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 #include "eachgapdist.h"
  13
  14 //********************************************************************************************************************
  15 //sorts lowest to highest
  16 inline bool compareQuanMembers(quanMember left, quanMember right){
  17         return (left.score < right.score);
  18 }
  19 //***************************************************************************************************************
  20
  21 Pintail::Pintail(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
  22 //***************************************************************************************************************
  23
  24 Pintail::~Pintail() {
  25         try {
  26                 for (int i = 0; i < querySeqs.size(); i++)              {  delete querySeqs[i];         }
  27                 for (int i = 0; i < templateSeqs.size(); i++)   {  delete templateSeqs[i];      }
  28                 for (int i = 0; i < bestfit.size(); i++)                {  delete bestfit[i];           }
  29         }
  30         catch(exception& e) {
  31                 errorOut(e, "Pintail", "~Pintail");
  32                 exit(1);
  33         }
  34 }
  35 //***************************************************************************************************************
  36 void Pintail::print(ostream& out) {
  37         try {
  38
  39                 mothurOutEndLine();
  40
  41                 for (int i = 0; i < querySeqs.size(); i++) {
  42
  43                         int index = ceil(deviation[i]);
  44
  45                         //is your DE value higher than the 95%
  46                         string chimera;
  47                         if (quantiles[index][4] == 0.0) {
  48                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
  49                         }else {
  50                                 if (DE[i] > quantiles[index][4])                {       chimera = "Yes";        }
  51                                 else                                                                    {       chimera = "No";         }
  52                         }
  53
  54                         out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
  55                         if (chimera == "Yes") {
  56                                 mothurOut(querySeqs[i]->getName() + "\tdiv: " + toString(deviation[i]) + "\tstDev: " + toString(DE[i]) + "\tchimera flag: " + chimera); mothurOutEndLine();
  57                         }
  58                         out << "Observed\t";
  59
  60                         for (int j = 0; j < obsDistance[i].size(); j++) {  out << obsDistance[i][j] << '\t';  }
  61                         out << endl;
  62
  63                         out << "Expected\t";
  64
  65                         for (int m = 0; m < expectedDistance[i].size(); m++) {  out << expectedDistance[i][m] << '\t';  }
  66                         out << endl;
  67
  68                 }
  69         }
  70         catch(exception& e) {
  71                 errorOut(e, "Pintail", "print");
  72                 exit(1);
  73         }
  74 }
  75
  76 //***************************************************************************************************************
  77 void Pintail::getChimeras() {
  78         try {
  79
  80                 //read in query sequences and subject sequences
  81                 mothurOut("Reading sequences and template file... "); cout.flush();
  82                 querySeqs = readSeqs(fastafile);
  83                 templateSeqs = readSeqs(templateFile);
  84                 mothurOut("Done."); mothurOutEndLine();
  85
  86                 int numSeqs = querySeqs.size();
  87
  88                 obsDistance.resize(numSeqs);
  89                 expectedDistance.resize(numSeqs);
  90                 seqCoef.resize(numSeqs);
  91                 DE.resize(numSeqs);
  92                 Qav.resize(numSeqs);
  93                 bestfit.resize(numSeqs);
  94                 deviation.resize(numSeqs);
  95                 trimmed.resize(numSeqs);
  96                 windowSizes.resize(numSeqs, window);
  97                 windowSizesTemplate.resize(templateSeqs.size(), window);
  98                 windowsForeachQuery.resize(numSeqs);
  99                 h.resize(numSeqs);
 100                 quantiles.resize(100);  //one for every percent mismatch
 101                 quantilesMembers.resize(100);  //one for every percent mismatch
 102
 103                 //break up file if needed
 104                 int linesPerProcess = numSeqs / processors ;
 105
 106                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 107                         //find breakup of sequences for all times we will Parallelize
 108                         if (processors == 1) {   lines.push_back(new linePair(0, numSeqs));  }
 109                         else {
 110                                 //fill line pairs
 111                                 for (int i = 0; i < (processors-1); i++) {
 112                                         lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
 113                                 }
 114                                 //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
 115                                 int i = processors - 1;
 116                                 lines.push_back(new linePair((i*linesPerProcess), numSeqs));
 117                         }
 118
 119                         //find breakup of templatefile for quantiles
 120                         if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
 121                         else {
 122                                 for (int i = 0; i < processors; i++) {
 123                                         templateLines.push_back(new linePair());
 124                                         templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
 125                                         templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
 126                                 }
 127                         }
 128                 #else
 129                         lines.push_back(new linePair(0, numSeqs));
 130                         templateLines.push_back(new linePair(0, templateSeqs.size()));
 131                 #endif
 132
 133                 distcalculator = new eachGapDist();
 134                 decalc = new DeCalculator();
 135
 136                 //if the user does enter a mask then you want to keep all the spots in the alignment
 137                 if (seqMask.length() == 0)      {       decalc->setAlignmentLength(querySeqs[0]->getAligned().length());        }
