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 o) {
  22         fastafile = filename;  outputDir = o;
  23         distcalculator = new eachGapDist();
  24         decalc = new DeCalculator();
  25 }
  26 //***************************************************************************************************************
  27
  28 Pintail::~Pintail() {
  29         try {
  30
  31                 delete distcalculator;
  32                 delete decalc;
  33         }
  34         catch(exception& e) {
  35                 errorOut(e, "Pintail", "~Pintail");
  36                 exit(1);
  37         }
  38 }
  39 //***************************************************************************************************************
  40 void Pintail::doPrep() {
  41         try {
  42
  43                 mergedFilterString = "";
  44                 windowSizesTemplate.resize(templateSeqs.size(), window);
  45                 quantiles.resize(100);  //one for every percent mismatch
  46                 quantilesMembers.resize(100);  //one for every percent mismatch
  47
  48                 //if the user does not enter a mask then you want to keep all the spots in the alignment
  49                 if (seqMask.length() == 0)      {       decalc->setAlignmentLength(templateSeqs[0]->getAligned().length());     }
  50                 else                                            {       decalc->setAlignmentLength(seqMask.length());                                           }
  51
  52                 decalc->setMask(seqMask);
  53
  54                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  55                         //find breakup of templatefile for quantiles
  56                         if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
  57                         else {
  58                                 for (int i = 0; i < processors; i++) {
  59                                         templateLines.push_back(new linePair());
  60                                         templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
  61                                         templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
  62                                 }
  63                         }
  64                 #else
  65                         templateLines.push_back(new linePair(0, templateSeqs.size()));
  66                 #endif
  67
  68
  69                 mothurOut("Getting conservation... "); cout.flush();
  70                 if (consfile == "") {
  71                         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();
  72                         probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName));
  73                         mothurOut("Done."); mothurOutEndLine();
  74                 }else                           {   probabilityProfile = readFreq();    mothurOut("Done.");               }
  75                 mothurOutEndLine();
  76
  77                 //make P into Q
  78                 for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];  }  //cout << i << '\t' << probabilityProfile[i] << endl;
  79
  80                 bool reRead = false;
  81                 //create filter if needed for later
  82                 if (filter) {
  83
  84                         //read in all query seqs
  85                         ifstream in;
  86                         openInputFile(fastafile, in);
  87
  88                         vector<Sequence*> tempQuerySeqs;
  89                         while(!in.eof()){
  90                                 Sequence* s = new Sequence(in);
  91                                 gobble(in);
  92
  93                                 if (s->getName() != "") { tempQuerySeqs.push_back(s); }
  94                         }
  95                         in.close();
  96
  97                         vector<Sequence*> temp;
  98                         //merge query seqs and template seqs
  99                         temp = templateSeqs;
 100                         for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
 101
 102                         if (seqMask != "") {
 103                             reRead = true;
 104                                 //mask templates
 105                                 for (int i = 0; i < temp.size(); i++) {
 106                                         decalc->runMask(temp[i]);
 107                                 }
 108                         }
 109
 110                         mergedFilterString = createFilter(temp, 0.5);
 111
 112                         //reread template seqs
 113                         for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 114                 }
 115
 116
 117                 //quantiles are used to determine whether the de values found indicate a chimera
 118                 //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
 119                 //combination of sequences in the template
 120                 if (quanfile != "") {
 121                         quantiles = readQuantiles();
 122                 }else {
 123                         if ((!filter) && (seqMask != "")) { //if you didn't filter but you want to mask. if you filtered then you did mask first above.
