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
  32                                 //cout << q->getName() << endl << q->getAligned() << endl << endl;
  33                                 //cout << leftParent->getName() << endl << leftParent->getAligned() << endl << endl;
  34                                 //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
  35                                 //cout << " length = " << rightParent->getAligned().length() << endl;
  36
  37                                 map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
  38                                 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
  39
  40                                 if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  41 //                              cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
  42                                 vector<data_struct> selectedDivs;
  43                                 for (int k = 0; k < divs.size(); k++) {
  44
  45                                         vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  46                                         vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  47
  48                                         if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  49
  50                                         int numSNPSLeft = snpsLeft.size();
  51                                         int numSNPSRight = snpsRight.size();
  52
  53 //                                      cout << numSNPSLeft << '\t' << numSNPSRight << endl;
  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 //                                                      bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
  71 //
  72 //                                                      if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  73 //
  74 //                                                      divs[k].bsa = BS_A;
  75 //                                                      divs[k].bsb = BS_B;
  76 //                                                      divs[k].bsMax = max(BS_A, BS_B);
  77 //                                                      divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  78 //                                              }
  79
  80                                                 //so results reflect orignal alignment
  81                                                 divs[k].winLStart = spots[divs[k].winLStart];
  82                                                 divs[k].winLEnd = spots[divs[k].winLEnd];
  83                                                 divs[k].winRStart = spots[divs[k].winRStart];
  84                                                 divs[k].winREnd = spots[divs[k].winREnd];
  85
  86                                                 selectedDivs.push_back(divs[k]);
  87                                         }
  88                                 }
  89
  90                                 //save selected
  91                                 for (int mi = 0; mi < selectedDivs.size(); mi++) {  all.push_back(selectedDivs[mi]);    }
  92
  93                                 delete q;
  94                                 delete leftParent;
  95                                 delete rightParent;
  96                         }
  97                 }
  98
  99
 100                 // compute bootstrap support
 101                 if (all.size() > 0) {
 102                         //sort them
 103                         sort(all.begin(), all.end(), compareDataStruct);
 104                         reverse(all.begin(), all.end());
 105
 106                         outputResults = all;
 107                         return "yes";
 108                 }else {
 109                         outputResults = all;
 110                         return "no";
 111                 }
 112         }
 113         catch(exception& e) {
 114                 m->errorOut(e, "Slayer", "getResults");
 115                 exit(1);
 116         }
 117 }
 118 /***********************************************************************/
 119 vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
 120         try{
 121
 122                 vector<data_struct> data;
 123
 124                 //vertical filter
 125                 vector<Sequence*> temp;
 126                 temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
 127
 128                 //maps spot in new alignment to spot in alignment before filter
 129                 spots = verticalFilter(temp);  //fills baseSpots
 130
 131                 //get these to avoid numerous function calls
 132                 string query = q->getAligned();
 133                 string parentA = pA->getAligned();
 134                 string parentB = pB->getAligned();
 135                 int length = query.length();
 136 //cout << q->getName() << endl << q->getAligned() << endl << endl;
 137 //cout << pA->getName() << endl << pA->getUnaligned() << endl << endl;
 138 //cout << pB->getName() << endl << pB->getUnaligned() << endl << endl;
 139 //cout << " length = " << length << endl;
 140
 141                 //check window size
 142                 if (length < (2*windowSize+windowStep)) {
 143 //                      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();
 144                         windowSize = length / 4;
 145                 }
 146
 147                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 148
 149                         if (m->control_pressed) { return data; }
 150
 151                         int breakpoint = i;
 152                         int leftLength = breakpoint + 1;
 153                         int rightLength = length - leftLength;
 154
 155                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 156                         float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
 157
 158                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 159                         float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
 160
 161                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 162                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1);
 163
 164                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 165                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 166                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 167
 168                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 169                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 170
 171                         //in original and not used
 172                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 173
 174                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 175                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 176
 177
 178                         //cout << q->getName() << '\t';
 179                         //cout << pA->getName() << '\t';
 180                         //cout << pB->getName() << '\t';
 181                     //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
 182                         //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
 183 //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;
 184
 185 //cout << divRThreshold << endl;
 186 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 187                         //is one of them above the
 188                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 189
 190                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 191                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 192
 193                                         data_struct member;
 194
 195                                         member.divr_qla_qrb = divR_QLA_QRB;
 196                                         member.divr_qlb_qra = divR_QLB_QRA;
 197                                         member.qla_qrb = QLA_QRB;
 198                                         member.qlb_qra = QLB_QRA;
 199                                         member.qla = QLA;
 200                                         member.qrb = QRB;
 201                                         member.ab = AB;
 202                                         member.qa = QA;
 203                                         member.qb = QB;
 204                                         member.lab = LAB;
 205                                         member.rab = RAB;
 206                                         member.qra = QRA;
 207                                         member.qlb = QLB;
 208                                         member.winLStart = 0;
 209                                         member.winLEnd = breakpoint;
 210                                         member.winRStart = breakpoint+1;
 211                                         member.winREnd = length-1;
 212                                         member.querySeq = *(q);
 213                                         member.parentA = *(pA);
 214                                         member.parentB = *(pB);
 215                                         member.bsa = 0;
 216                                         member.bsb = 0;
 217                                         member.bsMax = 0;
 218                                         member.chimeraMax = 0;
 219
 220                                         data.push_back(member);
 221
 222                                 }//if
 223                         }//if
 224                 }//for
 225
 226
 227                 return data;
 228
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "Slayer", "runBellerophon");
 232                 exit(1);
 233         }
 234 }
 235 /***********************************************************************/
 236 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 237         try {
 238
 239                 vector<snps> data;
 240
 241                 for (int i = left; i <= right; i++) {
 242
 243                         char A = parentA[i];
 244                         char Q = query[i];
 245                         char B = parentB[i];
 246
 247                         if ((A != Q) || (B != Q)) {
 248
 249                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 250
 251
 252                                 if (
 253                                         //did query loose a base here during filter??
