bellerophon.cpp

   1 /*
   2  *  bellerophon.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 "bellerophon.h"
  11 #include "eachgapdist.h"
  12 #include "ignoregaps.h"
  13 #include "onegapdist.h"
  14
  15
  16 //***************************************************************************************************************
  17
  18 Bellerophon::Bellerophon(string name, string o)  {
  19         try {
  20                 fastafile = name;
  21                 outputDir = o;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "Bellerophon", "Bellerophon");
  25                 exit(1);
  26         }
  27 }
  28
  29 //***************************************************************************************************************
  30 int Bellerophon::print(ostream& out, ostream& outAcc) {
  31         try {
  32                 int above1 = 0;
  33                 out << "Name\tScore\tLeft\tRight\t" << endl;
  34                 //output prefenence structure to .chimeras file
  35                 for (int i = 0; i < pref.size(); i++) {
  36
  37                         if (m->control_pressed) {  return 0; }
  38
  39                         out << pref[i].name << '\t' << setprecision(3) << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
  40
  41                         //calc # of seqs with preference above 1.0
  42                         if (pref[i].score[0] > 1.0) {
  43                                 above1++;
  44                                 outAcc << pref[i].name << endl;
  45                                 m->mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); m->mothurOutEndLine();
  46                                 m->mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); m->mothurOutEndLine();
  47                         }
  48                 }
  49
  50                 //output results to screen
  51                 m->mothurOutEndLine();
  52                 m->mothurOut("Sequence with preference score above 1.0: " + toString(above1)); m->mothurOutEndLine();
  53                 int spot;
  54                 spot = pref.size()-1;
  55                 m->mothurOut("Minimum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  56                 spot = pref.size() * 0.975;
  57                 m->mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  58                 spot = pref.size() * 0.75;
  59                 m->mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  60                 spot = pref.size() * 0.50;
  61                 m->mothurOut("Median: \t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  62                 spot = pref.size() * 0.25;
  63                 m->mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  64                 spot = pref.size() * 0.025;
  65                 m->mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  66                 spot = 0;
  67                 m->mothurOut("Maximum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
  68
  69                 return 1;
  70
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "Bellerophon", "print");
  74                 exit(1);
  75         }
  76 }
  77
  78 //********************************************************************************************************************
  79 //sorts highest score to lowest
  80 inline bool comparePref(Preference left, Preference right){
  81         return (left.score[0] > right.score[0]);
  82 }
  83
  84 //***************************************************************************************************************
  85 int Bellerophon::getChimeras() {
  86         try {
  87
  88                 //do soft filter
  89                 if (filter)  {
  90                         string optionString = "fasta=" + fastafile + ", soft=50";
  91                         if (outputDir != "") { optionString += ", outputdir=" + outputDir; }
  92
  93                         filterSeqs = new FilterSeqsCommand(optionString);
  94                         filterSeqs->execute();
  95                         delete filterSeqs;
  96
  97                         if (m->control_pressed) { return 0; }
  98
  99                         //reset fastafile to filtered file
 100                         if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
 101                         else                             { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
 102
 103                 }
 104
 105                 distCalculator = new eachGapDist();
 106
 107                 //read in sequences
 108                 seqs = readSeqs(fastafile);
 109
 110                 if (m->control_pressed) { return 0; }
 111
 112                 if (unaligned) { m->mothurOut("Your sequences need to be aligned when you use the bellerophon method."); m->mothurOutEndLine(); return 1;  }
 113
 114                 int numSeqs = seqs.size();
 115
 116                 if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); }
 117
 118                 //set default window to 25% of sequence length
 119                 string seq0 = seqs[0]->getAligned();
 120                 if (window == 0) { window = seq0.length() / 4;  }
 121                 else if (window > (seq0.length() / 2)) {
 122                         m->mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); m->mothurOutEndLine();
 123                         window = (seq0.length() / 2);
 124                 }
 125
 126                 if (increment > (seqs[0]->getAlignLength() - (2*window))) {
 127                         if (increment != 10) {
 128
 129                                 m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine();
 130                                 increment = 10;
 131                                 if (increment > (seqs[0]->getAlignLength() - (2*window))) {  increment = 0;  }
 132
 133                         }else{ increment = 0; }
 134                 }
 135
 136                 if (increment == 0) { iters = 1; }
 137                 else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
 138
 139                 //initialize pref
 140                 pref.resize(numSeqs);
 141
 142                 for (int i = 0; i < numSeqs; i++ ) {
 143                         pref[i].leftParent.resize(2); pref[i].rightParent.resize(2); pref[i].score.resize(2);   pref[i].closestLeft.resize(2); pref[i].closestRight.resize(3);
 144                         pref[i].name = seqs[i]->getName();
 145                         pref[i].score[0] = 0.0;  pref[i].score[1] = 0.0;
 146                         pref[i].closestLeft[0] = 100000.0;  pref[i].closestLeft[1] = 100000.0;
 147                         pref[i].closestRight[0] = 100000.0;  pref[i].closestRight[1] = 100000.0;
 148                 }
 149
 150                 int midpoint = window;
 151                 int count = 0;
 152                 while (count < iters) {
 153
 154                                 if (m->control_pressed) { return 0; }
 155
 156                                 //create 2 vectors of sequences, 1 for left side and one for right side
 157                                 vector<Sequence> left;  vector<Sequence> right;
 158
 159                                 for (int i = 0; i < seqs.size(); i++) {
 160
 161                                         if (m->control_pressed) { return 0; }
 162
 163 //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
 164 //cout << "whole = " << seqs[i]->getAligned().length() << endl;
 165                                         //save left side
 166                                         string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
