chimeraccodecommand.cpp

   1 /*
   2  *  chimeraccodecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/30/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraccodecommand.h"
  11 #include "ccode.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraCcodeCommand::ChimeraCcodeCommand(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", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir", };
  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                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 string path;
  43                                 it = parameters.find("fasta");
  44                                 //user has given a template file
  45                                 if(it != parameters.end()){
  46                                         path = hasPath(it->second);
  47                                         //if the user has not given a path then, add inputdir. else leave path alone.
  48                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  49                                 }
  50
  51                                 it = parameters.find("template");
  52                                 //user has given a template file
  53                                 if(it != parameters.end()){
  54                                         path = hasPath(it->second);
  55                                         //if the user has not given a path then, add inputdir. else leave path alone.
  56                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  57                                 }
  58                         }
  59
  60
  61                         //check for required parameters
  62                         fastafile = validParameter.validFile(parameters, "fasta", true);
  63                         if (fastafile == "not open") { abort = true; }
  64                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true;  }
  65
  66                         //if the user changes the output directory command factory will send this info to us in the output parameter
  67                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  68                                 outputDir = "";
  69                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  70                         }
  71
  72                         templatefile = validParameter.validFile(parameters, "template", true);
  73                         if (templatefile == "not open") { abort = true; }
  74                         else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true;  }
  75
  76                         maskfile = validParameter.validFile(parameters, "mask", false);
  77                         if (maskfile == "not found") { maskfile = "";  }
  78                         else if (maskfile != "default")  {
  79                                 if (inputDir != "") {
  80                                         string path = hasPath(maskfile);
  81                                         //if the user has not given a path then, add inputdir. else leave path alone.
  82                                         if (path == "") {       maskfile = inputDir + maskfile;         }
  83                                 }
  84
  85                                 ifstream in;
  86                                 int     ableToOpen = openInputFile(maskfile, in);
  87                                 if (ableToOpen == 1) { abort = true; }
  88                                 in.close();
  89                         }
  90
  91                         string temp;
  92                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
  93                         filter = isTrue(temp);
  94
  95                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  96                         convert(temp, processors);
  97
  98                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  99                         convert(temp, window);
 100
 101                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
 102                         convert(temp, numwanted);
 103
 104                 }
 105         }
 106         catch(exception& e) {
 107                 m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
 108                 exit(1);
 109         }
 110 }
 111 //**********************************************************************************************************************
 112
 113 void ChimeraCcodeCommand::help(){
 114         try {
 115
 116                 m->mothurOut("The chimera.ccode command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 117                 m->mothurOut("This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n");
 118                 m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n");
 119                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 120                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 121                 m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
 122                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 123                 #ifdef USE_MPI
 124                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 125                 #endif
 126                 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");
 127                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n");
 128                 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
 129                 m->mothurOut("The chimera.ccode command should be in the following format: \n");
 130                 m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n");
 131                 m->mothurOut("Example: chimera.seqs(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n");
 132                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 133         }
 134         catch(exception& e) {
 135                 m->errorOut(e, "ChimeraCcodeCommand", "help");
 136                 exit(1);
 137         }
 138 }
 139
 140 //***************************************************************************************************************
 141
 142 ChimeraCcodeCommand::~ChimeraCcodeCommand(){    /*      do nothing      */      }
 143
 144 //***************************************************************************************************************
 145
 146 int ChimeraCcodeCommand::execute(){
 147         try{
 148
 149                 if (abort == true) { return 0; }
 150
 151                 int start = time(NULL);
 152
 153                 //set user options
 154                 if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }
 155
 156                 chimera = new Ccode(fastafile, templatefile, filter, maskfile, window, numwanted, outputDir);
 157
 158                 //is your template aligned?
