slayer.cpp

   1 /*
   2  *  slayer.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/25/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "slayer.h"
  11
  12 /***********************************************************************/
  13 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
  14                 minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
  15 /***********************************************************************/
  16 string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
  17         try {
  18                 vector<data_struct> all; all.clear();
  19                 myQuery = *query;
  20
  21                 for (int i = 0; i < refSeqs.size(); i++) {
  22
  23                         for (int j = i+1; j < refSeqs.size(); j++) {
  24
  25                                 if (m->control_pressed) { return "no";  }
  26
  27                                 //make copies of query and each parent because runBellerophon removes gaps and messes them up
  28                                 Sequence* q = new Sequence(query->getName(), query->getAligned());
  29                                 Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
  30                                 Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
  31                 //cout << "parents: (" << refSeqs[i]->getName() << ", " << refSeqs[j]->getName() << ")\n";
  32                                 map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
  33                                 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
  34                                 //cout << divs.size() << endl;
  35                                 if (m->control_pressed) {
  36                                         delete q;
  37                                         delete leftParent;
  38                                         delete rightParent;
  39                                         return "no";
  40                                 }
  41
  42 //                              cout << divs.size() << endl;
  43                                 vector<data_struct> selectedDivs;
  44                                 for (int k = 0; k < divs.size(); k++) {
  45
  46                                         vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  47                                         vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  48                                         //cout << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << '\t' << k << divs[k].parentA.getAligned() << endl << divs[k].parentB.getAligned() << endl;
  49                                         if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  50
  51                                         int numSNPSLeft = snpsLeft.size();
  52                                         int numSNPSRight = snpsRight.size();
  53
  54                                         //require at least 4 SNPs on each side of the break
  55                                         if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
  56
  57                                                 float BS_A, BS_B;
  58                                                 bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
  59
  60                                                 if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  61
  62                                                 divs[k].bsa = BS_A;
  63                                                 divs[k].bsb = BS_B;
  64                                                 divs[k].bsMax = max(BS_A, BS_B);
  65                                                 divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  66
  67
  68                                                 //are we within 10 points of the bootstrap cutoff?
  69                                                 if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
  70                                                         snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  71                                                         snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  72
  73                                                         if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  74
  75                                                         numSNPSLeft = snpsLeft.size();
  76                                                         numSNPSRight = snpsRight.size();
  77
  78                                                         //require at least 4 SNPs on each side of the break
  79                                                         if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
  80                                                                 float BS_A, BS_B;
  81                                                                 bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
  82
  83                                                                 if (m->control_pressed) { return "no"; }
  84
  85                                                                 divs[k].bsa = BS_A;
  86                                                                 divs[k].bsb = BS_B;
  87                                                                 divs[k].bsMax = max(BS_A, BS_B);
  88                                                                 divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  89                                                         }
  90                                                 }
  91
  92                                                 //so results reflect orignal alignment
  93                                                 divs[k].winLStart = spots[divs[k].winLStart];
  94                                                 divs[k].winLEnd = spots[divs[k].winLEnd];
  95                                                 divs[k].winRStart = spots[divs[k].winRStart];
  96                                                 divs[k].winREnd = spots[divs[k].winREnd];
  97
  98                                                 selectedDivs.push_back(divs[k]);
  99                                         }
 100                                 }
 101
 102                                 //save selected
 103                                 for (int mi = 0; mi < selectedDivs.size(); mi++) {  all.push_back(selectedDivs[mi]);    }
 104
 105                                 delete q;
 106                                 delete leftParent;
 107                                 delete rightParent;
 108                         }
 109                 }
 110
 111                 // compute bootstrap support
 112                 if (all.size() > 0) {
 113                         //sort them
 114                         sort(all.begin(), all.end(), compareDataStruct);
 115                         reverse(all.begin(), all.end());
 116
 117                         outputResults = all;
 118                         return "yes";
 119                 }else {
 120                         outputResults = all;