 138                 else                                            {       decalc->setAlignmentLength(seqMask.length());                                           }
 139
 140                 decalc->setMask(seqMask);
 141
 142                 //find pairs
 143                 if (processors == 1) {
 144                         mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
 145                         bestfit = findPairs(lines[0]->start, lines[0]->end);
 146                         mothurOut("Done."); mothurOutEndLine();
 147                 }else {         createProcessesPairs();         }
 148
 149 //string o = "closestmatch.eachgap.fasta";
 150 //ofstream out7;
 151 //openOutputFile(o, out7);
 152
 153 //for (int i = 0; i < bestfit.size(); i++) {
 154         //out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
 155         //out7 << bestfit[i]->getAligned() << endl;
 156 //}
 157 //out7.close();
 158                 //find P
 159                 mothurOut("Getting conservation... "); cout.flush();
 160                 if (consfile == "") {
 161                         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();
 162                         probabilityProfile = decalc->calcFreq(templateSeqs, templateFile);
 163                         mothurOut("Done."); mothurOutEndLine();
 164                 }else                           {   probabilityProfile = readFreq();                      }
 165
 166                 //make P into Q
 167                 for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];  }  //cout << i << '\t' << probabilityProfile[i] << endl;
 168                 mothurOut("Done."); mothurOutEndLine();
 169
 170                 //mask sequences if the user wants to
 171                 if (seqMask != "") {
 172                         //mask querys
 173                         for (int i = 0; i < querySeqs.size(); i++) {
 174                                 decalc->runMask(querySeqs[i]);
 175                         }
 176
 177                         //mask templates
 178                         for (int i = 0; i < templateSeqs.size(); i++) {
 179                                 decalc->runMask(templateSeqs[i]);
 180                         }
 181
 182                         for (int i = 0; i < bestfit.size(); i++) {
 183                                 decalc->runMask(bestfit[i]);
 184                         }
 185
 186                 }
 187
 188                 if (filter) {
 189                         vector<Sequence*> temp = templateSeqs;
 190                         for (int i = 0; i < querySeqs.size(); i++) { temp.push_back(querySeqs[i]);  }
 191
 192                         createFilter(temp);
 193
 194                         runFilter(querySeqs);
 195                         runFilter(templateSeqs);
 196                         runFilter(bestfit);
 197                 }
 198
 199
 200                 if (processors == 1) {
 201
 202                         for (int j = 0; j < bestfit.size(); j++) {
 203                                 decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
 204                         }
 205
 206                         mothurOut("Finding window breaks... "); cout.flush();
 207                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 208                                 it = trimmed[i].begin();
 209                                 vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 210                                 windowsForeachQuery[i] = win;
 211                         }
 212                         mothurOut("Done."); mothurOutEndLine();
 213
 214                 }else {         createProcessesSpots();         }
 215
 216                 if (processors == 1) {
 217
 218                         mothurOut("Calculating observed distance... "); cout.flush();
 219                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 220                                 vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
 221
 222                                 obsDistance[i] = obsi;
 223                         }
 224                         mothurOut("Done."); mothurOutEndLine();
 225
 226
 227                         mothurOut("Finding variability... "); cout.flush();
 228                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 229                                 vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
 230
 231                                 Qav[i] = q;
 232                         }
 233                         mothurOut("Done."); mothurOutEndLine();
 234
 235
 236                         mothurOut("Calculating alpha... "); cout.flush();
 237                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 238                                 float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
 239                                 seqCoef[i] = alpha;
 240                         }
 241                         mothurOut("Done."); mothurOutEndLine();
 242
 243
 244                         mothurOut("Calculating expected distance... "); cout.flush();
 245                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 246                                 vector<float> exp = decalc->calcExpected(Qav[i], seqCoef[i]);
 247                                 expectedDistance[i] = exp;
 248                         }
 249                         mothurOut("Done."); mothurOutEndLine();
 250
 251
 252                         mothurOut("Finding deviation... "); cout.flush();
 253                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 254                                 float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
 255                                 DE[i] = de;
 256
 257                                 it = trimmed[i].begin();
 258                                 float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 259                                 deviation[i] = dist;
 260                         }
 261                         mothurOut("Done."); mothurOutEndLine();
 262
 263                 }
 264                 else {          createProcesses();              }
 265
 266                 //quantiles are used to determine whether the de values found indicate a chimera
 267                 //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
 268                 //combination of sequences in the template
 269                 if (quanfile != "") {  quantiles = readQuantiles();  }
 270                 else {
 271
 272                         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();
 273                         if (processors == 1) {
