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 //                              cout << divs.size() << 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) {
  49                                                 delete q;
  50                                                 delete leftParent;
  51                                                 delete rightParent;
  52                                                 return "no";
  53                                         }
  54
  55                                         int numSNPSLeft = snpsLeft.size();
  56                                         int numSNPSRight = snpsRight.size();
  57
  58                                         //require at least 3 SNPs on each side of the break
  59 //                                      if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
  60                                         if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
  61
  62                                                 //removed in 12/09 version of chimeraSlayer
  63                                                 //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
  64                                                 //int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1;
  65
  66                                                 //float snpRateLeft = numSNPSLeft / (float) winSizeLeft;
  67                                                 //float snpRateRight = numSNPSRight / (float) winSizeRight;
  68                                                 //float logR = log(snpRateLeft / snpRateRight) / log(2.0);
  69
  70                                                 // do not accept excess snp ratio on either side of the break
  71                                                 //if (abs(logR) < 1 ) {
  72
  73                                                         float BS_A, BS_B;
  74                                                         bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
  75
  76                                                         if (m->control_pressed) {
  77                                                                 delete q;
  78                                                                 delete leftParent;
  79                                                                 delete rightParent;
  80                                                                 return "no";
  81                                                         }
  82
  83                                                         divs[k].bsa = BS_A;
  84                                                         divs[k].bsb = BS_B;
  85
  86                                                         divs[k].bsMax = max(BS_A, BS_B);
  87
  88                                                         divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  89
  90                                                         //so results reflect orignal alignment
  91                                                         divs[k].winLStart = spots[divs[k].winLStart];
  92                                                         divs[k].winLEnd = spots[divs[k].winLEnd];
  93                                                         divs[k].winRStart = spots[divs[k].winRStart];
  94                                                         divs[k].winREnd = spots[divs[k].winREnd];
  95
  96                                                         selectedDivs.push_back(divs[k]);
  97                                                 //}
  98                                         }
  99                                 }
 100
 101                                 //save selected
 102                                 for (int m = 0; m < selectedDivs.size(); m++) {  all.push_back(selectedDivs[m]);        }
 103
 104                                 delete q;
 105                                 delete leftParent;
 106                                 delete rightParent;
 107                         }
 108                 }
 109
 110                 // compute bootstrap support
 111                 if (all.size() > 0) {
 112                         //sort them
 113                         sort(all.begin(), all.end(), compareDataStruct);
 114                         reverse(all.begin(), all.end());
 115
 116                         outputResults = all;
 117                         return "yes";
 118                 }
 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->getAligned() << endl << endl;
 149 cout << pB->getName() << endl << pB->getAligned() << endl << endl;
 150 cout << " length = " << length << endl;
 151 cout << q->getName() << endl;
 152 cout << pA->getName() << '\t';
 153 cout << pB->getName() << endl;*/
 154
 155                 //check window size
 156                 if (length < (2*windowSize+windowStep)) {
 157 //                      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();
 158                         windowSize = length / 4;
 159                 }
 160
 161                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 162
 163                         if (m->control_pressed) { return data; }
 164
 165                         int breakpoint = i;
 166                         int leftLength = breakpoint + 1;
 167                         int rightLength = length - leftLength;
 168
 169                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 170                         float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
 171
 172                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 173                         float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
 174
 175                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 176                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
 177
 178                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 179                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 180                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 181
 182                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 183                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 184
 185                         //in original and not used
 186                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 187
 188                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 189                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 190 //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;
 191
 192 //cout << divRThreshold << endl;
 193 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 194                         //is one of them above the
 195                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 196
 197                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 198                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 199
 200                                         data_struct member;
 201
 202                                         member.divr_qla_qrb = divR_QLA_QRB;
 203                                         member.divr_qlb_qra = divR_QLB_QRA;
 204                                         member.qla_qrb = QLA_QRB;
 205                                         member.qlb_qra = QLB_QRA;
 206                                         member.qla = QLA;
 207                                         member.qrb = QRB;
 208                                         member.ab = AB;
 209                                         member.qa = QA;
 210                                         member.qb = QB;
 211                                         member.lab = LAB;
 212                                         member.rab = RAB;
 213                                         member.qra = QRA;
 214                                         member.qlb = QLB;
 215                                         member.winLStart = 0;
 216                                         member.winLEnd = breakpoint;
 217                                         member.winRStart = breakpoint+1;
 218                                         member.winREnd = length-1;
 219                                         member.querySeq = *(q);
 220                                         member.parentA = *(pA);
 221                                         member.parentB = *(pB);
 222                                         member.bsa = 0;
 223                                         member.bsb = 0;
 224                                         member.bsMax = 0;
 225                                         member.chimeraMax = 0;
 226
 227                                         data.push_back(member);
 228
 229                                 }//if
 230                         }//if
 231                 }//for
 232
 233                 return data;
 234
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "Slayer", "runBellerophon");
 238                 exit(1);
 239         }
 240 }
 241 /***********************************************************************/
 242 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 243         try {
 244
 245                 vector<snps> data;
 246 //cout << left << '\t' << right << endl;
 247                 for (int i = left; i <= right; i++) {
 248
 249                         char A = parentA[i];
 250                         char Q = query[i];
 251                         char B = parentB[i];
 252
 253                         if ((A != Q) || (B != Q)) {
 254 //cout << "not equal " << Q << '\t' << A << '\t' << B << endl;
 255
 256                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 257                                 if (
 258                                         //did query loose a base here during filter??