 124                                 reRead = true;
 125                                 //mask templates
 126                                 for (int i = 0; i < templateSeqs.size(); i++) {
 127                                         decalc->runMask(templateSeqs[i]);
 128                                 }
 129                         }
 130
 131                         if (filter) {
 132                                 reRead = true;
 133                                 for (int i = 0; i < templateSeqs.size(); i++) {
 134                                         runFilter(templateSeqs[i]);
 135                                 }
 136                         }
 137
 138                         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();
 139                         if (processors == 1) {
 140                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 141                         }else {         createProcessesQuan();          }
 142
 143
 144                         ofstream out4, out5;
 145                         string noOutliers, outliers;
 146
 147                         if ((!filter) && (seqMask == "")) {
 148                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
 149                         }else if ((!filter) && (seqMask != "")) {
 150                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
 151                         }else if ((filter) && (seqMask != "")) {
 152                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "masked.quan";
 153                         }else if ((filter) && (seqMask == "")) {
 154                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
 155                         }
 156
 157
 158
 159
 160                         decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
 161
 162                         openOutputFile(noOutliers, out5);
 163                         //adjust quantiles
 164                         for (int i = 0; i < quantilesMembers.size(); i++) {
 165                                 vector<float> temp;
 166
 167                                 if (quantilesMembers[i].size() == 0) {
 168                                         //in case this is not a distance found in your template files
 169                                         for (int g = 0; g < 6; g++) {
 170                                                 temp.push_back(0.0);
 171                                         }
 172                                 }else{
 173
 174                                         sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
 175
 176                                         //save 10%
 177                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
 178                                         //save 25%
 179                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
 180                                         //save 50%
 181                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
 182                                         //save 75%
 183                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
 184                                         //save 95%
 185                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
 186                                         //save 99%
 187                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
 188
 189                                 }
 190
 191                                 //output quan value
 192                                 out5 << i+1 << '\t';
 193                                 for (int u = 0; u < temp.size(); u++) {   out5 << temp[u] << '\t'; }
 194                                 out5 << endl;
 195
 196                                 quantiles[i] = temp;
 197
 198                         }
 199
 200                         mothurOut("Done."); mothurOutEndLine();
 201                 }
 202
 203                 if (reRead) {
 204                         for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  }
 205                         templateSeqs.clear();
 206                         templateSeqs = readSeqs(templateFileName);
 207                 }
 208
 209
 210                 //free memory
 211                 for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i];  }
 212
 213         }
 214         catch(exception& e) {
 215                 errorOut(e, "Pintail", "doPrep");
 216                 exit(1);
 217         }
 218 }
 219 //***************************************************************************************************************
 220 void Pintail::print(ostream& out, ostream& outAcc) {
 221         try {
 222                 int index = ceil(deviation);
 223
 224                 //is your DE value higher than the 95%
 225                 string chimera;
 226                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 227                         if (quantiles[index][4] == 0.0) {
 228                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 229                         }else {
 230                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 231                                 else                                                            {       chimera = "No";         }
 232                         }
 233                 }else{ chimera = "No";          }
 234
 235                 out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
 236                 if (chimera == "Yes") {
 237                         mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); mothurOutEndLine();
 238                         outAcc << querySeq->getName() << endl;
 239                 }
 240                 out << "Observed\t";
 241
 242                 for (int j = 0; j < obsDistance.size(); j++) {  out << obsDistance[j] << '\t';  }
 243                 out << endl;
 244
 245                 out << "Expected\t";
 246
 247                 for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 248                 out << endl;
 249
 250
 251         }
 252         catch(exception& e) {
 253                 errorOut(e, "Pintail", "print");
 254                 exit(1);
 255         }
 256 }
 257
 258 //***************************************************************************************************************
 259 int Pintail::getChimeras(Sequence* query) {
 260         try {
 261                 querySeq = query;
 262                 trimmed.clear();
 263                 windowSizes = window;
 264
 265                 //find pairs has to be done before a mask
 266                 bestfit = findPairs(query);
 267
 268                 //if they mask
 269                 if (seqMask != "") {
 270                         decalc->runMask(query);
 271                         decalc->runMask(bestfit);
 272                 }
 273
 274                 if (filter) { //must be done after a mask
 275                         runFilter(query);
 276                         runFilter(bestfit);
 277                 }
 278
 279
 280                 //trim seq
 281                 decalc->trimSeqs(query, bestfit, trimmed);
 282
 283                 //find windows
 284                 it = trimmed.begin();
 285                 windowsForeachQuery = decalc->findWindows(query, it->first, it->second, windowSizes, increment);
 286
 287                 //find observed distance
 288                 obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
 289
 290                 Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
 291
 292                 //find alpha
 293                 seqCoef = decalc->getCoef(obsDistance, Qav);
 294
 295                 //calculating expected distance
 296                 expectedDistance = decalc->calcExpected(Qav, seqCoef);
 297
 298                 //finding de
 299                 DE = decalc->calcDE(obsDistance, expectedDistance);
 300
 301                 //find distance between query and closest match
 302                 it = trimmed.begin();
 303                 deviation = decalc->calcDist(query, bestfit, it->first, it->second);
 304
 305                 delete bestfit;
 306
 307                 return 0;
 308         }
 309         catch(exception& e) {
 310                 errorOut(e, "Pintail", "getChimeras");
 311                 exit(1);
 312         }
 313 }
 314
 315 //***************************************************************************************************************
 316
 317 vector<float> Pintail::readFreq() {
 318         try {
 319
 320                 ifstream in;
 321                 openInputFile(consfile, in);
 322
 323                 vector<float> prob;
 324                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 325
 326                 //read in probabilities and store in vector
 327                 int pos; float num;
 328
 329                 while(!in.eof()){
 330
 331                         in >> pos >> num;
 332
 333                         if (h.count(pos) > 0) {
 334                                 float Pi;
 335                                 Pi =  (num - 0.25) / 0.75;
 336
 337                                 //cannot have probability less than 0.