 121                         return "no";
 122                 }
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "Slayer", "getResults");
 126                 exit(1);
 127         }
 128 }
 129 /***********************************************************************/
 130 vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
 131         try{
 132
 133                 vector<data_struct> data;
 134
 135                 //vertical filter
 136                 vector<Sequence*> temp;
 137                 temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
 138
 139                 //maps spot in new alignment to spot in alignment before filter
 140                 spots = verticalFilter(temp);  //fills baseSpots
 141
 142                 //get these to avoid numerous function calls
 143                 string query = q->getAligned();
 144                 string parentA = pA->getAligned();
 145                 string parentB = pB->getAligned();
 146                 int length = query.length();
 147 //cout << q->getName() << endl << q->getAligned() << endl << endl;
 148 //cout << pA->getName() << endl << pA->getUnaligned() << endl << endl;
 149 //cout << pB->getName() << endl << pB->getUnaligned() << endl << endl;
 150 //cout << " length = " << length << endl;
 151
 152                 //check window size
 153                 if (length < (2*windowSize+windowStep)) {
 154 //                      m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();
 155                         windowSize = length / 4;
 156                 }
 157
 158                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 159
 160                         if (m->control_pressed) { return data; }
 161
 162                         int breakpoint = i;
 163                         int leftLength = breakpoint + 1;
 164                         int rightLength = length - leftLength;
 165
 166                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 167                         float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
 168
 169                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 170                         float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
 171
 172                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 173                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
 174
 175                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 176                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 177                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 178
 179                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 180                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 181
 182                         //in original and not used
 183                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 184
 185                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 186                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 187                         //cout << q->getName() << '\t';
 188                         //cout << pA->getName() << '\t';
 189                         //cout << pB->getName() << '\t';
 190                    // cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
 191                         //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
 192 //cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA  << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' <<  QLB_QRA <<    endl;
 193
 194 //cout << divRThreshold << endl;
 195 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 196                         //is one of them above the
 197                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 198
 199                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 200                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 201
 202                                         data_struct member;
 203
 204                                         member.divr_qla_qrb = divR_QLA_QRB;
 205                                         member.divr_qlb_qra = divR_QLB_QRA;
 206                                         member.qla_qrb = QLA_QRB;
 207                                         member.qlb_qra = QLB_QRA;
 208                                         member.qla = QLA;
 209                                         member.qrb = QRB;
 210                                         member.ab = AB;
 211                                         member.qa = QA;
 212                                         member.qb = QB;
 213                                         member.lab = LAB;
 214                                         member.rab = RAB;
 215                                         member.qra = QRA;
 216                                         member.qlb = QLB;
 217                                         member.winLStart = 0;
 218                                         member.winLEnd = breakpoint;
 219                                         member.winRStart = breakpoint+1;
 220                                         member.winREnd = length-1;
 221                                         member.querySeq = *(q);
 222                                         member.parentA = *(pA);
 223                                         member.parentB = *(pB);
 224                                         member.bsa = 0;
 225                                         member.bsb = 0;
 226                                         member.bsMax = 0;
 227                                         member.chimeraMax = 0;
 228
 229                                         data.push_back(member);
 230
 231                                 }//if
 232                         }//if
 233                 }//for
 234
 235                 return data;
 236
 237         }
 238         catch(exception& e) {
 239                 m->errorOut(e, "Slayer", "runBellerophon");
 240                 exit(1);
 241         }
 242 }
 243 /***********************************************************************/
 244 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 245         try {
 246
 247                 vector<snps> data;
 248 //cout << left << '\t' << right << endl;
 249                 for (int i = left; i <= right; i++) {
 250
 251                         char A = parentA[i];
 252                         char Q = query[i];
 253                         char B = parentB[i];
 254
 255                         if ((A != Q) || (B != Q)) {
 256 //cout << "not equal " << Q << '\t' << A << '\t' << B << endl;
 257
 258                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 259                                 if (
 260                                         //did query loose a base here during filter??
 261                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 262                                         ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 263                                         &&
 264                                         //did parentA loose a base here during filter??