 254                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 255                                         ( i == query.length()-1 || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 256                                         &&
 257                                         //did parentA loose a base here during filter??
 258                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 259                                         ( i == parentA.length()-1 || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 260                                         &&
 261                                         //did parentB loose a base here during filter??
 262                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 263                                         ( i == parentB.length()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 264                                         )
 265                                 {
 266                                         snps member;
 267                                         member.queryChar = Q;
 268                                         member.parentAChar = A;
 269                                         member.parentBChar = B;
 270                                         data.push_back(member);
 271                                 }
 272                         }
 273                 }
 274
 275                 return data;
 276
 277         }
 278         catch(exception& e) {
 279                 m->errorOut(e, "Slayer", "getSNPS");
 280                 exit(1);
 281         }
 282 }
 283 /***********************************************************************/
 284 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
 285         try {
 286
 287                 srand((unsigned)time( NULL ));
 288
 289                 int count_A = 0; // sceneario QLA,QRB supported
 290                 int count_B = 0; // sceneario QLB,QRA supported
 291
 292                 int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
 293                 int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
 294
 295                 for (int i = 0; i < numIters; i++) {
 296                         //random sampling with replacement.
 297
 298                         if (m->control_pressed) { return 0;  }
 299
 300                         vector<snps> selectedLeft;
 301
 302                         for (int j = 0; j < numLeft; j++) {
 303                                 int index = int(rand() % left.size());
 304                                 selectedLeft.push_back(left[index]);
 305                         }
 306
 307                         vector<snps> selectedRight;
 308                         for (int j = 0; j < numRight; j++) {
 309                                 int index = int(rand() % right.size());
 310                                 selectedRight.push_back(right[index]);
 311                         }
 312
 313                         /* A  ------------------------------------------
 314                         #       QLA                     QRA
 315                         # Q  ------------------------------------------
 316                         #                      |
 317                         #                      |
 318                         # Q  ------------------------------------------
 319                         #       QLB                     QRB
 320                         # B  ------------------------------------------ */
 321
 322
 323                         float QLA = snpQA(selectedLeft);
 324                         float QRA = snpQA(selectedRight);
 325
 326                         float QLB = snpQB(selectedLeft);
 327                         float QRB = snpQB(selectedRight);
 328
 329                         //in original - not used - not sure why?
