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, filter, mask, 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 mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
 148                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
 149                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
 150                 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
 151                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
 152                 m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
 153                 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");
 154                 m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
 155                 m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
 156                 m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
 157                 m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
 158                 m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
 159                 m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
 160                 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");
 161                 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");
 162                 //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");
 163                 m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
 164                 m->mothurOut("The chimera.slayer command should be in the following format: \n");
 165                 m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
 166                 m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
 167                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 168         }
 169         catch(exception& e) {
 170                 m->errorOut(e, "ChimeraSlayerCommand", "help");
 171                 exit(1);
 172         }
 173 }
 174
 175 //***************************************************************************************************************
 176
 177 ChimeraSlayerCommand::~ChimeraSlayerCommand(){  /*      do nothing      */      }
 178
 179 //***************************************************************************************************************
 180
 181 int ChimeraSlayerCommand::execute(){
 182         try{
 183
 184                 if (abort == true) { return 0; }
 185
 186                 int start = time(NULL);
 187
 188                 chimera = new ChimeraSlayer(fastafile, templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 189
 190                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras";
 191                 string accnosFileName = outputDir + getRootName(getSimpleName(fastafile))  + "slayer.accnos";
 192                 bool hasAccnos = true;
 193
 194                 if (m->control_pressed) { delete chimera;       return 0;       }
 195
 196                 if (chimera->getUnaligned()) {
 197                         m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 198                         delete chimera;
 199                         return 0;
 200                 }
 201                 templateSeqsLength = chimera->getLength();
 202
 203         #ifdef USE_MPI
 204                 int pid, end, numSeqsPerProcessor;
 205                         int tag = 2001;
 206                         vector<long> MPIPos;
 207                         MPIWroteAccnos = false;
 208
 209                         MPI_Status status;
 210                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 211                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 212
 213                         MPI_File inMPI;
 214                         MPI_File outMPI;
 215                         MPI_File outMPIAccnos;
 216
 217                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 218                         int inMode=MPI_MODE_RDONLY;
 219
 220                         char* outFilename = new char[outputFileName.length()];
 221                         memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 222
 223                         char* outAccnosFilename = new char[accnosFileName.length()];
 224                         memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 225
 226                         char* inFileName = new char[fastafile.length()];
 227                         memcpy(inFileName, fastafile.c_str(), fastafile.length());
 228
 229                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 230                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 231                         MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 232
 233                         delete inFileName;
 234                         delete outFilename;
 235                         delete outAccnosFilename;
 236
 237                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 238
 239                         if (pid == 0) { //you are the root process
 240                                 m->mothurOutEndLine();
 241                                 m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 242                                 m->mothurOutEndLine();
 243
 244                                 string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 245
 246                                 //print header
 247                                 int length = outTemp.length();
 248                                 char* buf2 = new char[length];
 249                                 memcpy(buf2, outTemp.c_str(), length);
 250
 251                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 252                                 delete buf2;
 253
 254                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 255
 256                                 //send file positions to all processes
 257                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 258                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 259
 260                                 //figure out how many sequences you have to align
 261                                 numSeqsPerProcessor = numSeqs / processors;
 262                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 263                                 int startIndex =  pid * numSeqsPerProcessor;
 264
 265                                 //align your part
 266                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 267
 268                                 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;  }
 269
 270                                 for (int i = 1; i < processors; i++) {
 271                                         bool tempResult;
 272                                         MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 273                                         if (tempResult != 0) { MPIWroteAccnos = true; }
 274                                 }
 275                         }else{ //you are a child process
 276                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 277                                 MPIPos.resize(numSeqs+1);
 278                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 279
 280                                 //figure out how many sequences you have to align