 159                 if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
 160                 templateSeqsLength = chimera->getLength();
 161
 162                 string outputFileName, accnosFileName;
 163                 if (maskfile != "") {
 164                         outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.chimeras";
 165                         accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.accnos";
 166                 }else {
 167                         outputFileName = outputDir + getRootName(getSimpleName(fastafile))  + "ccode.chimeras";
 168                         accnosFileName = outputDir + getRootName(getSimpleName(fastafile))  + "ccode.accnos";
 169                 }
 170
 171                 string mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
 172                 bool hasAccnos = true;
 173
 174                 if (m->control_pressed) { delete chimera;       return 0;       }
 175
 176         #ifdef USE_MPI
 177
 178                         int pid, end, numSeqsPerProcessor;
 179                         int tag = 2001;
 180                         vector<long> MPIPos;
 181                         MPIWroteAccnos = false;
 182
 183                         MPI_Status status;
 184                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 185                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 186
 187                         MPI_File inMPI;
 188                         MPI_File outMPI;
 189                         MPI_File outMPIAccnos;
 190
 191                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 192                         int inMode=MPI_MODE_RDONLY;
 193
 194                         //char* outFilename = new char[outputFileName.length()];
 195                         //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 196
 197                         char outFilename[1024];
 198                         strcpy(outFilename, outputFileName.c_str());
 199
 200                         //char* outAccnosFilename = new char[accnosFileName.length()];
 201                         //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 202
 203                         char outAccnosFilename[1024];
 204                         strcpy(outAccnosFilename, accnosFileName.c_str());
 205
 206                         //char* inFileName = new char[fastafile.length()];
 207                         //memcpy(inFileName, fastafile.c_str(), fastafile.length());
 208
 209                         char inFileName[1024];
 210                         strcpy(inFileName, fastafile.c_str());
 211
 212                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 213                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 214                         MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 215
 216                         //delete inFileName;
 217                         //delete outFilename;
 218                         //delete outAccnosFilename;
 219
 220                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 221
 222                         if (pid == 0) { //you are the root process
 223                                 string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
 224
 225                                 //print header
 226                                 int length = outTemp.length();
 227                                 char* buf2 = new char[length];
 228                                 memcpy(buf2, outTemp.c_str(), length);
 229
 230                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 231                                 delete buf2;
 232
 233                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 234
 235                                 //send file positions to all processes
 236                                 for(int i = 1; i < processors; i++) {
 237                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 238                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 239                                 }
 240
 241                                 //figure out how many sequences you have to align
 242                                 numSeqsPerProcessor = numSeqs / processors;
 243                                 int startIndex =  pid * numSeqsPerProcessor;
 244                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 245
 246
 247                                 //align your part
 248                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 249
 250                                 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;  }
 251
 252                                 for (int i = 1; i < processors; i++) {
 253                                         bool tempResult;
 254                                         MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 255                                         if (tempResult != 0) { MPIWroteAccnos = true; }
 256                                 }
 257                         }else{ //you are a child process
 258                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 259                                 MPIPos.resize(numSeqs+1);
 260                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 261
 262                                 //figure out how many sequences you have to align
 263                                 numSeqsPerProcessor = numSeqs / processors;
 264                                 int startIndex =  pid * numSeqsPerProcessor;
 265                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 266
 267
 268                                 //align your part
 269                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 270
 271                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 272
 273                                 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 274                         }
 275
 276                         //close files
 277                         MPI_File_close(&inMPI);
 278                         MPI_File_close(&outMPI);
 279                         MPI_File_close(&outMPIAccnos);
 280
 281                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 282
 283                         //delete accnos file if blank
 284                         if (pid == 0) {
 285                                 if (!MPIWroteAccnos) {
 286                                         //MPI_Info info;
 287                                         //MPI_File_delete(outAccnosFilename, info);
 288                                         hasAccnos = false;
 289                                         remove(accnosFileName.c_str());
 290                                 }
 291                         }
 292
 293         #else
 294                 ofstream outHeader;
 295                 string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + "ccode.chimeras.tempHeader";
 296                 openOutputFile(tempHeader, outHeader);
 297
 298                 outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
 299
 300                 outHeader.close();
 301
 302                 //break up file
 303                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 304                         if(processors == 1){
 305                                 ifstream inFASTA;
 306                                 openInputFile(fastafile, inFASTA);
 307                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 308                                 inFASTA.close();
 309
 310                                 lines.push_back(new linePair(0, numSeqs));
 311
 312                                 driver(lines[0], outputFileName, fastafile, accnosFileName);
 313
 314                                 if (m->control_pressed) {
 315                                         remove(outputFileName.c_str());
 316                                         remove(tempHeader.c_str());
 317                                         remove(accnosFileName.c_str());
 318                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 319                                         delete chimera;
 320                                         return 0;
 321                                 }
 322
 323                                 //delete accnos file if its blank
 324                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 325
 326                         }else{
 327                                 vector<int> positions;
 328                                 processIDS.resize(0);
 329
 330                                 ifstream inFASTA;
 331                                 openInputFile(fastafile, inFASTA);
 332
 333                                 string input;
 334                                 while(!inFASTA.eof()){
 335                                         input = getline(inFASTA);
 336                                         if (input.length() != 0) {
 337                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 338                                         }
 339                                 }
 340                                 inFASTA.close();
 341
 342                                 numSeqs = positions.size();
 343
 344                                 int numSeqsPerProcessor = numSeqs / processors;
 345
 346                                 for (int i = 0; i < processors; i++) {
 347                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 348                                         if(i == processors - 1){
 349                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 350                                         }
 351                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 352                                 }
 353
 354
 355                                 createProcesses(outputFileName, fastafile, accnosFileName);
 356
 357                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 358
 359                                 //append output files
 360                                 for(int i=1;i<processors;i++){
