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