 167                                         Sequence tempLeft;
 168                                         tempLeft.setName(seqs[i]->getName());
 169                                         tempLeft.setAligned(seqLeft);
 170                                         left.push_back(tempLeft);
 171 //cout << "left = " << tempLeft.getAligned().length() << endl;
 172                                         //save right side
 173                                         string seqRight = seqs[i]->getAligned().substr(midpoint, window);
 174                                         Sequence tempRight;
 175                                         tempRight.setName(seqs[i]->getName());
 176                                         tempRight.setAligned(seqRight);
 177                                         right.push_back(tempRight);
 178 //cout << "right = " << seqRight.length() << endl;
 179                                 }
 180
 181                                 //adjust midpoint by increment
 182                                 midpoint += increment;
 183
 184
 185                                 //this should be parallelized
 186                                 //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
 187                                 //create a matrix containing the distance from left to left and right to right
 188                                 //calculate distances
 189                                 SparseMatrix* SparseLeft = new SparseMatrix();
 190                                 SparseMatrix* SparseRight = new SparseMatrix();
 191
 192                                 createSparseMatrix(0, left.size(), SparseLeft, left);
 193
 194                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 195
 196                                 createSparseMatrix(0, right.size(), SparseRight, right);
 197
 198                                 if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 199
 200                                 vector<SeqMap> distMapRight;
 201                                 vector<SeqMap> distMapLeft;
 202
 203                                 // Create a data structure to quickly access the distance information.
 204                                 //this is from thallingers reimplementation on get.oturep
 205                                 // It consists of a vector of distance maps, where each map contains
 206                                 // all distances of a certain sequence. Vector and maps are accessed
 207                                 // via the index of a sequence in the distance matrix
 208                                 distMapRight = vector<SeqMap>(numSeqs);
 209                                 distMapLeft = vector<SeqMap>(numSeqs);
 210                                 //cout << "left" << endl << endl;
 211                                 for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
 212                                         distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
 213                                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 214                                         //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 215                                 }
 216                                 //cout << "right" << endl << endl;
 217                                 for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
 218                                         distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
 219                                         if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
 220                                         //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 221                                 }
 222
 223                                 delete SparseLeft;
 224                                 delete SparseRight;
 225
 226                                 //fill preference structure
 227                                 generatePreferences(distMapLeft, distMapRight, midpoint);
 228
 229                                 count++;
 230
 231                 }
 232
 233                 delete distCalculator;
 234
 235                 //rank preference score to eachother
 236                 float dme = 0.0;
 237                 float expectedPercent = 1 / (float) (pref.size());
 238
 239                 for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[0];  }
 240
 241                 for (int i = 0; i < pref.size(); i++) {
 242
 243                         //gives the actual percentage of the dme this seq adds
 244                         pref[i].score[0] = pref[i].score[0] / dme;
 245
 246                         //how much higher or lower is this than expected
 247                         pref[i].score[0] = pref[i].score[0] / expectedPercent;
 248
 249                 }
 250
 251                 //sort Preferences highest to lowest
 252                 sort(pref.begin(), pref.end(), comparePref);
 253
 254                 return 0;
 255
 256         }
 257         catch(exception& e) {
 258                 m->errorOut(e, "Bellerophon", "getChimeras");
 259                 exit(1);
 260         }
 261 }
 262
 263 /***************************************************************************************************************/
 264 int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
 265         try {
 266
 267                 for(int i=startSeq; i<endSeq; i++){
 268
 269                         for(int j=0;j<i;j++){
 270
 271                                 if (m->control_pressed) { return 0; }
 272
 273                                 distCalculator->calcDist(s[i], s[j]);
 274                                 float dist = distCalculator->getDist();
 275
 276                                 PCell temp(i, j, dist);
 277                                 sparse->addCell(temp);
 278
 279                         }
 280                 }
 281
 282                 return 1;
 283         }
 284         catch(exception& e) {
 285                 m->errorOut(e, "Bellerophon", "createSparseMatrix");
 286                 exit(1);
 287         }
 288 }
 289 /***************************************************************************************************************/
 290 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
 291         try {
 292
 293                 float dme = 0.0;
 294                 SeqMap::iterator itR;
 295                 SeqMap::iterator itL;
 296
 297                 //initialize pref[i]
 298                 for (int i = 0; i < pref.size(); i++) {
 299                         pref[i].score[1] = 0.0;
 300                         pref[i].closestLeft[1] = 100000.0;
 301                         pref[i].closestRight[1] = 100000.0;
 302                         pref[i].leftParent[1] = "";
 303                         pref[i].rightParent[1] = "";
 304                 }
 305
 306                 for (int i = 0; i < left.size(); i++) {
 307
 308                         SeqMap currentLeft = left[i];    //example i = 3;   currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
 309                                                                                                 //                                                                              1 to the distance of sequence 3 to sequence 1,
 310                                                                                                 //                                                                              2 to the distance of sequence 3 to sequence 2.