 330                         //float ALB = snpAB(selectedLeft);
 331                         //float ARB = snpAB(selectedRight);
 332
 333                         if ((QLA > QLB) && (QRB > QRA)) {
 334                                 count_A++;
 335                         }
 336
 337                         if ((QLB > QLA) && (QRA > QRB)) {
 338                                 count_B++;
 339                         }
 340
 341 //cout << "selected left snp: \n";
 342 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 343 //cout << endl;
 344 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 345 //cout << endl;
 346 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 347 //cout << endl;
 348 //cout << "selected right snp: \n";
 349 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 350 //cout << endl;
 351 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 352 //cout << endl;
 353 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 354 //cout << endl;
 355                 }
 356
 357
 358                 //cout << count_A << '\t' << count_B << endl;
 359
 360                 BSA = (float) count_A / (float) numIters * 100;
 361                 BSB = (float) count_B / (float) numIters * 100;
 362 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 363
 364                 return 0;
 365
 366         }
 367         catch(exception& e) {
 368                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 369                 exit(1);
 370         }
 371 }
 372 /***********************************************************************/
 373 float Slayer::snpQA(vector<snps> data) {
 374         try {
 375
 376                 int numIdentical = 0;
 377
 378                 for (int i = 0; i < data.size(); i++) {
 379                         if (data[i].parentAChar == data[i].queryChar) {
 380                                 numIdentical++;
 381                         }
 382                 }
 383
 384                 float percentID = (numIdentical / (float) data.size()) * 100;
 385
 386                 return percentID;
 387         }
 388         catch(exception& e) {
 389                 m->errorOut(e, "Slayer", "snpQA");
 390                 exit(1);
 391         }
 392 }
 393 /***********************************************************************/
 394 float Slayer::snpQB(vector<snps> data) {
 395         try {
 396
 397                 int numIdentical = 0;
 398
 399                 for (int i = 0; i < data.size(); i++) {
 400                         if (data[i].parentBChar == data[i].queryChar) {
 401                                 numIdentical++;
 402                         }
 403                 }
 404
 405                 float percentID = (numIdentical / (float) data.size()) * 100;
 406
 407                 return percentID;
 408
 409         }
 410         catch(exception& e) {
 411                 m->errorOut(e, "Slayer", "snpQB");
 412                 exit(1);
 413         }
 414 }
 415 /***********************************************************************/
 416 float Slayer::snpAB(vector<snps> data) {
 417         try {
 418                 int numIdentical = 0;
 419
 420                 for (int i = 0; i < data.size(); i++) {
 421                         if (data[i].parentAChar == data[i].parentBChar) {
 422                                 numIdentical++;
 423                         }
 424                 }
 425
 426                 float percentID = (numIdentical / (float) data.size()) * 100;
 427
 428                 return percentID;
 429
 430         }
 431         catch(exception& e) {
 432                 m->errorOut(e, "Slayer", "snpAB");
 433                 exit(1);
 434         }
 435 }
 436 /***********************************************************************/
 437 float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) {
 438         try {
 439
 440                 int numIdentical = 0;
 441                 int countA = 0;
 442                 int countB = 0;
 443                 for (int i = left; i <= right; i++) {
 444                         if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
 445                                 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
 446                         else {
 447
 448                                 bool charA = false; bool charB = false;
 449                                 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
 450                                 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
 451
 452                                 if (charA || charB) {
 453
 454                                         if (charA) { countA++; }
 455                                         if (charB) { countB++; }
 456
 457                                         if (queryAlign[i] == chimera[i]) {
 458                                                 numIdentical++;
 459                                         }
 460                                 }
 461                         }
 462
 463                 }
 464
 465                 float numBases = (countA + countB) /(float) 2;
 466
 467                 if (numBases == 0) { return 0; }
 468
 469                 float percentIdentical = (numIdentical/(float)numBases) * 100;
 470
 471                 return percentIdentical;
 472
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "Slayer", "computePercentID");
 476                 exit(1);
 477         }
 478 }
 479 /***********************************************************************/
 480 //remove columns that contain any gaps
 481 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 482         try {
 483                 //find baseSpots
 484                 baseSpots.clear();
 485                 baseSpots.resize(3);  //query, parentA, parentB
 486
 487                 vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
 488
 489                 string filterString = (string(seqs[0]->getAligned().length(), '1'));
 490
 491                 //for each sequence
 492                 for (int i = 0; i < seqs.size(); i++) {
 493
 494                         string seqAligned = seqs[i]->getAligned();
 495
 496                         for (int j = 0; j < seqAligned.length(); j++) {
 497                                 //if this spot is a gap
 498                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 499                         }
 500                 }
 501
 502                 //zero out spot where any sequences have blanks
 503                 int numColRemoved = 0;
 504                 int count = 0;
 505                 map<int, int> maskMap; maskMap.clear();
 506
 507                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 508                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 509                         else {
 510                                 maskMap[count] = i;
 511                                 count++;
 512                         }
 513                 }
 514
 515                 //for each sequence
 516                 for (int i = 0; i < seqs.size(); i++) {
 517
 518                         string seqAligned = seqs[i]->getAligned();
 519                         string newAligned = "";
 520
 521                         int baseCount = 0;
 522                         int count = 0;
 523                         for (int j = 0; j < seqAligned.length(); j++) {
 524                                 //are you a base
 525                                 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 526
 527                                 //if this spot is not a gap
 528                                 if (filterString[j] == '1') {
 529                                         newAligned += seqAligned[j];
 530                                         baseSpots[i][count] = baseCount;
 531                                         count++;
 532                                 }
 533                         }
 534
 535                         seqs[i]->setAligned(newAligned);
 536                 }
 537
 538                 return maskMap;
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "Slayer", "verticalFilter");
 542                 exit(1);
 543         }
 544 }
 545 /***********************************************************************/