 265                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 266                                         ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 267                                         &&
 268                                         //did parentB loose a base here during filter??
 269                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 270                                         ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 271                                         )
 272                                 {
 273
 274                                         snps member;
 275                                         member.queryChar = Q;
 276                                         member.parentAChar = A;
 277                                         member.parentBChar = B;
 278 //cout << "not neighboring a gap " << Q << '\t' << A << '\t' << B << '\t' << baseSpots[0][i] << '\t' << baseSpots[0][i+1] << '\t' << baseSpots[0][i-1] << '\t' << baseSpots[1][i] << '\t' << baseSpots[1][i+1] << '\t' << baseSpots[1][i-1] << '\t' << baseSpots[2][i] << '\t' << baseSpots[2][i+1] << '\t' << baseSpots[2][i-1] << endl;
 279                                         data.push_back(member);
 280                                 }
 281                         }
 282 //                      cout << i << '\t' << data.size() << endl;
 283                 }
 284
 285                 return data;
 286
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "Slayer", "getSNPS");
 290                 exit(1);
 291         }
 292 }
 293 /***********************************************************************/
 294 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
 295         try {
 296
 297                 srand((unsigned)time( NULL ));
 298
 299                 int count_A = 0; // sceneario QLA,QRB supported
 300                 int count_B = 0; // sceneario QLB,QRA supported
 301
 302                 int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
 303                 int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
 304                 //cout << numLeft << '\t' << numRight << endl;
 305                 for (int i = 0; i < numIters; i++) {
 306                         //random sampling with replacement.
 307
 308                         if (m->control_pressed) { return 0;  }
 309
 310                         vector<snps> selectedLeft;
 311
 312                         for (int j = 0; j < numLeft; j++) {
 313                                 int index = int(rand() % left.size());
 314                                 selectedLeft.push_back(left[index]);
 315                         }
 316
 317                         vector<snps> selectedRight;
 318                         for (int j = 0; j < numRight; j++) {
 319                                 int index = int(rand() % right.size());
 320                                 selectedRight.push_back(right[index]);
 321                         }
 322
 323                         /* A  ------------------------------------------
 324                         #       QLA                     QRA
 325                         # Q  ------------------------------------------
 326                         #                      |
 327                         #                      |
 328                         # Q  ------------------------------------------
 329                         #       QLB                     QRB
 330                         # B  ------------------------------------------ */
 331
 332
 333                         float QLA = snpQA(selectedLeft);
 334                         float QRA = snpQA(selectedRight);
 335
 336                         float QLB = snpQB(selectedLeft);
 337                         float QRB = snpQB(selectedRight);
 338
 339                         //in original - not used - not sure why?
 340                         //float ALB = snpAB(selectedLeft);
 341                         //float ARB = snpAB(selectedRight);
 342
 343                         if ((QLA > QLB) && (QRB > QRA)) {
 344                                 count_A++;
 345                         }
 346
 347                         if ((QLB > QLA) && (QRA > QRB)) {
 348                                 count_B++;
 349                         }
 350
 351 //cout << "selected left snp: \n";
 352 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 353 //cout << endl;
 354 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 355 //cout << endl;
 356 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 357 //cout << endl;
 358 //cout << "selected right snp: \n";
 359 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 360 //cout << endl;
 361 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 362 //cout << endl;
 363 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 364 //cout << endl;
 365                 }
 366
 367
 368                 //cout << count_A << '\t' << count_B << endl;
 369
 370                 BSA = (float) count_A / (float) numIters * 100;
 371                 BSB = (float) count_B / (float) numIters * 100;
 372 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 373
 374                 return 0;
 375
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 379                 exit(1);
 380         }
 381 }
 382 /***********************************************************************/
 383 float Slayer::snpQA(vector<snps> data) {
 384         try {
 385
 386                 int numIdentical = 0;
 387
 388                 for (int i = 0; i < data.size(); i++) {
