                                         vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
 706                                         obsDistance[i] = obsi;
 707
 708                                         //calc Qav
 709                                         vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
 710
 711                                         //get alpha
 712                                         float alpha = decalc->getCoef(obsDistance[i], q);
 713
 714                                         //find expected
 715                                         vector<float> exp = decalc->calcExpected(q, alpha);
 716                                         expectedDistance[i] = exp;
 717
 718                                         //get de and deviation
 719                                         float dei = decalc->calcDE(obsi, exp);
 720                                         DE[i] = dei;
 721
 722                                         it = trimmed[i].begin();
 723                                         float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 724                                         deviation[i] = dist;
 725                                 }
 726                                 mothurOut("Done calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 727
 728                                 //write out data to file so parent can read it
 729                                 ofstream out;
 730                                 string s = toString(getpid()) + ".temp";
 731                                 openOutputFile(s, out);
 732
 733                                 int size = lines[process]->end - lines[process]->start;
 734                                 out << size << endl;
 735
 736                                 //output observed distances
 737                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 738                                         out << obsDistance[i].size() << '\t';
 739                                         for (int j = 0; j < obsDistance[i].size(); j++) {
 740                                                 out << obsDistance[i][j] << '\t';
 741                                         }
 742                                         out << endl;
 743                                 }
 744
 745
 746                                 //output expected distances
 747                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 748                                         out << expectedDistance[i].size() << '\t';
 749                                         for (int j = 0; j < expectedDistance[i].size(); j++) {
 750                                                 out << expectedDistance[i][j] << '\t';
 751                                         }
 752                                         out << endl;
 753                                 }
 754
 755
 756                                 //output de values
 757                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 758                                         out << DE[i] << '\t';
 759                                 }
 760                                 out << endl;
 761
 762                                 //output de values
 763                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 764                                         out << deviation[i] << '\t';
 765                                 }
 766                                 out << endl;
 767
 768                                 out.close();
 769
 770                                 exit(0);
 771                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 772                 }
 773
 774                 //force parent to wait until all the processes are done
 775                 for (int i=0;i<processors;i++) {
 776                         int temp = processIDS[i];
 777                         wait(&temp);
 778                 }
 779
 780                 //get data created by processes
 781                 for (int i=0;i<processors;i++) {
 782                         ifstream in;
 783                         string s = toString(processIDS[i]) + ".temp";
 784                         openInputFile(s, in);
 785
 786                         int size;
 787                         in >> size;  gobble(in);
 788
 789                         //get observed distances
 790                         int count = lines[i]->start;
 791                         for (int m = 0; m < size; m++) {
 792                                 int num;
 793                                 in >> num;
 794
 795                                 vector<float> obs;  float w;
 796                                 for (int j = 0; j < num; j++) {
 797                                         in >> w;
 798                                         obs.push_back(w);
 799                                 }
 800
 801                                 obsDistance[count] = obs;
 802                                 count++;
 803                                 gobble(in);
 804                         }
 805
 806                         gobble(in);
 807
 808                         //get expected distances
 809                         count = lines[i]->start;
 810                         for (int m = 0; m < size; m++) {
 811                                 int num;
 812                                 in >> num;
 813
 814                                 vector<float> exp;  float w;
 815                                 for (int j = 0; j < num; j++) {
 816                                         in >> w;
 817                                         exp.push_back(w);
 818                                 }
 819
 820                                 expectedDistance[count] = exp;
 821                                 count++;
 822                                 gobble(in);
 823                         }
 824
 825                         gobble(in);
 826
 827                         count = lines[i]->start;
 828                         for (int m = 0; m < size; m++) {
 829                                 float num;
 830                                 in >> num;
 831
 832                                 DE[count] = num;
 833                                 count++;
 834                         }
 835
 836                         gobble(in);
 837
 838                         count = lines[i]->start;
 839                         for (int m = 0; m < size; m++) {
 840                                 float num;
 841                                 in >> num;
 842
 843                                 deviation[count] = num;
 844                                 count++;
 845                         }
 846