 259                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 260                                         ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 261                                         &&
 262                                         //did parentA loose a base here during filter??
 263                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 264                                         ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 265                                         &&
 266                                         //did parentB loose a base here during filter??
 267                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 268                                         ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 269                                         )
 270                                 {
 271
 272                                         snps member;
 273                                         member.queryChar = Q;
 274                                         member.parentAChar = A;
 275                                         member.parentBChar = B;
 276 //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;
 277                                         data.push_back(member);
 278                                 }
 279                         }
 280 //                      cout << i << '\t' << data.size() << endl;
 281                 }
 282
 283                 return data;
 284
 285         }
 286         catch(exception& e) {
 287                 m->errorOut(e, "Slayer", "getSNPS");
 288                 exit(1);
 289         }
 290 }
 291 /***********************************************************************/
 292 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
 293         try {
 294
 295                 srand((unsigned)time( NULL ));
 296
 297                 int count_A = 0; // sceneario QLA,QRB supported
 298                 int count_B = 0; // sceneario QLB,QRA supported
 299
 300                 int numLeft = max(1, int(left.size() * (percentSNPSample/(float)100) + 0.5));
 301                 int numRight = max(1, int(right.size() * (percentSNPSample/(float)100) + 0.5));
 302
 303                 for (int i = 0; i < iters; i++) {
 304                         //random sampling with replacement.
 305
 306                         if (m->control_pressed) { return 0;  }
 307
 308                         vector<snps> selectedLeft;
 309
 310                         for (int j = 0; j < numLeft; j++) {
 311                                 int index = int(rand() % left.size());
 312                                 selectedLeft.push_back(left[index]);
 313                         }
 314
 315                         vector<snps> selectedRight;
 316                         for (int j = 0; j < numRight; j++) {
 317                                 int index = int(rand() % right.size());
 318                                 selectedRight.push_back(right[index]);
 319                         }
 320
 321                         /* A  ------------------------------------------
 322                         #       QLA                     QRA
 323                         # Q  ------------------------------------------
 324                         #                      |
 325                         #                      |
 326                         # Q  ------------------------------------------
 327                         #       QLB                     QRB
 328                         # B  ------------------------------------------ */
 329
 330
 331                         float QLA = snpQA(selectedLeft);
 332                         float QRA = snpQA(selectedRight);
 333
 334                         float QLB = snpQB(selectedLeft);
 335                         float QRB = snpQB(selectedRight);
 336
 337                         //in original - not used - not sure why?
