chimeraslayercommand.cpp

   1 /*
   2  *  chimeraslayercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraslayercommand.h"
  11 #include "chimeraslayer.h"
  12
  13
  14 //***************************************************************************************************************
  15
  16 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
  17         try {
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch",
  26                         "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string,string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33                         map<string,string>::iterator it;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  42                         if (inputDir == "not found"){   inputDir = "";          }
  43                         else {
  44                                 string path;
  45                                 it = parameters.find("fasta");
  46                                 //user has given a template file
  47                                 if(it != parameters.end()){
  48                                         path = hasPath(it->second);
  49                                         //if the user has not given a path then, add inputdir. else leave path alone.
  50                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  51                                 }
  52
  53                                 it = parameters.find("template");
  54                                 //user has given a template file
  55                                 if(it != parameters.end()){
  56                                         path = hasPath(it->second);
  57                                         //if the user has not given a path then, add inputdir. else leave path alone.
  58                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  59                                 }
  60                         }
  61
  62
  63                         //check for required parameters
  64                         fastafile = validParameter.validFile(parameters, "fasta", true);
  65                         if (fastafile == "not open") { abort = true; }
  66                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
  67
  68                         //if the user changes the output directory command factory will send this info to us in the output parameter
  69                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  70                                 outputDir = "";
  71                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  72                         }
  73
  74                         templatefile = validParameter.validFile(parameters, "template", true);
  75                         if (templatefile == "not open") { abort = true; }
  76                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
  77
  78                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
  79                         convert(temp, processors);
  80
  81                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
  82                         convert(temp, ksize);
  83
  84                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
  85                         convert(temp, window);
  86
  87                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
  88                         convert(temp, match);
  89
  90                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
  91                         convert(temp, mismatch);
  92
  93                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
  94                         convert(temp, divR);
  95
  96                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
  97                         convert(temp, minSimilarity);
  98
  99                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 100                         convert(temp, minCoverage);
 101
 102                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 103                         convert(temp, minBS);
 104
 105                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
 106                         convert(temp, minSNP);
 107
 108                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 109                         convert(temp, parents);
 110
 111                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
 112                         realign = isTrue(temp);
 113
 114                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
 115
 116                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "100"; }
 117                         convert(temp, iters);
 118
 119                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 120                         convert(temp, increment);
 121
 122                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 123                         convert(temp, numwanted);
 124
 125                         if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 126                 }
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 130                 exit(1);
 131         }
 132 }
 133 //**********************************************************************************************************************
 134
 135 void ChimeraSlayerCommand::help(){
 136         try {
 137
 138                 m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 139                 m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
 140                 m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
 141                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 142                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 143                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 144                 #ifdef USE_MPI
 145                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 146                 #endif
 147                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
 148                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
 149                 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
 150                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
 151                 m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
 152                 m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n");
 153                 m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
 154                 m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
 155                 m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
 156                 m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
 157                 m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
 158                 m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
 159                 m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
 160                 m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
 161                 //m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. Found to make results worse. \n");
 162                 m->mothurOut("The chimera.slayer command should be in the following format: \n");
 163                 m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
 164                 m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
 165                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "ChimeraSlayerCommand", "help");
 169                 exit(1);
 170         }
 171 }
 172
 173 //***************************************************************************************************************
 174
 175 ChimeraSlayerCommand::~ChimeraSlayerCommand(){  /*      do nothing      */      }
 176
 177 //***************************************************************************************************************
 178
 179 int ChimeraSlayerCommand::execute(){
 180         try{
 181
 182                 if (abort == true) { return 0; }
 183
 184                 int start = time(NULL);
 185
 186                 chimera = new ChimeraSlayer(fastafile, templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 187
 188                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras";
 189                 string accnosFileName = outputDir + getRootName(getSimpleName(fastafile))  + "slayer.accnos";
 190                 bool hasAccnos = true;
 191
 192                 if (m->control_pressed) { delete chimera;       return 0;       }
 193
 194                 if (chimera->getUnaligned()) {
 195                         m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 196                         delete chimera;
 197                         return 0;
 198                 }
 199                 templateSeqsLength = chimera->getLength();
 200
 201         #ifdef USE_MPI
 202                 int pid, end, numSeqsPerProcessor;
 203                         int tag = 2001;
 204                         vector<long> MPIPos;
 205                         MPIWroteAccnos = false;
 206
 207                         MPI_Status status;
 208                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 209                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 210
 211                         MPI_File inMPI;
 212                         MPI_File outMPI;