 847                         in.close();
 848                         remove(s.c_str());
 849                 }
 850
 851
 852 #else
 853                         mothurOut("Calculating observed distance... "); cout.flush();
 854                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 855                                 vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windows[i], windowSizes[i]);
 856                                 obsDistance[i] = obsi;
 857                         }
 858                         mothurOut("Done."); mothurOutEndLine();
 859
 860
 861
 862                         mothurOut("Finding variability... "); cout.flush();
 863                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 864                                 vector<float> q = decalc->findQav(windows[i], windowSizes[i], probabilityProfile, h[i]);
 865                                 Qav[i] = q;
 866                         }
 867                         mothurOut("Done."); mothurOutEndLine();
 868
 869
 870
 871                         mothurOut("Calculating alpha... "); cout.flush();
 872                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 873                                 float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
 874                                 seqCoef.push_back(alpha);
 875                         }
 876                         mothurOut("Done."); mothurOutEndLine();
 877
 878
 879
 880                         mothurOut("Calculating expected distance... "); cout.flush();
 881                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 882                                 vector<float> exp = decalc->calcExpected(Qav[i], seqCoef[i]);
 883                                 expectedDistance[i] = exp;
 884                         }
 885                         mothurOut("Done."); mothurOutEndLine();
 886
 887
 888
 889                         mothurOut("Finding deviation... "); cout.flush();
 890                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 891                                 float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
 892                                 DE[i] = de;
 893
 894                                 it = trimmed[i].begin();
 895                                 float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 896                                 deviation[i] = dist;
 897                         }
 898                         mothurOut("Done."); mothurOutEndLine();
 899
 900 #endif
 901         }
 902         catch(exception& e) {
 903                 errorOut(e, "Pintail", "createProcesses");
 904                 exit(1);
 905         }
 906 }
 907
 908
 909 /**************************************************************************************************/
 910
 911 void Pintail::createProcessesQuan() {
 912         try {
 913 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 914                 int process = 0;
 915                 vector<int> processIDS;
 916
 917                 //loop through and create all the processes you want
 918                 while (process != processors) {
 919                         int pid = fork();
 920
 921                         if (pid > 0) {
 922                                 processIDS.push_back(pid);
 923                                 process++;
 924                         }else if (pid == 0){
 925
 926                                 quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 927
 928                                 //write out data to file so parent can read it
 929                                 ofstream out;
 930                                 string s = toString(getpid()) + ".temp";
 931                                 openOutputFile(s, out);
 932
 933
 934                                 //output observed distances
 935                                 for (int i = 0; i < quantiles.size(); i++) {
 936                                         out << quantiles[i].size() << '\t';
 937                                         for (int j = 0; j < quantiles[i].size(); j++) {
 938                                                 out << quantiles[i][j] << '\t';
 939                                         }
 940                                         out << endl;
 941                                 }
 942
 943                                 out.close();
 944
 945                                 exit(0);
 946                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 947                 }
 948
 949                 //force parent to wait until all the processes are done
 950                 for (int i=0;i<processors;i++) {
 951                         int temp = processIDS[i];
 952                         wait(&temp);
 953                 }
 954
 955                 //get data created by processes
 956                 for (int i=0;i<processors;i++) {
 957                         ifstream in;
 958                         string s = toString(processIDS[i]) + ".temp";
 959                         openInputFile(s, in);
 960
 961                         vector< vector<float> > quan; quan.resize(100);
 962
 963                         //get quantiles
 964                         for (int m = 0; m < quan.size(); m++) {
 965                                 int num;
 966                                 in >> num;
 967
 968                                 vector<float> q;  float w;
 969                                 for (int j = 0; j < num; j++) {
 970                                         in >> w;
 971                                         q.push_back(w);
 972                                 }
 973
 974                                 quan[m] = q;
 975                                 gobble(in);
 976                         }
 977
 978
 979                         //save quan in quantiles
 980                         for (int i = 0; i < quan.size(); i++) {
 981                                 //put all values of q[i] into quan[i]
 982                                 quantiles[i].insert(quantiles[i].begin(), quan[i].begin(), quan[i].end());
 983                         }
 984
 985                         in.close();
 986                         remove(s.c_str());
 987                 }
 988
 989 #else
 990                 quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 991 #endif
 992         }
 993         catch(exception& e) {
 994                 errorOut(e, "Pintail", "createProcessesQuan");
 995                 exit(1);
 996         }
 997 }
 998
 999
1000 //***************************************************************************************************************
1001
1002