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