chimeraseqscommand.cpp

   1 /*
   2  *  chimeraseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/29/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraseqscommand.h"
  11 #include "eachgapdist.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment" };
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //check for required parameters
  38                         fastafile = validParameter.validFile(parameters, "fasta", true);
  39                         if (fastafile == "not open") { abort = true; }
  40                         else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true;  }
  41
  42                         string temp;
  43                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "T"; }
  44                         filter = isTrue(temp);
  45
  46                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
  47                         correction = isTrue(temp);
  48
  49                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  50                         convert(temp, processors);
  51
  52                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  53                         convert(temp, window);
  54
  55                         temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "10"; }
  56                         convert(temp, increment);
  57
  58                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "bellerophon"; }
  59
  60                         if (method != "bellerophon") { mothurOut(method + " is not a valid method."); mothurOutEndLine();  abort = true; }
  61
  62                 }
  63         }
  64         catch(exception& e) {
  65                 errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 void ChimeraSeqsCommand::help(){
  72         try {
  73                 mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
  74                 mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method.  fasta is required.\n");
  75                 mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
  76                 mothurOut("The correction parameter allows you to .....  The default is true. \n");
  77                 mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
  78                 mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is bellerophon. \n");
  79                 mothurOut("The chimera.seqs command should be in the following format: \n");
  80                 mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
  81                 mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
  82                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
  83         }
  84         catch(exception& e) {
  85                 errorOut(e, "ChimeraSeqsCommand", "help");
  86                 exit(1);
  87         }
  88 }
  89 //********************************************************************************************************************
  90 //sorts highest score to lowest
  91 inline bool comparePref(Preference left, Preference right){
  92         return (left.score[0] > right.score[0]);
  93 }
  94
  95 //***************************************************************************************************************
  96
  97 ChimeraSeqsCommand::~ChimeraSeqsCommand(){      /*      do nothing      */      }
  98
  99 //***************************************************************************************************************
 100
 101 int ChimeraSeqsCommand::execute(){
 102         try{
 103
 104                 if (abort == true) { return 0; }
 105
 106
 107                 //do soft filter
 108                 if (filter)  {
 109                         string optionString = "fasta=" + fastafile + ", soft=50, vertical=F";
 110                         filterSeqs = new FilterSeqsCommand(optionString);
 111                         filterSeqs->execute();
 112                         delete filterSeqs;
 113
 114                         //reset fastafile to filtered file
 115                         fastafile = getRootName(fastafile) + "filter.fasta";
 116                 }
 117
 118                 distCalculator = new eachGapDist();
 119
 120                 //read in sequences
 121                 readSeqs();
 122
 123                 int numSeqs = seqs.size();
 124
 125                 if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); return 0; }
 126
 127                 //set default window to 25% of sequence length
 128                 string seq0 = seqs[0].getAligned();
 129                 if (window == 0) { window = seq0.length() / 4;  }
 130                 else if (window > (seq0.length() / 2)) {
 131                         mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); mothurOutEndLine();
 132                         window = (seq0.length() / 2);
 133                 }
 134
 135                 if (increment > (seqs[0].getAlignLength() - (2*window))) {
 136                         if (increment != 10) {
 137
 138                                 mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
 139                                 increment = 10;
 140                                 if (increment > (seqs[0].getAlignLength() - (2*window))) {  increment = 0;  }
 141
 142                         }else{ increment = 0; }
 143                 }
 144 cout << "increment = " << increment << endl;
 145                 if (increment == 0) { iters = 1; }
 146                 else { iters = ((seqs[0].getAlignLength() - (2*window)) / increment); }
 147
 148                 //initialize pref