 213                         MPI_File outMPIAccnos;
 214
 215                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 216                         int inMode=MPI_MODE_RDONLY;
 217
 218                         //char* outFilename = new char[outputFileName.length()];
 219                         //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 220
 221                         char outFilename[1024];
 222                         strcpy(outFilename, outputFileName.c_str());
 223
 224                         //char* outAccnosFilename = new char[accnosFileName.length()];
 225                         //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 226
 227                         char outAccnosFilename[1024];
 228                         strcpy(outAccnosFilename, accnosFileName.c_str());
 229
 230                         //char* inFileName = new char[fastafile.length()];
 231                         //memcpy(inFileName, fastafile.c_str(), fastafile.length());
 232
 233                         char inFileName[1024];
 234                         strcpy(inFileName, fastafile.c_str());
 235
 236                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 237                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 238                         MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 239
 240                         //delete inFileName;
 241                         //delete outFilename;
 242                         //delete outAccnosFilename;
 243
 244                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 245
 246                         if (pid == 0) { //you are the root process
 247                                 m->mothurOutEndLine();
 248                                 m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 249                                 m->mothurOutEndLine();
 250
 251                                 string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 252
 253                                 //print header
 254                                 int length = outTemp.length();
 255                                 char* buf2 = new char[length];
 256                                 memcpy(buf2, outTemp.c_str(), length);
 257
 258                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 259                                 delete buf2;
 260
 261                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 262
 263                                 //send file positions to all processes
 264                                 for(int i = 1; i < processors; i++) {
 265                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 266                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 267                                 }
 268
 269                                 //figure out how many sequences you have to align
 270                                 numSeqsPerProcessor = numSeqs / processors;
 271                                 int startIndex =  pid * numSeqsPerProcessor;
 272                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 273
 274
 275                                 //align your part
 276                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 277
 278                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 279
 280                                 for (int i = 1; i < processors; i++) {
 281                                         bool tempResult;
 282                                         MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 283                                         if (tempResult != 0) { MPIWroteAccnos = true; }
 284                                 }
 285                         }else{ //you are a child process
 286                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 287                                 MPIPos.resize(numSeqs+1);
 288                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 289
 290                                 //figure out how many sequences you have to align
 291                                 numSeqsPerProcessor = numSeqs / processors;
 292                                 int startIndex =  pid * numSeqsPerProcessor;
 293                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 294
 295
 296                                 //align your part
 297                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 298
 299                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 300
 301                                 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 302                         }
 303
 304                         //close files
 305                         MPI_File_close(&inMPI);
 306                         MPI_File_close(&outMPI);
 307                         MPI_File_close(&outMPIAccnos);
 308                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 309
 310                         //delete accnos file if blank
 311                         if (pid == 0) {
 312                                 if (!MPIWroteAccnos) {
 313                                         //MPI_Info info;
 314                                         //MPI_File_delete(outAccnosFilename, info);
 315                                         hasAccnos = false;
 316                                         remove(accnosFileName.c_str());
 317                                 }
 318                         }
 319
 320         #else
 321                 ofstream outHeader;
 322                 string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras.tempHeader";
 323                 openOutputFile(tempHeader, outHeader);
 324
 325                 chimera->printHeader(outHeader);
 326                 outHeader.close();
 327
 328                 //break up file
 329                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 330                         if(processors == 1){
 331                                 ifstream inFASTA;
 332                                 openInputFile(fastafile, inFASTA);
 333                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 334                                 inFASTA.close();
 335
 336                                 lines.push_back(new linePair(0, numSeqs));
 337
 338                                 driver(lines[0], outputFileName, fastafile, accnosFileName);
 339
 340                                 if (m->control_pressed) {
 341                                         remove(outputFileName.c_str());
 342                                         remove(tempHeader.c_str());
 343                                         remove(accnosFileName.c_str());
 344                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 345                                         delete chimera;
 346                                         return 0;
 347                                 }
 348
 349                                 //delete accnos file if its blank
 350                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 351
 352                         }else{
 353                                 vector<int> positions;
 354                                 processIDS.resize(0);
 355
 356                                 ifstream inFASTA;
 357                                 openInputFile(fastafile, inFASTA);
 358
 359                                 string input;
 360                                 while(!inFASTA.eof()){
 361                                         input = getline(inFASTA);
 362                                         if (input.length() != 0) {
 363                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 364                                         }
 365                                 }
 366                                 inFASTA.close();
 367
 368                                 numSeqs = positions.size();
 369
 370                                 int numSeqsPerProcessor = numSeqs / processors;
 371
 372                                 for (int i = 0; i < processors; i++) {
 373                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 374                                         if(i == processors - 1){
 375                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 376                                         }
 377                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 378                                 }
 379
 380
 381                                 createProcesses(outputFileName, fastafile, accnosFileName);
 382
 383                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 384
 385                                 //append output files
 386                                 for(int i=1;i<processors;i++){
 387                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 388                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 389                                 }
 390
 391                                 vector<string> nonBlankAccnosFiles;
 392                                 //delete blank accnos files generated with multiple processes
 393                                 for(int i=0;i<processors;i++){
 394                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 395                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 396                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 397                                 }