 274                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 275                         }else {         createProcessesQuan();          }
 276
 277
 278                         ofstream out4, out5;
 279                         string noOutliers, outliers;
 280
 281                         if ((!filter) && (seqMask == "")) {
 282                                 noOutliers = getRootName(templateFile) + "pintail.quan";
 283                         }else if ((filter) && (seqMask == "")) {
 284                                 noOutliers = getRootName(templateFile) + "pintail.filtered.quan";
 285                         }else if ((!filter) && (seqMask != "")) {
 286                                 noOutliers = getRootName(templateFile) + "pintail.masked.quan";
 287                         }else if ((filter) && (seqMask != "")) {
 288                                 noOutliers = getRootName(templateFile) + "pintail.filtered.masked.quan";
 289                         }
 290
 291                         //outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";
 292
 293                         /*openOutputFile(outliers, out4);
 294
 295                         //adjust quantiles
 296                         for (int i = 0; i < quantilesMembers.size(); i++) {
 297                                 vector<float> temp;
 298
 299                                 if (quantilesMembers[i].size() == 0) {
 300                                         //in case this is not a distance found in your template files
 301                                         for (int g = 0; g < 6; g++) {
 302                                                 temp.push_back(0.0);
 303                                         }
 304                                 }else{
 305
 306                                         sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
 307
 308                                         //save 10%
 309                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
 310                                         //save 25%
 311                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
 312                                         //save 50%
 313                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
 314                                         //save 75%
 315                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
 316                                         //save 95%
 317                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
 318                                         //save 99%
 319                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
 320
 321                                 }
 322
 323                                 //output quan value
 324                                 out4 << i+1 << '\t';
 325                                 for (int u = 0; u < temp.size(); u++) {   out4 << temp[u] << '\t'; }
 326                                 out4 << endl;
 327
 328                                 quantiles[i] = temp;
 329
 330                         }
 331
 332                         out4.close();*/
 333
 334                         decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
 335
 336                         openOutputFile(noOutliers, out5);
 337
 338                         //adjust quantiles
 339                         for (int i = 0; i < quantilesMembers.size(); i++) {
 340                                 vector<float> temp;
 341
 342                                 if (quantilesMembers[i].size() == 0) {
 343                                         //in case this is not a distance found in your template files
 344                                         for (int g = 0; g < 6; g++) {
 345                                                 temp.push_back(0.0);
 346                                         }
 347                                 }else{
 348
 349                                         sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
 350
 351                                         //save 10%
 352                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
 353                                         //save 25%
 354                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
 355                                         //save 50%
 356                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
 357                                         //save 75%
 358                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
 359                                         //save 95%
 360                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
 361                                         //save 99%
 362                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
 363
 364                                 }
 365
 366                                 //output quan value
 367                                 out5 << i+1 << '\t';
 368                                 for (int u = 0; u < temp.size(); u++) {   out5 << temp[u] << '\t'; }
 369                                 out5 << endl;
 370
 371                                 quantiles[i] = temp;
 372
 373                         }
 374
 375                         mothurOut("Done."); mothurOutEndLine();
 376
 377                 }
 378
 379                 //free memory
 380                 for (int i = 0; i < lines.size(); i++)                                  {       delete lines[i];                                }
 381                 for (int i = 0; i < templateLines.size(); i++)                  {       delete templateLines[i];                }
 382
 383                 delete distcalculator;
 384                 delete decalc;
 385         }
 386         catch(exception& e) {
 387                 errorOut(e, "Pintail", "getChimeras");
 388                 exit(1);
 389         }
 390 }
 391
 392 //***************************************************************************************************************
 393
 394 vector<float> Pintail::readFreq() {
 395         try {
 396
 397                 ifstream in;
 398                 openInputFile(consfile, in);
 399
 400                 vector<float> prob;
 401                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 402
 403                 //read in probabilities and store in vector
 404                 int pos; float num;
 405
 406                 while(!in.eof()){
 407
 408                         in >> pos >> num;
 409
 410                         if (h.count(pos) > 0) {
 411                                 float Pi;
 412                                 Pi =  (num - 0.25) / 0.75;
 413
 414                                 //cannot have probability less than 0.
