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) :
  14                 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
  20                 for (int i = 0; i < refSeqs.size(); i++) {
  21
  22                         for (int j = i+1; j < refSeqs.size(); j++) {
  23
  24                                 if (m->control_pressed) { return "no";  }
  25
  26                                 //make copies of query and each parent because runBellerophon removes gaps and messes them up
  27                                 Sequence* q = new Sequence(query->getName(), query->getAligned());
  28                                 Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
  29                                 Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
  30
  31                                 map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
  32                                 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
  33
  34                                 if (m->control_pressed) {
  35                                         delete q;
  36                                         delete leftParent;
  37                                         delete rightParent;
  38                                         return "no";
  39                                 }
  40
  41                                 vector<data_struct> selectedDivs;
  42                                 for (int k = 0; k < divs.size(); k++) {
  43
  44                                         vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  45                                         vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  46
  47                                         if (m->control_pressed) {
  48                                                 delete q;
  49                                                 delete leftParent;
  50                                                 delete rightParent;
  51                                                 return "no";
  52                                         }
  53
  54                                         int numSNPSLeft = snpsLeft.size();
  55                                         int numSNPSRight = snpsRight.size();
  56
  57                                         //require at least 3 SNPs on each side of the break
  58                                         if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
  59
  60                                                 //removed in 12/09 version of chimeraSlayer
  61                                                 //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
  62                                                 //int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1;
  63
  64                                                 //float snpRateLeft = numSNPSLeft / (float) winSizeLeft;
  65                                                 //float snpRateRight = numSNPSRight / (float) winSizeRight;
  66                                                 //float logR = log(snpRateLeft / snpRateRight) / log(2.0);
  67
  68                                                 // do not accept excess snp ratio on either side of the break
  69                                                 //if (abs(logR) < 1 ) {
  70
  71                                                         float BS_A, BS_B;
  72                                                         bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
  73
  74                                                         if (m->control_pressed) {
  75                                                                 delete q;
  76                                                                 delete leftParent;
  77                                                                 delete rightParent;
  78                                                                 return "no";
  79                                                         }
  80
  81                                                         divs[k].bsa = BS_A;
  82                                                         divs[k].bsb = BS_B;
  83
  84                                                         divs[k].bsMax = max(BS_A, BS_B);
  85
  86                                                         divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  87
  88                                                         //so results reflect orignal alignment
  89                                                         divs[k].winLStart = spots[divs[k].winLStart];
  90                                                         divs[k].winLEnd = spots[divs[k].winLEnd];
  91                                                         divs[k].winRStart = spots[divs[k].winRStart];
  92                                                         divs[k].winREnd = spots[divs[k].winREnd];
  93
  94                                                         selectedDivs.push_back(divs[k]);
  95                                                 //}
  96                                         }
  97                                 }
  98
  99                                 //save selected
 100                                 for (int m = 0; m < selectedDivs.size(); m++) {  all.push_back(selectedDivs[m]);        }
 101
 102                                 delete q;
 103                                 delete leftParent;
 104                                 delete rightParent;
 105                         }
 106                 }
 107
 108
 109                 // compute bootstrap support
 110                 if (all.size() > 0) {
 111                         //sort them
 112                         sort(all.begin(), all.end(), compareDataStruct);
 113                         reverse(all.begin(), all.end());
 114
 115                         outputResults = all;
 116                         return "yes";
 117                 }
 118                 else {
 119                         outputResults = all;
 120                         return "no";
 121                 }
 122         }
 123         catch(exception& e) {
 124                 m->errorOut(e, "Slayer", "getResults");
 125                 exit(1);
 126         }
 127 }
 128 /***********************************************************************/
 129 vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
 130         try{
 131
 132                 vector<data_struct> data;
 133
 134                 //vertical filter
 135                 vector<Sequence*> temp;
 136                 temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
 137
 138                 //maps spot in new alignment to spot in alignment before filter
 139                 spots = verticalFilter(temp);  //fills baseSpots
 140
 141                 //get these to avoid numerous function calls
 142                 string query = q->getAligned();
 143                 string parentA = pA->getAligned();
 144                 string parentB = pB->getAligned();
 145                 int length = query.length();
 146 //cout << q->getName() << endl << q->getAligned() << endl << endl;
 147 //cout << pA->getName() << endl << pA->getAligned() << endl << endl;
 148 //cout << pB->getName() << endl << pB->getAligned() << endl << endl;
 149 //cout << " length = " << length << endl;
 150 //cout << q->getName() << endl;
 151 //cout << pA->getName() << '\t';
 152 //cout << pB->getName() << endl;
 153
 154                 //check window size
 155                 if (length < (2*windowSize+windowStep)) {
 156                         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();
 157                         windowSize = length / 4;
 158                 }
 159
 160                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 161
 162                         if (m->control_pressed) { return data; }
 163
 164                         int breakpoint = i;
 165                         int leftLength = breakpoint + 1;
 166                         int rightLength = length - leftLength;
 167
 168                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 169                         float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