 281                                 numSeqsPerProcessor = numSeqs / processors;
 282                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 283                                 int startIndex =  pid * numSeqsPerProcessor;
 284
 285                                 //align your part
 286                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 287
 288                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 289
 290                                 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 291                         }
 292
 293                         //close files
 294                         MPI_File_close(&inMPI);
 295                         MPI_File_close(&outMPI);
 296                         MPI_File_close(&outMPIAccnos);
 297
 298                         //delete accnos file if blank
 299                         if (pid == 0) {
 300                                 if (!MPIWroteAccnos) {
 301                                         //MPI_Info info;
 302                                         //MPI_File_delete(outAccnosFilename, info);
 303                                         hasAccnos = false;
 304                                         remove(accnosFileName.c_str());
 305                                 }
 306                         }
 307
 308         #else
 309                 ofstream outHeader;
 310                 string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras.tempHeader";
 311                 openOutputFile(tempHeader, outHeader);
 312
 313                 chimera->printHeader(outHeader);
 314                 outHeader.close();
 315
 316                 //break up file
 317                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 318                         if(processors == 1){
 319                                 ifstream inFASTA;
 320                                 openInputFile(fastafile, inFASTA);
 321                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 322                                 inFASTA.close();
 323
 324                                 lines.push_back(new linePair(0, numSeqs));
 325
 326                                 driver(lines[0], outputFileName, fastafile, accnosFileName);
 327
 328                                 if (m->control_pressed) {
 329                                         remove(outputFileName.c_str());
 330                                         remove(tempHeader.c_str());
 331                                         remove(accnosFileName.c_str());
 332                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 333                                         delete chimera;
 334                                         return 0;
 335                                 }
 336
 337                                 //delete accnos file if its blank
 338                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 339
 340                         }else{
 341                                 vector<int> positions;
 342                                 processIDS.resize(0);
 343
 344                                 ifstream inFASTA;
 345                                 openInputFile(fastafile, inFASTA);
 346
 347                                 string input;
 348                                 while(!inFASTA.eof()){
 349                                         input = getline(inFASTA);
 350                                         if (input.length() != 0) {
 351                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 352                                         }
 353                                 }
 354                                 inFASTA.close();
 355
 356                                 numSeqs = positions.size();
 357
 358                                 int numSeqsPerProcessor = numSeqs / processors;
 359
 360                                 for (int i = 0; i < processors; i++) {
 361                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 362                                         if(i == processors - 1){
 363                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 364                                         }
 365                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 366                                 }
 367
 368
 369                                 createProcesses(outputFileName, fastafile, accnosFileName);
 370
 371                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 372
 373                                 //append output files
 374                                 for(int i=1;i<processors;i++){
 375                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 376                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 377                                 }
 378
 379                                 vector<string> nonBlankAccnosFiles;
 380                                 //delete blank accnos files generated with multiple processes
 381                                 for(int i=0;i<processors;i++){
 382                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 383                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 384                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 385                                 }
 386
 387                                 //append accnos files
 388                                 if (nonBlankAccnosFiles.size() != 0) {
 389                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 390
 391                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 392                                                 appendFiles(nonBlankAccnosFiles[h], accnosFileName);
 393                                                 remove(nonBlankAccnosFiles[h].c_str());
 394                                         }
 395                                 }else{ hasAccnos = false;  }
 396
 397                                 if (m->control_pressed) {
 398                                         remove(outputFileName.c_str());
 399                                         remove(accnosFileName.c_str());
 400                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 401                                         delete chimera;
 402                                         return 0;
 403                                 }
 404
 405                         }
 406
 407                 #else
 408                         ifstream inFASTA;
 409                         openInputFile(fastafile, inFASTA);
 410                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 411                         inFASTA.close();
 412                         lines.push_back(new linePair(0, numSeqs));
 413
 414                         driver(lines[0], outputFileName, fastafile, accnosFileName);
 415
 416                         if (m->control_pressed) {
 417                                         remove(outputFileName.c_str());
 418                                         remove(tempHeader.c_str());
 419                                         remove(accnosFileName.c_str());
 420                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 421                                         delete chimera;
 422                                         return 0;