 415                                 if (Pi < 0) { Pi = 0.0; }
 416
 417                                 //do you want this spot
 418                                 prob.push_back(Pi);
 419                         }
 420
 421                         gobble(in);
 422                 }
 423
 424                 in.close();
 425                 return prob;
 426
 427         }
 428         catch(exception& e) {
 429                 errorOut(e, "Pintail", "readFreq");
 430                 exit(1);
 431         }
 432 }
 433
 434 //***************************************************************************************************************
 435 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 436 vector<Sequence*> Pintail::findPairs(int start, int end) {
 437         try {
 438
 439                 vector<Sequence*> seqsMatches;
 440
 441                 for(int i = start; i < end; i++){
 442
 443                         vector<Sequence*> copy = decalc->findClosest(querySeqs[i], templateSeqs, 1);
 444                         seqsMatches.push_back(copy[0]);
 445                 }
 446
 447                 return seqsMatches;
 448
 449         }
 450         catch(exception& e) {
 451                 errorOut(e, "Pintail", "findPairs");
 452                 exit(1);
 453         }
 454 }
 455
 456 /**************************************************************************************************/
 457
 458 void Pintail::createProcessesSpots() {
 459         try {
 460 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 461                 int process = 0;
 462                 vector<int> processIDS;
 463
 464                 //loop through and create all the processes you want
 465                 while (process != processors) {
 466                         int pid = fork();
 467
 468                         if (pid > 0) {
 469                                 processIDS.push_back(pid);
 470                                 process++;
 471                         }else if (pid == 0){
 472
 473                                 for (int j = lines[process]->start; j < lines[process]->end; j++) {
 474
 475                                         //chops off beginning and end of sequences so they both start and end with a base
 476                                         map<int, int> trim;
 477
 478                                         decalc->trimSeqs(querySeqs[j], bestfit[j], trim);
 479                                         trimmed[j] = trim;
 480
 481                                 }
 482
 483                                 mothurOut("Finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 484                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 485                                         it = trimmed[i].begin();
 486                                         windowsForeachQuery[i] = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 487                                 }
 488                                 mothurOut("Done finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 489
 490                                 //write out data to file so parent can read it
 491                                 ofstream out;
 492                                 string s = toString(getpid()) + ".temp";
 493                                 openOutputFile(s, out);
 494
 495                                 //output windowsForeachQuery
 496                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 497                                         out << windowsForeachQuery[i].size() << '\t';
 498                                         for (int j = 0; j < windowsForeachQuery[i].size(); j++) {
 499                                                 out << windowsForeachQuery[i][j] << '\t';
 500                                         }
 501                                         out << endl;
 502                                 }
 503
 504                                 //output windowSizes
 505                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 506                                         out << windowSizes[i] << '\t';
 507                                 }
 508                                 out << endl;
 509
 510                                 //output trimmed values
 511                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 512                                         it = trimmed[i].begin();
 513                                         out << it->first << '\t' << it->second << endl;
 514                                 }
 515                                 out.close();
 516
 517                                 exit(0);
 518                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 519                 }
 520
 521                 //force parent to wait until all the processes are done
 522                 for (int i=0;i<processors;i++) {
 523                         int temp = processIDS[i];
 524                         wait(&temp);
 525                 }
 526
 527                 //get data created by processes
 528                 for (int i=0;i<processors;i++) {
 529                         ifstream in;
 530                         string s = toString(processIDS[i]) + ".temp";
 531                         openInputFile(s, in);
 532
 533                         int size = lines[i]->end - lines[i]->start;
 534
 535                         int count = lines[i]->start;
 536                         for (int m = 0; m < size; m++) {
 537                                 int num;
 538                                 in >> num;
 539
 540                                 vector<int> win;  int w;
 541                                 for (int j = 0; j < num; j++) {
 542                                         in >> w;
 543                                         win.push_back(w);
 544                                 }
 545
 546                                 windowsForeachQuery[count] = win;
 547                                 count++;
 548                                 gobble(in);
 549                         }
 550
 551                         gobble(in);
 552                         count = lines[i]->start;
 553                         for (int m = 0; m < size; m++) {
 554                                 int num;
 555                                 in >> num;
 556
 557                                 windowSizes[count] = num;
 558                                 count++;
 559                         }
 560
 561                         gobble(in);
 562
