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()];\r
 195                         memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 196
 197                         char* outAccnosFilename = new char[accnosFileName.length()];\r
 198                         memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 199
 200                         char* inFileName = new char[fastafile.length()];\r
 201                         memcpy(inFileName, fastafile.c_str(), fastafile.length());
 202
 203                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 204                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 205                         MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 206
 207                         delete inFileName;
 208                         delete outFilename;
 209                         delete outAccnosFilename;
 210
 211                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 212
 213                         if (pid == 0) { //you are the root process
 214                                 string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
 215
 216                                 //print header
 217                                 int length = outTemp.length();
 218                                 char* buf2 = new char[length];\r
 219                                 memcpy(buf2, outTemp.c_str(), length);
 220
 221                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 222                                 delete buf2;
 223
 224                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 225
 226                                 //send file positions to all processes
 227                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 228                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 229
 230                                 //figure out how many sequences you have to align
 231                                 numSeqsPerProcessor = numSeqs / processors;
 232                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 233                                 int startIndex =  pid * numSeqsPerProcessor;
 234
 235                                 //align your part
 236                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 237
 238                                 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;  }
 239
 240                                 for (int i = 1; i < processors; i++) {
 241                                         bool tempResult;
 242                                         MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 243                                         if (tempResult != 0) { MPIWroteAccnos = true; }
 244                                 }
 245                         }else{ //you are a child process
 246                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 247                                 MPIPos.resize(numSeqs+1);
 248                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 249
 250                                 //figure out how many sequences you have to align
 251                                 numSeqsPerProcessor = numSeqs / processors;
 252                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 253                                 int startIndex =  pid * numSeqsPerProcessor;
 254
 255                                 //align your part
 256                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 257
 258                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 259
 260                                 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 261                         }
 262
 263                         //close files
 264                         MPI_File_close(&inMPI);
 265                         MPI_File_close(&outMPI);
 266                         MPI_File_close(&outMPIAccnos);
 267
 268                         //delete accnos file if blank
 269                         if (pid == 0) {
 270                                 if (!MPIWroteAccnos) {
 271                                         //MPI_Info info;
 272                                         //MPI_File_delete(outAccnosFilename, info);
 273                                         hasAccnos = false;
 274                                         remove(accnosFileName.c_str());
 275                                 }
 276                         }
 277
 278         #else
 279                 ofstream outHeader;
 280                 string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + "ccode.chimeras.tempHeader";
 281                 openOutputFile(tempHeader, outHeader);
 282
 283                 outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
 284
 285                 outHeader.close();
 286
 287                 //break up file
 288                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 289                         if(processors == 1){
 290                                 ifstream inFASTA;
 291                                 openInputFile(fastafile, inFASTA);
 292                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 293                                 inFASTA.close();
 294
 295                                 lines.push_back(new linePair(0, numSeqs));
 296
 297                                 driver(lines[0], outputFileName, fastafile, accnosFileName);
 298
 299                                 if (m->control_pressed) {
 300                                         remove(outputFileName.c_str());
 301                                         remove(tempHeader.c_str());
 302                                         remove(accnosFileName.c_str());
 303                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 304                                         delete chimera;
 305                                         return 0;
 306                                 }
 307
 308                                 //delete accnos file if its blank
 309                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 310
 311                         }else{
 312                                 vector<int> positions;
 313                                 processIDS.resize(0);
 314
 315                                 ifstream inFASTA;
 316                                 openInputFile(fastafile, inFASTA);
 317
 318                                 string input;
 319                                 while(!inFASTA.eof()){
 320                                         input = getline(inFASTA);
 321                                         if (input.length() != 0) {
 322                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 323                                         }
 324                                 }
 325                                 inFASTA.close();
 326
 327                                 numSeqs = positions.size();
 328
 329                                 int numSeqsPerProcessor = numSeqs / processors;
 330
 331                                 for (int i = 0; i < processors; i++) {
 332                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 333                                         if(i == processors - 1){
 334                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 335                                         }
 336                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 337                                 }
 338
 339
 340                                 createProcesses(outputFileName, fastafile, accnosFileName);
 341
 342                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 343
 344                                 //append output files
 345                                 for(int i=1;i<processors;i++){
 346                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 347                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 348                                 }
 349
 350                                 vector<string> nonBlankAccnosFiles;
 351                                 //delete blank accnos files generated with multiple processes
 352                                 for(int i=0;i<processors;i++){
 353                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 354                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 355                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 356                                 }
 357
 358                                 //append accnos files
 359                                 if (nonBlankAccnosFiles.size() != 0) {
 360                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 361
 362                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 363                                                 appendFiles(nonBlankAccnosFiles[h], accnosFileName);
 364                                                 remove(nonBlankAccnosFiles[h].c_str());
 365                                         }