 149                 pref.resize(numSeqs);
 150
 151                 for (int i = 0; i < numSeqs; i++ ) {
 152                         pref[i].leftParent.resize(2); pref[i].rightParent.resize(2); pref[i].score.resize(2);   pref[i].closestLeft.resize(2); pref[i].closestRight.resize(3);
 153                         pref[i].name = seqs[i].getName();
 154                         pref[i].score[0] = 0.0;  pref[i].score[1] = 0.0;
 155                         pref[i].closestLeft[0] = 100000.0;  pref[i].closestLeft[1] = 100000.0;
 156                         pref[i].closestRight[0] = 100000.0;  pref[i].closestRight[1] = 100000.0;
 157                 }
 158
 159                 int midpoint = window;
 160                 int count = 0;
 161                 while (count < iters) {
 162
 163                                 //create 2 vectors of sequences, 1 for left side and one for right side
 164                                 vector<Sequence> left;  vector<Sequence> right;
 165
 166                                 for (int i = 0; i < seqs.size(); i++) {
 167 //cout << "whole = " << seqs[i].getAligned() << endl;
 168                                         //save left side
 169                                         string seqLeft = seqs[i].getAligned().substr(midpoint-window, window);
 170                                         Sequence tempLeft;
 171                                         tempLeft.setName(seqs[i].getName());
 172                                         tempLeft.setAligned(seqLeft);
 173                                         left.push_back(tempLeft);
 174 //cout << "left = " << tempLeft.getAligned() << endl;
 175                                         //save right side
 176                                         string seqRight = seqs[i].getAligned().substr(midpoint, window);
 177                                         Sequence tempRight;
 178                                         tempRight.setName(seqs[i].getName());
 179                                         tempRight.setAligned(seqRight);
 180                                         right.push_back(tempRight);
 181 //cout << "right = " << seqRight << endl;
 182                                 }
 183
 184                                 //adjust midpoint by increment
 185                                 midpoint += increment;
 186
 187
 188                                 //this should be parallelized
 189                                 //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
 190                                 //create a matrix containing the distance from left to left and right to right
 191                                 //calculate distances
 192                                 SparseMatrix* SparseLeft = new SparseMatrix();
 193                                 SparseMatrix* SparseRight = new SparseMatrix();
 194
 195                                 createSparseMatrix(0, left.size(), SparseLeft, left);
 196                                 createSparseMatrix(0, right.size(), SparseRight, right);
 197
 198                                 vector<SeqMap> distMapRight;
 199                                 vector<SeqMap> distMapLeft;
 200
 201                                 // Create a data structure to quickly access the distance information.
 202                                 // It consists of a vector of distance maps, where each map contains
 203                                 // all distances of a certain sequence. Vector and maps are accessed
 204                                 // via the index of a sequence in the distance matrix
 205                                 distMapRight = vector<SeqMap>(numSeqs);
 206                                 distMapLeft = vector<SeqMap>(numSeqs);
 207                                 //cout << "left" << endl << endl;
 208                                 for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
 209                                         distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
 210                                         //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 211                                 }
 212                                 //cout << "right" << endl << endl;
 213                                 for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
 214                                         distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
 215                                         //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
 216                                 }
 217
 218                                 delete SparseLeft;
 219                                 delete SparseRight;
 220
 221
 222                                 //fill preference structure
 223                                 generatePreferences(distMapLeft, distMapRight, midpoint);
 224
 225                                 count++;
 226
 227                 }
 228
 229                 delete distCalculator;
 230
 231                 //find average pref score across windows
 232                 //if (increment != 0) {
 233
 234                         //for (int i = 0; i < pref.size(); i++) {
 235                                 //pref[i].score[0] = pref[i].score[0] / iters;
 236                         //}
 237                 //}
 238
 239                 //sort Preferences highest to lowest
 240                 sort(pref.begin(), pref.end(), comparePref);
 241
 242                 string outputFileName = getRootName(fastafile) + "chimeras";