 563                         count = lines[i]->start;
 564                         for (int m = 0; m < size; m++) {
 565                                 int front, back;
 566                                 in >> front >> back;
 567
 568                                 map<int, int> t;
 569
 570                                 t[front] = back;
 571
 572                                 trimmed[count] = t;
 573                                 count++;
 574
 575                                 gobble(in);
 576                         }
 577
 578
 579                         in.close();
 580                         remove(s.c_str());
 581                 }
 582
 583
 584 #else
 585                 for (int j = 0; j < bestfit.size(); j++) {
 586                         //chops off beginning and end of sequences so they both start and end with a base
 587                         decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
 588                 }
 589
 590                 for (int i = lines[0]->start; i < lines[0]->end; i++) {
 591                                 it = trimmed[i].begin();
 592                                 vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
 593                                 windowsForeachQuery[i] = win;
 594                 }
 595
 596 #endif
 597         }
 598         catch(exception& e) {
 599                 errorOut(e, "Pintail", "createProcessesSpots");
 600                 exit(1);
 601         }
 602 }
 603 /**************************************************************************************************/
 604
 605 void Pintail::createProcessesPairs() {
 606         try {
 607 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 608                 int process = 0;
 609                 vector<int> processIDS;
 610
 611                 //loop through and create all the processes you want
 612                 while (process != processors) {
 613                         int pid = fork();
 614
 615                         if (pid > 0) {
 616                                 processIDS.push_back(pid);
 617                                 process++;
 618                         }else if (pid == 0){
 619
 620                                 mothurOut("Finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 621                                 bestfit = findPairs(lines[process]->start, lines[process]->end);
 622                                 mothurOut("Done finding pairs for sequences " +  toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 623
 624                                 //write out data to file so parent can read it
 625                                 ofstream out;
 626                                 string s = toString(getpid()) + ".temp";
 627                                 openOutputFile(s, out);
 628
 629                                 //output range and size
 630                                 out << bestfit.size() << endl;
 631
 632                                 //output pairs
 633                                 for (int i = 0; i < bestfit.size(); i++) {
 634                                         out << ">" << bestfit[i]->getName() << endl << bestfit[i]->getAligned() << endl;
 635                                 }
 636                                 out.close();
 637
 638                                 exit(0);
 639                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 640                 }
 641
 642                 //force parent to wait until all the processes are done
 643                 for (int i=0;i<processors;i++) {
 644                         int temp = processIDS[i];
 645                         wait(&temp);
 646                 }
 647
 648                 //get data created by processes
 649                 for (int i=0;i<processors;i++) {
 650                         ifstream in;
 651                         string s = toString(processIDS[i]) + ".temp";
 652                         openInputFile(s, in);
 653
 654                         int size;
 655                         in >> size;  gobble(in);
 656
 657                         //get pairs
 658                         int count = lines[i]->start;
 659                         for (int m = 0; m < size; m++) {
 660                                 Sequence* temp = new Sequence(in);
 661                                 bestfit[count] = temp;
 662
 663                                 count++;
 664                                 gobble(in);
 665                         }
 666
 667                         in.close();
 668                         remove(s.c_str());
 669                 }
 670
 671
 672 #else
 673                 bestfit = findPairs(lines[0]->start, lines[0]->end);
 674 #endif
 675         }
 676         catch(exception& e) {
 677                 errorOut(e, "Pintail", "createProcessesPairs");
 678                 exit(1);
 679         }
 680 }
 681 /**************************************************************************************************/
 682
 683 void Pintail::createProcesses() {
 684         try {
 685 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 686                 int process = 0;
 687                 vector<int> processIDS;
 688
 689                 //loop through and create all the processes you want
 690                 while (process != processors) {
 691                         int pid = fork();
 692
 693                         if (pid > 0) {
 694                                 processIDS.push_back(pid);
 695                                 process++;
 696                         }else if (pid == 0){
 697
 698                                 mothurOut("Calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 699                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 700
 701                                         vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
 702                                         obsDistance[i] = obsi;
 703
 704                                         //calc Qav
 705                                         vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
 706
 707                                         //get alpha
 708                                         float alpha = decalc->getCoef(obsDistance[i], q);
 709
 710                                         //find expected
 711                                         vector<float> exp = decalc->calcExpected(q, alpha);
 712                                         expectedDistance[i] = exp;
 713