 366                                 }else{ hasAccnos = false;  }
 367
 368                                 if (m->control_pressed) {
 369                                         remove(outputFileName.c_str());
 370                                         remove(accnosFileName.c_str());
 371                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 372                                         delete chimera;
 373                                         return 0;
 374                                 }
 375
 376                         }
 377
 378                 #else
 379                         ifstream inFASTA;
 380                         openInputFile(fastafile, inFASTA);
 381                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 382                         inFASTA.close();
 383                         lines.push_back(new linePair(0, numSeqs));
 384
 385                         driver(lines[0], outputFileName, fastafile, accnosFileName);
 386
 387                         if (m->control_pressed) {
 388                                         remove(outputFileName.c_str());
 389                                         remove(tempHeader.c_str());
 390                                         remove(accnosFileName.c_str());
 391                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 392                                         delete chimera;
 393                                         return 0;
 394                         }
 395
 396                         //delete accnos file if its blank
 397                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 398                 #endif
 399
 400                 //m->mothurOut("Output File Names: ");
 401                 //if ((filter) && (method == "bellerophon")) { m->mothurOut(
 402                 //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
 403                 //      else                             { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
 404
 405                 appendFiles(outputFileName, tempHeader);
 406
 407                 remove(outputFileName.c_str());
 408                 rename(tempHeader.c_str(), outputFileName.c_str());
 409         #endif
 410
 411                 delete chimera;
 412
 413
 414                 m->mothurOutEndLine();
 415                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 416                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 417                 if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
 418                 m->mothurOutEndLine();
 419
 420                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 421
 422                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 423
 424                 return 0;
 425
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "ChimeraCcodeCommand", "execute");
 429                 exit(1);
 430         }
 431 }
 432 //**********************************************************************************************************************
 433
 434 int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 435         try {
 436                 ofstream out;
 437                 openOutputFile(outputFName, out);
 438
 439                 ofstream out2;
 440                 openOutputFile(accnos, out2);
 441
 442                 ifstream inFASTA;
 443                 openInputFile(filename, inFASTA);
 444
 445                 inFASTA.seekg(line->start);
 446
 447                 for(int i=0;i<line->numSeqs;i++){
 448
 449                         if (m->control_pressed) {       return 1;       }
 450
 451                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 452
 453                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 454
 455                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 456                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 457                                 }else{
 458                                         //find chimeras
 459                                         chimera->getChimeras(candidateSeq);
 460
 461                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 462
 463                                         //print results
 464                                         chimera->print(out, out2);
 465                                 }
 466                         }
 467                         delete candidateSeq;
 468
 469                         //report progress
 470                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 471                 }
 472                 //report progress
 473                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 474
 475                 out.close();
 476                 out2.close();
 477                 inFASTA.close();
 478
 479                 return 0;
 480         }
 481         catch(exception& e) {
 482                 m->errorOut(e, "ChimeraCcodeCommand", "driver");
 483                 exit(1);
 484         }
 485 }
 486 //**********************************************************************************************************************
 487 #ifdef USE_MPI
 488 int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 489         try {
 490
 491                 MPI_Status status;
 492                 int pid;
 493                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 494
 495                 for(int i=0;i<num;i++){
 496
 497                         if (m->control_pressed) { return 0; }
 498
 499                         //read next sequence
 500                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 501
 502                         char* buf4 = new char[length];\r
 503
 504                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 505
 506                         string tempBuf = buf4;
 507                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 508                         istringstream iss (tempBuf,istringstream::in);
 509                         delete buf4;
 510
 511                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 512
 513                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 514
 515                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 516                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 517                                 }else{
 518                                         //find chimeras
 519                                         chimera->getChimeras(candidateSeq);
 520
 521                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 522
 523                                         //print results
 524                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 525                                         if (isChimeric) { MPIWroteAccnos = true;  }
 526                                 }
 527                         }
 528                         delete candidateSeq;
 529
 530                         //report progress
 531                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 532                 }
 533                 //report progress
 534                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 535
 536
 537                 return 0;
 538         }
 539         catch(exception& e) {
 540                 m->errorOut(e, "ChimeraCcodeCommand", "driverMPI");
 541                 exit(1);
 542         }
 543 }
 544 #endif
 545
 546 /**************************************************************************************************/
 547
 548 int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 549         try {
 550 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 551                 int process = 0;
 552                 //              processIDS.resize(0);
 553
 554                 //loop through and create all the processes you want
 555                 while (process != processors) {
 556                         int pid = fork();
 557
 558                         if (pid > 0) {
 559                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 560                                 process++;
 561                         }else if (pid == 0){
 562                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 563                                 exit(0);
 564                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 565                 }
 566
 567                 //force parent to wait until all the processes are done
 568                 for (int i=0;i<processors;i++) {
 569                         int temp = processIDS[i];
 570                         wait(&temp);
 571                 }
 572
 573                 return 0;
 574 #endif
 575         }
 576         catch(exception& e) {
 577                 m->errorOut(e, "ChimeraCcodeCommand", "createProcesses");
 578                 exit(1);
 579         }
 580 }
 581 //**********************************************************************************************************************
 582