 338                         //float ALB = snpAB(selectedLeft);
 339                         //float ARB = snpAB(selectedRight);
 340
 341                         if ((QLA > QLB) && (QRB > QRA)) {
 342                                 count_A++;
 343                         }
 344
 345                         if ((QLB > QLA) && (QRA > QRB)) {
 346                                 count_B++;
 347                         }
 348
 349 //cout << "selected left snp: \n";
 350 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 351 //cout << endl;
 352 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 353 //cout << endl;
 354 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 355 //cout << endl;
 356 //cout << "selected right snp: \n";
 357 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 358 //cout << endl;
 359 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 360 //cout << endl;
 361 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 362 //cout << endl;
 363                 }
 364
 365
 366
 367
 368                 BSA = ((float) count_A / (float) iters) * 100;
 369                 BSB = ((float) count_B / (float) iters) * 100;
 370 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 371
 372                 return 0;
 373
 374         }
 375         catch(exception& e) {
 376                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 377                 exit(1);
 378         }
 379 }
 380 /***********************************************************************/
 381 float Slayer::snpQA(vector<snps> data) {
 382         try {
 383
 384                 int numIdentical = 0;
 385
 386                 for (int i = 0; i < data.size(); i++) {
 387                         if (data[i].parentAChar == data[i].queryChar) {
 388                                 numIdentical++;
 389                         }
 390                 }
 391
 392                 float percentID = (numIdentical / (float) data.size()) * 100;
 393
 394                 return percentID;
 395         }
 396         catch(exception& e) {
 397                 m->errorOut(e, "Slayer", "snpQA");
 398                 exit(1);
 399         }
 400 }
 401 /***********************************************************************/
 402 float Slayer::snpQB(vector<snps> data) {
 403         try {
 404
 405                 int numIdentical = 0;
 406
 407                 for (int i = 0; i < data.size(); i++) {
 408                         if (data[i].parentBChar == data[i].queryChar) {
 409                                 numIdentical++;
 410                         }
 411                 }
 412
 413                 float percentID = (numIdentical / (float) data.size()) * 100;
 414
 415                 return percentID;
 416
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "Slayer", "snpQB");
 420                 exit(1);
 421         }
 422 }
 423 /***********************************************************************/
 424 float Slayer::snpAB(vector<snps> data) {
 425         try {
 426                 int numIdentical = 0;
 427
 428                 for (int i = 0; i < data.size(); i++) {
 429                         if (data[i].parentAChar == data[i].parentBChar) {
 430                                 numIdentical++;
 431                         }
 432                 }
 433
 434                 float percentID = (numIdentical / (float) data.size()) * 100;
 435
 436                 return percentID;
 437
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "Slayer", "snpAB");
 441                 exit(1);
 442         }
 443 }
 444 /***********************************************************************/
 445 float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
 446         try {
 447                 int total = 0;
 448                 int matches = 0;
 449
 450                 for (int i = left; i <= right; i++) {
 451                         total++;
 452                         if (queryFrag[i] == parent[i]) {
 453                                 matches++;
 454                         }
 455                 }
 456
 457                 float percentID =( matches/(float)total) * 100;
 458
 459                 return percentID;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "Slayer", "computePercentID");
 463                 exit(1);
 464         }
 465 }
 466 /***********************************************************************/
 467 //remove columns that contain any gaps
 468 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 469         try {
 470                 //find baseSpots
 471                 baseSpots.clear();
 472                 baseSpots.resize(3);  //query, parentA, parentB
 473
 474                 vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
 475
 476                 string filterString = (string(seqs[0]->getAligned().length(), '1'));
 477
 478                 //for each sequence
 479                 for (int i = 0; i < seqs.size(); i++) {
 480
 481                         string seqAligned = seqs[i]->getAligned();
 482
 483                         for (int j = 0; j < seqAligned.length(); j++) {
 484                                 //if this spot is a gap
 485                                 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 486                         }
 487                 }
 488
 489                 //zero out spot where any sequences have blanks
 490                 int numColRemoved = 0;
 491                 int count = 0;
 492                 map<int, int> maskMap; maskMap.clear();
 493
 494                 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
 495                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 496                         else {
 497                                 maskMap[count] = i;
 498                                 count++;
 499                         }
 500                 }
 501
 502                 //for each sequence
 503                 for (int i = 0; i < seqs.size(); i++) {
 504
 505                         string seqAligned = seqs[i]->getAligned();
 506                         string newAligned = "";
 507
 508                         int baseCount = 0;
 509                         int count = 0;
 510                         for (int j = 0; j < seqAligned.length(); j++) {
 511                                 //are you a base
 512                                 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 513
 514                                 //if this spot is not a gap
 515                                 if (filterString[j] == '1') {
 516                                         newAligned += seqAligned[j];
 517                                         baseSpots[i][count] = baseCount;
 518                                         count++;
 519                                 }
 520                         }
 521
 522                         seqs[i]->setAligned(newAligned);
 523                 }
 524
 525                 return maskMap;
 526         }
 527         catch(exception& e) {
 528                 m->errorOut(e, "Slayer", "verticalFilter");
 529                 exit(1);
 530         }
 531 }
 532 /***********************************************************************/