 714                                         //get de and deviation
 715                                         float dei = decalc->calcDE(obsi, exp);
 716                                         DE[i] = dei;
 717
 718                                         it = trimmed[i].begin();
 719                                         float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 720                                         deviation[i] = dist;
 721                                 }
 722                                 mothurOut("Done calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
 723
 724                                 //write out data to file so parent can read it
 725                                 ofstream out;
 726                                 string s = toString(getpid()) + ".temp";
 727                                 openOutputFile(s, out);
 728
 729                                 int size = lines[process]->end - lines[process]->start;
 730                                 out << size << endl;
 731
 732                                 //output observed distances
 733                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 734                                         out << obsDistance[i].size() << '\t';
 735                                         for (int j = 0; j < obsDistance[i].size(); j++) {
 736                                                 out << obsDistance[i][j] << '\t';
 737                                         }
 738                                         out << endl;
 739                                 }
 740
 741
 742                                 //output expected distances
 743                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 744                                         out << expectedDistance[i].size() << '\t';
 745                                         for (int j = 0; j < expectedDistance[i].size(); j++) {
 746                                                 out << expectedDistance[i][j] << '\t';
 747                                         }
 748                                         out << endl;
 749                                 }
 750
 751
 752                                 //output de values
 753                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 754                                         out << DE[i] << '\t';
 755                                 }
 756                                 out << endl;
 757
 758                                 //output de values
 759                                 for (int i = lines[process]->start; i < lines[process]->end; i++) {
 760                                         out << deviation[i] << '\t';
 761                                 }
 762                                 out << endl;
 763
 764                                 out.close();
 765
 766                                 exit(0);
 767                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 768                 }
 769
 770                 //force parent to wait until all the processes are done
 771                 for (int i=0;i<processors;i++) {
 772                         int temp = processIDS[i];
 773                         wait(&temp);
 774                 }
 775
 776                 //get data created by processes
 777                 for (int i=0;i<processors;i++) {
 778                         ifstream in;
 779                         string s = toString(processIDS[i]) + ".temp";
 780                         openInputFile(s, in);
 781
 782                         int size;
 783                         in >> size;  gobble(in);
 784
 785                         //get observed distances
 786                         int count = lines[i]->start;
 787                         for (int m = 0; m < size; m++) {
 788                                 int num;
 789                                 in >> num;
 790
 791                                 vector<float> obs;  float w;
 792                                 for (int j = 0; j < num; j++) {
 793                                         in >> w;
 794                                         obs.push_back(w);
 795                                 }
 796
 797                                 obsDistance[count] = obs;
 798                                 count++;
 799                                 gobble(in);
 800                         }
 801
 802                         gobble(in);
 803
 804                         //get expected distances
 805                         count = lines[i]->start;
 806                         for (int m = 0; m < size; m++) {
 807                                 int num;
 808                                 in >> num;
 809
 810                                 vector<float> exp;  float w;
 811                                 for (int j = 0; j < num; j++) {
 812                                         in >> w;
 813                                         exp.push_back(w);
 814                                 }
 815
 816                                 expectedDistance[count] = exp;
 817                                 count++;
 818                                 gobble(in);
 819                         }
 820
 821                         gobble(in);
 822
 823                         count = lines[i]->start;
 824                         for (int m = 0; m < size; m++) {
 825                                 float num;
 826                                 in >> num;
 827
 828                                 DE[count] = num;
 829                                 count++;
 830                         }
 831
 832                         gobble(in);
 833
 834                         count = lines[i]->start;
 835                         for (int m = 0; m < size; m++) {
 836                                 float num;
 837                                 in >> num;
 838
 839                                 deviation[count] = num;
 840                                 count++;
 841                         }
 842
 843                         in.close();
 844                         remove(s.c_str());
 845                 }
 846
 847
 848 #else
 849                         mothurOut("Calculating observed distance... "); cout.flush();
 850                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 851                                 vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
 852                                 obsDistance[i] = obsi;
 853                         }
 854                         mothurOut("Done."); mothurOutEndLine();
 855