 398
 399                                 //append accnos files
 400                                 if (nonBlankAccnosFiles.size() != 0) {
 401                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 402
 403                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 404                                                 appendFiles(nonBlankAccnosFiles[h], accnosFileName);
 405                                                 remove(nonBlankAccnosFiles[h].c_str());
 406                                         }
 407                                 }else{ hasAccnos = false;  }
 408
 409                                 if (m->control_pressed) {
 410                                         remove(outputFileName.c_str());
 411                                         remove(accnosFileName.c_str());
 412                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 413                                         delete chimera;
 414                                         return 0;
 415                                 }
 416
 417                         }
 418
 419                 #else
 420                         ifstream inFASTA;
 421                         openInputFile(fastafile, inFASTA);
 422                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 423                         inFASTA.close();
 424                         lines.push_back(new linePair(0, numSeqs));
 425
 426                         driver(lines[0], outputFileName, fastafile, accnosFileName);
 427
 428                         if (m->control_pressed) {
 429                                         remove(outputFileName.c_str());
 430                                         remove(tempHeader.c_str());
 431                                         remove(accnosFileName.c_str());
 432                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 433                                         delete chimera;
 434                                         return 0;
 435                         }
 436
 437                         //delete accnos file if its blank
 438                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 439                 #endif
 440
 441                 appendFiles(outputFileName, tempHeader);
 442
 443                 remove(outputFileName.c_str());
 444                 rename(tempHeader.c_str(), outputFileName.c_str());
 445
 446         #endif
 447                 delete chimera;
 448
 449                 m->mothurOutEndLine();
 450                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 451                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 452                 if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
 453                 m->mothurOutEndLine();
 454
 455                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 456
 457                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 458
 459                 return 0;
 460
 461         }
 462         catch(exception& e) {
 463                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 464                 exit(1);
 465         }
 466 }
 467 //**********************************************************************************************************************
 468
 469 int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 470         try {
 471                 ofstream out;
 472                 openOutputFile(outputFName, out);
 473
 474                 ofstream out2;
 475                 openOutputFile(accnos, out2);
 476
 477                 ifstream inFASTA;
 478                 openInputFile(filename, inFASTA);
 479
 480                 inFASTA.seekg(line->start);
 481
 482                 for(int i=0;i<line->numSeqs;i++){
 483
 484                         if (m->control_pressed) {       return 1;       }
 485
 486                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 487
 488                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 489
 490                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 491                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 492                                 }else{
 493                                         //find chimeras
 494                                         chimera->getChimeras(candidateSeq);
 495
 496                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 497
 498                                         //print results
 499                                         chimera->print(out, out2);
 500                                 }
 501                         }
 502                         delete candidateSeq;
 503
 504                         //report progress
 505                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 506                 }
 507                 //report progress
 508                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 509
 510                 out.close();
 511                 out2.close();
 512                 inFASTA.close();
 513
 514                 return 0;
 515         }
 516         catch(exception& e) {
 517                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 518                 exit(1);
 519         }
 520 }
 521 //**********************************************************************************************************************
 522 #ifdef USE_MPI
 523 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 524         try {
 525                 MPI_Status status;
 526                 int pid;
 527                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 528
 529                 for(int i=0;i<num;i++){
 530
 531                         if (m->control_pressed) {       return 1;       }
 532
 533                         //read next sequence
 534                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 535
 536                         char* buf4 = new char[length];
 537                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 538
 539                         string tempBuf = buf4;
 540                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 541                         istringstream iss (tempBuf,istringstream::in);
 542
 543                         delete buf4;
 544
 545                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 546
 547                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 548
 549                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 550                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 551                                 }else{
 552
 553                                         //find chimeras
 554                                         chimera->getChimeras(candidateSeq);
 555
 556                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 557                 //cout << "about to print" << endl;
 558                                         //print results
 559                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 560                                         if (isChimeric) { MPIWroteAccnos = true;  }
 561
 562                                 }
 563                         }
 564                         delete candidateSeq;
 565
 566                         //report progress
 567                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 568                 }
 569                 //report progress
 570                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 571
 572
 573                 return 0;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 577                 exit(1);
 578         }
 579 }
 580 #endif
 581
 582 /**************************************************************************************************/
 583
 584 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
 585         try {
 586 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 587                 int process = 0;
 588                 //              processIDS.resize(0);
 589
 590                 //loop through and create all the processes you want
 591                 while (process != processors) {
 592                         int pid = fork();
 593
 594                         if (pid > 0) {
 595                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 596                                 process++;
 597                         }else if (pid == 0){
 598                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 599                                 exit(0);
 600                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 601                 }
 602
 603                 //force parent to wait until all the processes are done
 604                 for (int i=0;i<processors;i++) {
 605                         int temp = processIDS[i];
 606                         wait(&temp);
 607                 }
 608
 609                 return 0;
 610 #endif
 611         }
 612         catch(exception& e) {
 613                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 614                 exit(1);
 615         }
 616 }
 617
 618 /**************************************************************************************************/
 619
 620