 311                         SeqMap currentRight = right[i];         // same as left but with distances on the right side.
 312
 313                         for (int j = 0; j < i; j++) {
 314
 315                                 if (m->control_pressed) {  return 0; }
 316
 317                                 itL = currentLeft.find(j);
 318                                 itR = currentRight.find(j);
 319 //cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
 320 //cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
 321
 322                                 //if you can find this entry update the preferences
 323                                 if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
 324
 325                                         if (!correction) {
 326                                                 pref[i].score[1] += abs((itL->second - itR->second));
 327                                                 pref[j].score[1] += abs((itL->second - itR->second));
 328 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 329 //cout << "abs = " << abs((itL->second - itR->second)) << endl;
 330 //cout << i << " score = " << pref[i].score[1] << endl;
 331 //cout << j << " score = " << pref[j].score[1] << endl;
 332                                         }else {
 333                                                 pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
 334                                                 pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
 335 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 336 //cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
 337 //cout << i << " score = " << pref[i].score[1] << endl;
 338 //cout << j << " score = " << pref[j].score[1] << endl;
 339                                         }
 340 //cout << "pref[" << i << "].closestLeft[1] = " <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
 341                                         //are you the closest left sequence
 342                                         if (itL->second < pref[i].closestLeft[1]) {
 343
 344                                                 pref[i].closestLeft[1] = itL->second;
 345                                                 pref[i].leftParent[1] = seqs[j]->getName();
 346 //cout << "updating closest left to " << pref[i].leftParent[1] << endl;
 347                                         }
 348 //cout << "pref[" << j << "].closestLeft[1] = " <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
 349                                         if (itL->second < pref[j].closestLeft[1]) {
 350                                                 pref[j].closestLeft[1] = itL->second;
 351                                                 pref[j].leftParent[1] = seqs[i]->getName();
 352 //cout << "updating closest left to " << pref[j].leftParent[1] << endl;
 353                                         }
 354
 355                                         //are you the closest right sequence
 356                                         if (itR->second < pref[i].closestRight[1]) {
 357                                                 pref[i].closestRight[1] = itR->second;
 358                                                 pref[i].rightParent[1] = seqs[j]->getName();
 359                                         }
 360                                         if (itR->second < pref[j].closestRight[1]) {
 361                                                 pref[j].closestRight[1] = itR->second;
 362                                                 pref[j].rightParent[1] = seqs[i]->getName();
 363                                         }
 364
 365                                 }
 366                         }
 367
 368                 }
 369
 370
 371
 372                 //calculate the dme
 373                 int count0 = 0;
 374                 for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[1];  if (pref[i].score[1] == 0.0) { count0++; }  }
 375
 376                 float expectedPercent = 1 / (float) (pref.size() - count0);
 377 //cout << endl << "dme = " << dme << endl;
 378                 //recalculate prefernences based on dme
 379                 for (int i = 0; i < pref.size(); i++) {
 380
 381                         if (m->control_pressed) {  return 0; }
 382 //cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;
 383                         // gives the actual percentage of the dme this seq adds
 384                         pref[i].score[1] = pref[i].score[1] / dme;
 385
 386                         //how much higher or lower is this than expected
 387                         pref[i].score[1] = pref[i].score[1] / expectedPercent;
 388
 389                         //pref[i].score[1] = dme / (dme - 2 * pref[i].score[1]);
 390
 391                         //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
 392 //cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
 393                 }
 394
 395                 //is this score bigger then the last score
 396                 for (int i = 0; i < pref.size(); i++) {
 397
 398                         if (m->control_pressed) {  return 0; }
 399
 400                         //update biggest score
 401                         if (pref[i].score[1] > pref[i].score[0]) {
 402                                 pref[i].score[0] = pref[i].score[1];
 403                                 pref[i].leftParent[0] = pref[i].leftParent[1];
 404                                 pref[i].rightParent[0] = pref[i].rightParent[1];
 405                                 pref[i].closestLeft[0] = pref[i].closestLeft[1];
 406                                 pref[i].closestRight[0] = pref[i].closestRight[1];
 407                                 pref[i].midpoint = mid;
 408                         }
 409
 410                 }
 411
 412                 return 1;
 413
 414         }
 415         catch(exception& e) {
 416                 m->errorOut(e, "Bellerophon", "generatePreferences");
 417                 exit(1);
 418         }
 419 }
 420 /**************************************************************************************************/
 421