 243                 ofstream out;
 244                 openOutputFile(outputFileName, out);
 245
 246                 int above1 = 0;
 247                 out << "Name\tScore\tLeft\tRight\t" << endl;
 248                 //output prefenence structure to .chimeras file
 249                 for (int i = 0; i < pref.size(); i++) {
 250                         out << pref[i].name << '\t' << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
 251
 252                         //calc # of seqs with preference above 1.0
 253                         if (pref[i].score[0] > 1.0) {
 254                                 above1++;
 255                                 mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
 256                                 mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); mothurOutEndLine();
 257                         }
 258
 259
 260                 }
 261
 262                 //output results to screen
 263                 mothurOutEndLine();
 264                 mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
 265                 int spot;
 266                 spot = pref.size()-1;
 267                 mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 268                 spot = pref.size() * 0.975;
 269                 mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 270                 spot = pref.size() * 0.75;
 271                 mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 272                 spot = pref.size() * 0.50;
 273                 mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine();
 274                 spot = pref.size() * 0.25;
 275                 mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 276                 spot = pref.size() * 0.025;
 277                 mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 278                 spot = 0;
 279                 mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
 280
 281                 return 0;
 282         }
 283         catch(exception& e) {
 284                 errorOut(e, "ChimeraSeqsCommand", "execute");
 285                 exit(1);
 286         }
 287 }
 288
 289 //***************************************************************************************************************
 290 void ChimeraSeqsCommand::readSeqs(){
 291         try {
 292                 ifstream inFASTA;
 293                 openInputFile(fastafile, inFASTA);
 294
 295                 //read in seqs and store in vector
 296                 while(!inFASTA.eof()){
 297                         Sequence current(inFASTA);
 298
 299                         if (current.getAligned() == "") { current.setAligned(current.getUnaligned()); }
 300
 301                         seqs.push_back(current);
 302
 303                         gobble(inFASTA);
 304                 }
 305                 inFASTA.close();
 306
 307         }
 308         catch(exception& e) {
 309                 errorOut(e, "ChimeraSeqsCommand", "readSeqs");
 310                 exit(1);
 311         }
 312 }
 313
 314 /***************************************************************************************************************/
 315 int ChimeraSeqsCommand::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
 316         try {
 317
 318                 for(int i=startSeq; i<endSeq; i++){
 319
 320                         for(int j=0;j<i;j++){
 321
 322                                 distCalculator->calcDist(s[i], s[j]);
 323                                 float dist = distCalculator->getDist();
 324
 325                                 PCell temp(i, j, dist);
 326                                 sparse->addCell(temp);
 327
 328                         }
 329                 }
 330
 331
 332                 return 1;
 333         }
 334         catch(exception& e) {
 335                 errorOut(e, "ChimeraSeqsCommand", "createSparseMatrix");
 336                 exit(1);
 337         }
 338 }
 339 /***************************************************************************************************************/
 340 void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
 341         try {
 342
 343                 float dme = 0.0;
 344                 SeqMap::iterator itR;
 345                 SeqMap::iterator itL;
 346
 347                 //initialize pref[i]
 348                 for (int i = 0; i < pref.size(); i++) {
 349                         pref[i].score[1] = 0.0;
 350                         pref[i].closestLeft[1] = 100000.0;
 351                         pref[i].closestRight[1] = 100000.0;
 352                         pref[i].leftParent[1] = "";
 353                         pref[i].rightParent[1] = "";
 354                 }
 355
 356 //cout << "in generate left.size() = " << left.size() << endl;
 357                 for (int i = 0; i < left.size(); i++) {
 358
 359                         SeqMap currentLeft = left[i];    //example i = 3;   currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
 360                                                                                                 //                                                                              1 to the distance of sequence 3 to sequence 1,
 361                                                                                                 //                                                                              2 to the distance of sequence 3 to sequence 2.
 362                         SeqMap currentRight = right[i];         // same as left but with distances on the right side.