 338                                 if (Pi < 0) { Pi = 0.0; }
 339
 340                                 //do you want this spot
 341                                 prob.push_back(Pi);
 342                         }
 343
 344                         gobble(in);
 345                 }
 346
 347                 in.close();
 348                 return prob;
 349
 350         }
 351         catch(exception& e) {
 352                 errorOut(e, "Pintail", "readFreq");
 353                 exit(1);
 354         }
 355 }
 356
 357 //***************************************************************************************************************
 358 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 359 Sequence* Pintail::findPairs(Sequence* q) {
 360         try {
 361
 362                 Sequence* seqsMatches;
 363
 364                 seqsMatches = decalc->findClosest(q, templateSeqs);
 365                 return seqsMatches;
 366
 367         }
 368         catch(exception& e) {
 369                 errorOut(e, "Pintail", "findPairs");
 370                 exit(1);
 371         }
 372 }
 373 /**************************************************************************************************/
 374 void Pintail::createProcessesQuan() {
 375         try {
 376 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 377                 int process = 0;
 378                 vector<int> processIDS;
 379
 380                 //loop through and create all the processes you want
 381                 while (process != processors) {
 382                         int pid = fork();
 383
 384                         if (pid > 0) {
 385                                 processIDS.push_back(pid);
 386                                 process++;
 387                         }else if (pid == 0){
 388
 389                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 390
 391                                 //write out data to file so parent can read it
 392                                 ofstream out;
 393                                 string s = toString(getpid()) + ".temp";
 394                                 openOutputFile(s, out);
 395
 396
 397                                 //output observed distances
 398                                 for (int i = 0; i < quantilesMembers.size(); i++) {
 399                                         out << quantilesMembers[i].size() << '\t';
 400                                         for (int j = 0; j < quantilesMembers[i].size(); j++) {
 401                                                 out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
 402                                         }
 403                                         out << endl;
 404                                 }
 405
 406                                 out.close();
 407
 408                                 exit(0);
 409                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 410                 }
 411
 412                 //force parent to wait until all the processes are done
 413                 for (int i=0;i<processors;i++) {
 414                         int temp = processIDS[i];
 415                         wait(&temp);
 416                 }
 417
 418                 //get data created by processes
 419                 for (int i=0;i<processors;i++) {
 420                         ifstream in;
 421                         string s = toString(processIDS[i]) + ".temp";
 422                         openInputFile(s, in);
 423
 424                         vector< vector<quanMember> > quan;
 425                         quan.resize(100);
 426
 427                         //get quantiles
 428                         for (int m = 0; m < quan.size(); m++) {
 429                                 int num;
 430                                 in >> num;
 431
 432                                 gobble(in);
 433
 434                                 vector<quanMember> q;  float w; int b, n;
 435                                 for (int j = 0; j < num; j++) {
 436                                         in >> w >> b >> n;
 437         //cout << w << '\t' << b << '\t' n << endl;
 438                                         quanMember newMember(w, b, n);
 439                                         q.push_back(newMember);
 440                                 }
 441 //cout << "here" << endl;
 442                                 quan[m] = q;
 443 //cout << "now here" << endl;
 444                                 gobble(in);
 445                         }
 446
 447
 448                         //save quan in quantiles
 449                         for (int j = 0; j < quan.size(); j++) {
 450                                 //put all values of q[i] into quan[i]
 451                                 for (int l = 0; l < quan[j].size(); l++) {  quantilesMembers[j].push_back(quan[j][l]);   }
 452                                 //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
 453                         }
 454
 455                         in.close();
 456                         remove(s.c_str());
 457                 }
 458
 459 #else
 460                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 461 #endif
 462         }
 463         catch(exception& e) {
 464                 errorOut(e, "Pintail", "createProcessesQuan");
 465                 exit(1);
 466         }
 467 }
 468
 469
 470 //***************************************************************************************************************
 471
 472