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