 363
 364                         for (int j = 0; j < i; j++) {
 365
 366                                 itL = currentLeft.find(j);
 367                                 itR = currentRight.find(j);
 368 cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
 369 cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
 370
 371                                 //if you can find this entry update the preferences
 372                                 if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
 373
 374                                         if (!correction) {
 375                                                 pref[i].score[1] += abs((itL->second - itR->second));
 376                                                 pref[j].score[1] += abs((itL->second - itR->second));
 377 cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 378 cout << "abs = " << abs((itL->second - itR->second)) << endl;
 379 cout << i << " score = " << pref[i].score[1] << endl;
 380 cout << j << " score = " << pref[j].score[1] << endl;
 381                                         }else {
 382                                                 pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
 383                                                 pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
 384 cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
 385 cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
 386 cout << i << " score = " << pref[i].score[1] << endl;
 387 cout << j << " score = " << pref[j].score[1] << endl;
 388                                         }
 389 cout << "pref[" << i << "].closestLeft[1] = "   <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
 390                                         //are you the closest left sequence
 391                                         if (itL->second < pref[i].closestLeft[1]) {
 392
 393                                                 pref[i].closestLeft[1] = itL->second;
 394                                                 pref[i].leftParent[1] = seqs[j].getName();
 395 cout << "updating closest left to " << pref[i].leftParent[1] << endl;
 396                                         }
 397 cout << "pref[" << j << "].closestLeft[1] = "   <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
 398                                         if (itL->second < pref[j].closestLeft[1]) {
 399                                                 pref[j].closestLeft[1] = itL->second;
 400                                                 pref[j].leftParent[1] = seqs[i].getName();
 401 cout << "updating closest left to " << pref[j].leftParent[1] << endl;
 402                                         }
 403
 404                                         //are you the closest right sequence
 405                                         if (itR->second < pref[i].closestRight[1]) {
 406                                                 pref[i].closestRight[1] = itR->second;
 407                                                 pref[i].rightParent[1] = seqs[j].getName();
 408                                         }
 409                                         if (itR->second < pref[j].closestRight[1]) {
 410                                                 pref[j].closestRight[1] = itR->second;
 411                                                 pref[j].rightParent[1] = seqs[i].getName();
 412                                         }
 413
 414                                 }
 415                         }
 416
 417                 }
 418
 419
 420
 421                 //calculate the dme
 422                 int count0 = 0;
 423                 for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[1];  if (pref[i].score[1] == 0.0) { count0++; }  }
 424
 425                 float expectedPercent = 1 / (float) (pref.size() - count0);
 426 cout << endl << "dme = " << dme << endl;
 427                 //recalculate prefernences based on dme
 428                 for (int i = 0; i < pref.size(); i++) {
 429 cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;
 430                         // gives the actual percentage of the dme this seq adds
 431                         pref[i].score[1] = pref[i].score[1] / dme;
 432
 433                         //how much higher or lower is this than expected
 434                         pref[i].score[1] = pref[i].score[1] / expectedPercent;
 435
 436                         //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
 437 cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
 438                 }
 439
 440                 //is this score bigger then the last score
 441                 for (int i = 0; i < pref.size(); i++) {
 442
 443                         //update biggest score
 444                         if (pref[i].score[1] > pref[i].score[0]) {
 445                                 pref[i].score[0] = pref[i].score[1];
 446                                 pref[i].leftParent[0] = pref[i].leftParent[1];
 447                                 pref[i].rightParent[0] = pref[i].rightParent[1];
 448                                 pref[i].closestLeft[0] = pref[i].closestLeft[1];
 449                                 pref[i].closestRight[0] = pref[i].closestRight[1];
 450                                 pref[i].midpoint = mid;
 451                         }
 452
 453                         //total of preference scores across windows
 454                         //pref[i].score[0] += pref[i].score[1];
 455                 }
 456
 457         }
 458         catch(exception& e) {
 459                 errorOut(e, "ChimeraSeqsCommand", "generatePreferences");
 460                 exit(1);
 461         }
 462 }
 463 /**************************************************************************************************/
 464
 465 /**************************************************************************************************/
 466