 856
 857
 858                         mothurOut("Finding variability... "); cout.flush();
 859                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 860                                 vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
 861                                 Qav[i] = q;
 862                         }
 863                         mothurOut("Done."); mothurOutEndLine();
 864
 865
 866
 867                         mothurOut("Calculating alpha... "); cout.flush();
 868                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 869                                 float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
 870                                 seqCoef.push_back(alpha);
 871                         }
 872                         mothurOut("Done."); mothurOutEndLine();
 873
 874
 875
 876                         mothurOut("Calculating expected distance... "); cout.flush();
 877                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 878                                 vector<float> exp = decalc->calcExpected(Qav[i], seqCoef[i]);
 879                                 expectedDistance[i] = exp;
 880                         }
 881                         mothurOut("Done."); mothurOutEndLine();
 882
 883
 884
 885                         mothurOut("Finding deviation... "); cout.flush();
 886                         for (int i = lines[0]->start; i < lines[0]->end; i++) {
 887                                 float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
 888                                 DE[i] = de;
 889
 890                                 it = trimmed[i].begin();
 891                                 float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
 892                                 deviation[i] = dist;
 893                         }
 894                         mothurOut("Done."); mothurOutEndLine();
 895
 896 #endif
 897         }
 898         catch(exception& e) {
 899                 errorOut(e, "Pintail", "createProcesses");
 900                 exit(1);
 901         }
 902 }
 903
 904
 905 /**************************************************************************************************/
 906
 907 void Pintail::createProcessesQuan() {
 908         try {
 909 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 910                 int process = 0;
 911                 vector<int> processIDS;
 912
 913                 //loop through and create all the processes you want
 914                 while (process != processors) {
 915                         int pid = fork();
 916
 917                         if (pid > 0) {
 918                                 processIDS.push_back(pid);
 919                                 process++;
 920                         }else if (pid == 0){
 921
 922                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 923
 924                                 //write out data to file so parent can read it
 925                                 ofstream out;
 926                                 string s = toString(getpid()) + ".temp";
 927                                 openOutputFile(s, out);
 928
 929
 930                                 //output observed distances
 931                                 for (int i = 0; i < quantilesMembers.size(); i++) {
 932                                         out << quantilesMembers[i].size() << '\t';
 933                                         for (int j = 0; j < quantilesMembers[i].size(); j++) {
 934                                                 out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
 935                                         }
 936                                         out << endl;
 937                                 }
 938
 939                                 out.close();
 940
 941                                 exit(0);
 942                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 943                 }
 944
 945                 //force parent to wait until all the processes are done
 946                 for (int i=0;i<processors;i++) {
 947                         int temp = processIDS[i];
 948                         wait(&temp);
 949                 }
 950
 951                 //get data created by processes
 952                 for (int i=0;i<processors;i++) {
 953                         ifstream in;
 954                         string s = toString(processIDS[i]) + ".temp";
 955                         openInputFile(s, in);
 956
 957                         vector< vector<quanMember> > quan;
 958                         quan.resize(100);
 959
 960                         //get quantiles
 961                         for (int m = 0; m < quan.size(); m++) {
 962                                 int num;
 963                                 in >> num;
 964
 965                                 gobble(in);
 966
 967                                 vector<quanMember> q;  float w; int b, n;
 968                                 for (int j = 0; j < num; j++) {
 969                                         in >> w >> b >> n;
 970         //cout << w << '\t' << b << '\t' n << endl;
 971                                         quanMember newMember(w, b, n);
 972                                         q.push_back(newMember);
 973                                 }
 974 //cout << "here" << endl;
 975                                 quan[m] = q;
 976 //cout << "now here" << endl;
 977                                 gobble(in);
 978                         }
 979
 980
 981                         //save quan in quantiles
 982                         for (int j = 0; j < quan.size(); j++) {
 983                                 //put all values of q[i] into quan[i]
 984                                 for (int l = 0; l < quan[j].size(); l++) {  quantilesMembers[j].push_back(quan[j][l]);   }
 985                                 //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
 986                         }
 987
 988                         in.close();
 989                         remove(s.c_str());
 990                 }
 991
 992 #else
 993                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 994 #endif
 995         }
 996         catch(exception& e) {
 997                 errorOut(e, "Pintail", "createProcessesQuan");
 998                 exit(1);
 999         }
1000 }
1001
1002
1003 //***************************************************************************************************************
1004
1005