 170
 171                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 172                         float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
 173
 174                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 175                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
 176
 177                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 178                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 179                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 180
 181                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 182                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 183
 184                         //in original and not used
 185                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 186
 187                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 188                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 189 //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;
 190
 191 //cout << divRThreshold << endl;
 192 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 193                         //is one of them above the
 194                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 195
 196                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 197                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 198
 199                                         data_struct member;
 200
 201                                         member.divr_qla_qrb = divR_QLA_QRB;
 202                                         member.divr_qlb_qra = divR_QLB_QRA;
 203                                         member.qla_qrb = QLA_QRB;
 204                                         member.qlb_qra = QLB_QRA;
 205                                         member.qla = QLA;
 206                                         member.qrb = QRB;
 207                                         member.ab = AB;
 208                                         member.qa = QA;
 209                                         member.qb = QB;
 210                                         member.lab = LAB;
 211                                         member.rab = RAB;
 212                                         member.qra = QRA;
 213                                         member.qlb = QLB;
 214                                         member.winLStart = 0;
 215                                         member.winLEnd = breakpoint;
 216                                         member.winRStart = breakpoint+1;
 217                                         member.winREnd = length-1;
 218                                         member.querySeq = *(q);
 219                                         member.parentA = *(pA);
 220                                         member.parentB = *(pB);
 221                                         member.bsa = 0;
 222                                         member.bsb = 0;
 223                                         member.bsMax = 0;
 224                                         member.chimeraMax = 0;
 225
 226                                         data.push_back(member);
 227
 228                                 }//if
 229                         }//if
 230                 }//for
 231
 232                 return data;
 233
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "Slayer", "runBellerophon");
 237                 exit(1);
 238         }
 239 }
 240 /***********************************************************************/
 241 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 242         try {
 243
 244                 vector<snps> data;
 245 //cout << left << '\t' << right << endl;
 246                 for (int i = left; i <= right; i++) {
 247
 248                         char A = parentA[i];
 249                         char Q = query[i];
 250                         char B = parentB[i];
 251
 252                         if ((A != Q) || (B != Q)) {
 253 //cout << "not equal " << Q << '\t' << A << '\t' << B << endl;
 254
 255                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 256                                 if (
 257                                         //did query loose a base here during filter??
 258                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 259                                         ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 260                                         &&
 261                                         //did parentA loose a base here during filter??
 262                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 263                                         ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 264                                         &&
 265                                         //did parentB loose a base here during filter??
 266                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 267                                         ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 268                                         )
 269                                 {
 270
 271                                         snps member;
 272                                         member.queryChar = Q;
 273                                         member.parentAChar = A;
 274                                         member.parentBChar = B;
 275 //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;
 276                                         data.push_back(member);
 277                                 }
 278                         }
 279                 }
 280
 281                 return data;
 282
 283         }
 284         catch(exception& e) {
 285                 m->errorOut(e, "Slayer", "getSNPS");
 286                 exit(1);
 287         }
 288 }
 289 /***********************************************************************/
 290 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
 291         try {
 292
 293                 srand((unsigned)time( NULL ));
 294
 295                 int count_A = 0; // sceneario QLA,QRB supported
 296                 int count_B = 0; // sceneario QLB,QRA supported
 297
 298                 int numLeft = max(1, int(left.size() * (percentSNPSample/(float)100) + 0.5));
 299                 int numRight = max(1, int(right.size() * (percentSNPSample/(float)100) + 0.5));
 300
 301                 for (int i = 0; i < iters; i++) {
 302                         //random sampling with replacement.
 303
 304                         if (m->control_pressed) { return 0;  }
 305
 306                         vector<snps> selectedLeft;
 307
 308                         for (int j = 0; j < numLeft; j++) {
 309                                 int index = int(rand() % left.size());
 310                                 selectedLeft.push_back(left[index]);
 311                         }
 312
 313                         vector<snps> selectedRight;
 314                         for (int j = 0; j < numRight; j++) {
 315                                 int index = int(rand() % right.size());
 316                                 selectedRight.push_back(right[index]);
 317                         }
 318
 319                         /* A  ------------------------------------------
 320                         #       QLA                     QRA
 321                         # Q  ------------------------------------------
 322                         #                      |
 323                         #                      |
 324                         # Q  ------------------------------------------
 325                         #       QLB                     QRB
 326                         # B  ------------------------------------------ */
 327
 328
 329                         float QLA = snpQA(selectedLeft);
 330                         float QRA = snpQA(selectedRight);
 331
 332                         float QLB = snpQB(selectedLeft);
 333                         float QRB = snpQB(selectedRight);
 334
 335                         //in original - not used - not sure why?