 423                         }
 424
 425                         //delete accnos file if its blank
 426                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 427                 #endif
 428
 429                 appendFiles(outputFileName, tempHeader);
 430
 431                 remove(outputFileName.c_str());
 432                 rename(tempHeader.c_str(), outputFileName.c_str());
 433
 434         #endif
 435                 delete chimera;
 436
 437                 m->mothurOutEndLine();
 438                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 439                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 440                 if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
 441                 m->mothurOutEndLine();
 442
 443                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 444
 445                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 446
 447                 return 0;
 448
 449         }
 450         catch(exception& e) {
 451                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 452                 exit(1);
 453         }
 454 }
 455 //**********************************************************************************************************************
 456
 457 int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 458         try {
 459                 ofstream out;
 460                 openOutputFile(outputFName, out);
 461
 462                 ofstream out2;
 463                 openOutputFile(accnos, out2);
 464
 465                 ifstream inFASTA;
 466                 openInputFile(filename, inFASTA);
 467
 468                 inFASTA.seekg(line->start);
 469
 470                 for(int i=0;i<line->numSeqs;i++){
 471
 472                         if (m->control_pressed) {       return 1;       }
 473
 474                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 475
 476                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 477
 478                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 479                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 480                                 }else{
 481                                         //find chimeras
 482                                         chimera->getChimeras(candidateSeq);
 483
 484                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 485
 486                                         //print results
 487                                         chimera->print(out, out2);
 488                                 }
 489                         }
 490                         delete candidateSeq;
 491
 492                         //report progress
 493                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 494                 }
 495                 //report progress
 496                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 497
 498                 out.close();
 499                 out2.close();
 500                 inFASTA.close();
 501
 502                 return 0;
 503         }
 504         catch(exception& e) {
 505                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 506                 exit(1);
 507         }
 508 }
 509 //**********************************************************************************************************************
 510 #ifdef USE_MPI
 511 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 512         try {
 513                 MPI_Status status;
 514                 int pid;
 515                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 516
 517                 for(int i=0;i<num;i++){
 518
 519                         if (m->control_pressed) {       return 1;       }
 520
 521                         //read next sequence
 522                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 523
 524                         char* buf4 = new char[length];
 525                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 526
 527                         string tempBuf = buf4;
 528                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 529                         istringstream iss (tempBuf,istringstream::in);
 530
 531                         delete buf4;
 532
 533                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 534
 535                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 536
 537                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 538                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 539                                 }else{
 540
 541                                         //find chimeras
 542                                         chimera->getChimeras(candidateSeq);
 543
 544                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 545                 //cout << "about to print" << endl;
 546                                         //print results
 547                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 548                                         if (isChimeric) { MPIWroteAccnos = true;  }
 549
 550                                 }
 551                         }
 552                         delete candidateSeq;
 553
 554                         //report progress
 555                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 556                 }
 557                 //report progress
 558                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 559
 560
 561                 return 0;
 562         }
 563         catch(exception& e) {
 564                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 565                 exit(1);
 566         }
 567 }
 568 #endif
 569
 570 /**************************************************************************************************/
 571
 572 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
 573         try {
 574 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 575                 int process = 0;
 576                 //              processIDS.resize(0);
 577
 578                 //loop through and create all the processes you want
 579                 while (process != processors) {
 580                         int pid = fork();
 581
 582                         if (pid > 0) {
 583                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 584                                 process++;
 585                         }else if (pid == 0){
 586                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 587                                 exit(0);
 588                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 589                 }
 590
 591                 //force parent to wait until all the processes are done
 592                 for (int i=0;i<processors;i++) {
 593                         int temp = processIDS[i];
 594                         wait(&temp);
 595                 }
 596
 597                 return 0;
 598 #endif
 599         }
 600         catch(exception& e) {
 601                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 602                 exit(1);
 603         }
 604 }
 605
 606 /**************************************************************************************************/
 607
 608