 389                         if (data[i].parentAChar == data[i].queryChar) {
 390                                 numIdentical++;
 391                         }
 392                 }
 393
 394                 float percentID = (numIdentical / (float) data.size()) * 100;
 395
 396                 return percentID;
 397         }
 398         catch(exception& e) {
 399                 m->errorOut(e, "Slayer", "snpQA");
 400                 exit(1);
 401         }
 402 }
 403 /***********************************************************************/
 404 float Slayer::snpQB(vector<snps> data) {
 405         try {
 406
 407                 int numIdentical = 0;
 408
 409                 for (int i = 0; i < data.size(); i++) {
 410                         if (data[i].parentBChar == data[i].queryChar) {
 411                                 numIdentical++;
 412                         }
 413                 }
 414
 415                 float percentID = (numIdentical / (float) data.size()) * 100;
 416
 417                 return percentID;
 418
 419         }
 420         catch(exception& e) {
 421                 m->errorOut(e, "Slayer", "snpQB");
 422                 exit(1);
 423         }
 424 }
 425 /***********************************************************************/
 426 float Slayer::snpAB(vector<snps> data) {
 427         try {
 428                 int numIdentical = 0;
 429
 430                 for (int i = 0; i < data.size(); i++) {
 431                         if (data[i].parentAChar == data[i].parentBChar) {
 432                                 numIdentical++;
 433                         }
 434                 }
 435
 436                 float percentID = (numIdentical / (float) data.size()) * 100;
 437
 438                 return percentID;
 439
 440         }
 441         catch(exception& e) {
 442                 m->errorOut(e, "Slayer", "snpAB");
 443                 exit(1);
 444         }
 445 }
 446 /***********************************************************************/
 447 float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
 448         try {
 449                 int total = 0;
 450                 int matches = 0;
 451
 452                 for (int i = left; i <= right; i++) {
 453                         total++;
 454                         if (queryFrag[i] == parent[i]) {
 455                                 matches++;
 456                         }
 457                 }
 458
 459                 float percentID =( matches/(float)total) * 100;
 460
 461                 return percentID;
 462         }
 463         catch(exception& e) {
 464                 m->errorOut(e, "Slayer", "computePercentID");
 465                 exit(1);
 466         }
 467 }
 468 /***********************************************************************/
 469 //remove columns that contain any gaps
 470 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 471         try {
 472                 //find baseSpots
 473                 baseSpots.clear();
 474                 baseSpots.resize(3);  //query, parentA, parentB
 475
 476                 vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
 477
 478                 string filterString = (string(seqs[0]->getAligned().length(), '1'));
 479
 480                 //for each sequence
 481                 for (int i = 0; i < seqs.size(); i++) {
 482
 483                         string seqAligned = seqs[i]->getAligned();
 484
 485                         for (int j = 0; j < seqAligned.length(); j++) {
 486                                 //if this spot is a gap
 487                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 488                         }
 489                 }
 490
 491                 //zero out spot where any sequences have blanks
 492                 int numColRemoved = 0;
 493                 int count = 0;
 494                 map<int, int> maskMap; maskMap.clear();
 495
 496                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 497                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 498                         else {
 499                                 maskMap[count] = i;
 500                                 count++;
 501                         }
 502                 }
 503
 504                 //for each sequence
 505                 for (int i = 0; i < seqs.size(); i++) {
 506
 507                         string seqAligned = seqs[i]->getAligned();
 508                         string newAligned = "";
 509
 510                         int baseCount = 0;
 511                         int count = 0;
 512                         for (int j = 0; j < seqAligned.length(); j++) {
 513                                 //are you a base
 514                                 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 515
 516                                 //if this spot is not a gap
 517                                 if (filterString[j] == '1') {
 518                                         newAligned += seqAligned[j];
 519                                         baseSpots[i][count] = baseCount;
 520                                         count++;
 521                                 }
 522                         }
 523
 524                         seqs[i]->setAligned(newAligned);
 525                 }
 526
 527                 return maskMap;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "Slayer", "verticalFilter");
 531                 exit(1);
 532         }
 533 }
 534 /***********************************************************************/