 336                         //float ALB = snpAB(selectedLeft);
 337                         //float ARB = snpAB(selectedRight);
 338
 339                         if ((QLA > QLB) && (QRB > QRA)) {
 340                                 count_A++;
 341                         }
 342
 343                         if ((QLB > QLA) && (QRA > QRB)) {
 344                                 count_B++;
 345                         }
 346
 347 //cout << "selected left snp: \n";
 348 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 349 //cout << endl;
 350 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 351 //cout << endl;
 352 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 353 //cout << endl;
 354 //cout << "selected right snp: \n";
 355 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 356 //cout << endl;
 357 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 358 //cout << endl;
 359 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 360 //cout << endl;
 361                 }
 362
 363
 364
 365
 366                 BSA = ((float) count_A / (float) iters) * 100;
 367                 BSB = ((float) count_B / (float) iters) * 100;
 368 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 369
 370                 return 0;
 371
 372         }
 373         catch(exception& e) {
 374                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 375                 exit(1);
 376         }
 377 }
 378 /***********************************************************************/
 379 float Slayer::snpQA(vector<snps> data) {
 380         try {
 381
 382                 int numIdentical = 0;
 383
 384                 for (int i = 0; i < data.size(); i++) {
 385                         if (data[i].parentAChar == data[i].queryChar) {
 386                                 numIdentical++;
 387                         }
 388                 }
 389
 390                 float percentID = (numIdentical / (float) data.size()) * 100;
 391
 392                 return percentID;
 393         }
 394         catch(exception& e) {
 395                 m->errorOut(e, "Slayer", "snpQA");
 396                 exit(1);
 397         }
 398 }
 399 /***********************************************************************/
 400 float Slayer::snpQB(vector<snps> data) {
 401         try {
 402
 403                 int numIdentical = 0;
 404
 405                 for (int i = 0; i < data.size(); i++) {
 406                         if (data[i].parentBChar == data[i].queryChar) {
 407                                 numIdentical++;
 408                         }
 409                 }
 410
 411                 float percentID = (numIdentical / (float) data.size()) * 100;
 412
 413                 return percentID;
 414
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "Slayer", "snpQB");
 418                 exit(1);
 419         }
 420 }
 421 /***********************************************************************/
 422 float Slayer::snpAB(vector<snps> data) {
 423         try {
 424                 int numIdentical = 0;
 425
 426                 for (int i = 0; i < data.size(); i++) {
 427                         if (data[i].parentAChar == data[i].parentBChar) {
 428                                 numIdentical++;
 429                         }
 430                 }
 431
 432                 float percentID = (numIdentical / (float) data.size()) * 100;
 433
 434                 return percentID;
 435
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "Slayer", "snpAB");
 439                 exit(1);
 440         }
 441 }
 442 /***********************************************************************/
 443 float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
 444         try {
 445                 int total = 0;
 446                 int matches = 0;
 447
 448                 for (int i = left; i <= right; i++) {
 449                         total++;
 450                         if (queryFrag[i] == parent[i]) {
 451                                 matches++;
 452                         }
 453                 }
 454
 455                 float percentID =( matches/(float)total) * 100;
 456
 457                 return percentID;
 458         }
 459         catch(exception& e) {
 460                 m->errorOut(e, "Slayer", "computePercentID");
 461                 exit(1);
 462         }
 463 }
 464 /***********************************************************************/
 465 //remove columns that contain any gaps
 466 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 467         try {
 468                 //find baseSpots
 469                 baseSpots.clear();
 470                 baseSpots.resize(3);  //query, parentA, parentB
 471
 472                 vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
 473
 474                 string filterString = (string(seqs[0]->getAligned().length(), '1'));
 475
 476                 //for each sequence
 477                 for (int i = 0; i < seqs.size(); i++) {
 478
 479                         string seqAligned = seqs[i]->getAligned();
 480
 481                         for (int j = 0; j < seqAligned.length(); j++) {
 482                                 //if this spot is a gap
 483                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 484                         }
 485                 }
 486
 487                 //zero out spot where any sequences have blanks
 488                 int numColRemoved = 0;
 489                 int count = 0;
 490                 map<int, int> maskMap; maskMap.clear();
 491
 492                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 493                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 494                         else {
 495                                 maskMap[count] = i;
 496                                 count++;
 497                         }
 498                 }
 499
 500                 //for each sequence
 501                 for (int i = 0; i < seqs.size(); i++) {
 502
 503                         string seqAligned = seqs[i]->getAligned();
 504                         string newAligned = "";
 505
 506                         int baseCount = 0;
 507                         int count = 0;
 508                         for (int j = 0; j < seqAligned.length(); j++) {
 509                                 //are you a base
 510                                 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 511
 512                                 //if this spot is not a gap
 513                                 if (filterString[j] == '1') {
 514                                         newAligned += seqAligned[j];
 515                                         baseSpots[i][count] = baseCount;
 516                                         count++;
 517                                 }
 518                         }
 519
 520                         seqs[i]->setAligned(newAligned);
 521                 }
 522
 523                 return maskMap;
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "Slayer", "verticalFilter");
 527                 exit(1);
 528         }
 529 }
 530 /***********************************************************************/