 361                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 362                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 363                                 }
 364
 365                                 vector<string> nonBlankAccnosFiles;
 366                                 //delete blank accnos files generated with multiple processes
 367                                 for(int i=0;i<processors;i++){
 368                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 369                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 370                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 371                                 }
 372
 373                                 //append accnos files
 374                                 if (nonBlankAccnosFiles.size() != 0) {
 375                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 376
 377                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 378                                                 appendFiles(nonBlankAccnosFiles[h], accnosFileName);
 379                                                 remove(nonBlankAccnosFiles[h].c_str());
 380                                         }
 381                                 }else{ hasAccnos = false;  }
 382
 383                                 if (m->control_pressed) {
 384                                         remove(outputFileName.c_str());
 385                                         remove(accnosFileName.c_str());
 386                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 387                                         delete chimera;
 388                                         return 0;
 389                                 }
 390
 391                         }
 392
 393                 #else
 394                         ifstream inFASTA;
 395                         openInputFile(fastafile, inFASTA);
 396                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 397                         inFASTA.close();
 398                         lines.push_back(new linePair(0, numSeqs));
 399
 400                         driver(lines[0], outputFileName, fastafile, accnosFileName);
 401
 402                         if (m->control_pressed) {
 403                                         remove(outputFileName.c_str());
 404                                         remove(tempHeader.c_str());
 405                                         remove(accnosFileName.c_str());
 406                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 407                                         delete chimera;
 408                                         return 0;
 409                         }
 410
 411                         //delete accnos file if its blank
 412                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 413                 #endif
 414
 415                 //m->mothurOut("Output File Names: ");
 416                 //if ((filter) && (method == "bellerophon")) { m->mothurOut(
 417                 //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
 418                 //      else                             { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
 419
 420                 appendFiles(outputFileName, tempHeader);
 421
 422                 remove(outputFileName.c_str());
 423                 rename(tempHeader.c_str(), outputFileName.c_str());
 424         #endif
 425
 426                 delete chimera;
 427
 428
 429                 m->mothurOutEndLine();
 430                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 431                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 432                 if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
 433                 m->mothurOutEndLine();
 434
 435                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 436
 437                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 438
 439                 return 0;
 440
 441         }
 442         catch(exception& e) {
 443                 m->errorOut(e, "ChimeraCcodeCommand", "execute");
 444                 exit(1);
 445         }
 446 }
 447 //**********************************************************************************************************************
 448
 449 int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 450         try {
 451                 ofstream out;
 452                 openOutputFile(outputFName, out);
 453
 454                 ofstream out2;
 455                 openOutputFile(accnos, out2);
 456
 457                 ifstream inFASTA;
 458                 openInputFile(filename, inFASTA);
 459
 460                 inFASTA.seekg(line->start);
 461
 462                 for(int i=0;i<line->numSeqs;i++){
 463
 464                         if (m->control_pressed) {       return 1;       }
 465
 466                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 467
 468                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 469
 470                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 471                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 472                                 }else{
 473                                         //find chimeras
 474                                         chimera->getChimeras(candidateSeq);
 475
 476                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 477
 478                                         //print results
 479                                         chimera->print(out, out2);
 480                                 }
 481                         }
 482                         delete candidateSeq;
 483
 484                         //report progress
 485                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 486                 }
 487                 //report progress
 488                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 489
 490                 out.close();
 491                 out2.close();
 492                 inFASTA.close();
 493
 494                 return 0;
 495         }
 496         catch(exception& e) {
 497                 m->errorOut(e, "ChimeraCcodeCommand", "driver");
 498                 exit(1);
 499         }
 500 }
 501 //**********************************************************************************************************************
 502 #ifdef USE_MPI
 503 int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 504         try {
 505
 506                 MPI_Status status;
 507                 int pid;
 508                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 509
 510                 for(int i=0;i<num;i++){
 511
 512                         if (m->control_pressed) { return 0; }
 513
 514                         //read next sequence
 515                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 516
 517                         char* buf4 = new char[length];
 518
 519                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 520
 521                         string tempBuf = buf4;
 522                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 523                         istringstream iss (tempBuf,istringstream::in);
 524                         delete buf4;
 525
 526                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 527
 528                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 529
 530                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 531                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 532                                 }else{
 533                                         //find chimeras
 534                                         chimera->getChimeras(candidateSeq);
 535
 536                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 537
 538                                         //print results
 539                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 540                                         if (isChimeric) { MPIWroteAccnos = true;  }
 541                                 }
 542                         }
 543                         delete candidateSeq;
 544
 545                         //report progress
 546                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 547                 }
 548                 //report progress
 549                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 550
 551
 552                 return 0;
 553         }
 554         catch(exception& e) {
 555                 m->errorOut(e, "ChimeraCcodeCommand", "driverMPI");
 556                 exit(1);
 557         }
 558 }
 559 #endif
 560
 561 /**************************************************************************************************/
 562
 563 int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 564         try {
 565 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 566                 int process = 0;
 567                 //              processIDS.resize(0);
 568
 569                 //loop through and create all the processes you want
 570                 while (process != processors) {
 571                         int pid = fork();
 572
 573                         if (pid > 0) {
 574                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 575                                 process++;
 576                         }else if (pid == 0){
 577                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 578                                 exit(0);
 579                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 580                 }
 581
 582                 //force parent to wait until all the processes are done
 583                 for (int i=0;i<processors;i++) {
 584                         int temp = processIDS[i];
 585                         wait(&temp);
 586                 }
 587
 588                 return 0;
 589 #endif
 590         }
 591         catch(exception& e) {
 592                 m->errorOut(e, "ChimeraCcodeCommand", "createProcesses");
 593                 exit(1);
 594         }
 595 }
 596 //**********************************************************************************************************************
 597