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("template");
  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["template"] = inputDir + it->second;         }
  49                                 }
  50                         }
  51
  52                         //check for required parameters
  53                         fastafile = validParameter.validFile(parameters, "fasta", false);
  54                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true;  }
  55                         else {
  56                                 splitAtDash(fastafile, fastaFileNames);
  57
  58                                 //go through files and make sure they are good, if not, then disregard them
  59                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  60                                         if (inputDir != "") {
  61                                                 string path = hasPath(fastaFileNames[i]);
  62                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  63                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  64                                         }
  65
  66                                         int ableToOpen;
  67                                         ifstream in;
  68
  69                                         #ifdef USE_MPI
  70                                                 int pid;
  71                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
  72                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  73
  74                                                 if (pid == 0) {
  75                                         #endif
  76
  77                                         ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
  78
  79                                         //if you can't open it, try default location
  80                                         if (ableToOpen == 1) {
  81                                                 if (m->getDefaultPath() != "") { //default path is set
  82                                                         string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
  83                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  84                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  85                                                         fastaFileNames[i] = tryPath;
  86                                                 }
  87                                         }
  88                                         in.close();
  89
  90                                         #ifdef USE_MPI
  91                                                         for (int j = 1; j < processors; j++) {
  92                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
  93                                                         }
  94                                                 }else{
  95                                                         MPI_Status status;
  96                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
  97                                                 }
  98
  99                                         #endif
 100
 101                                         if (ableToOpen == 1) {
 102                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 103                                                 //erase from file list
 104                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 105                                                 i--;
 106                                         }
 107                                 }
 108
 109                                 //make sure there is at least one valid file left
 110                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 111                         }
 112
 113                         //if the user changes the output directory command factory will send this info to us in the output parameter
 114                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 115                                 outputDir = "";
 116                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
 117                         }
 118
 119                         templatefile = validParameter.validFile(parameters, "template", true);
 120                         if (templatefile == "not open") { abort = true; }
 121                         else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true;  }
 122
 123                         maskfile = validParameter.validFile(parameters, "mask", false);
 124                         if (maskfile == "not found") { maskfile = "";  }
 125                         else if (maskfile != "default")  {
 126                                 if (inputDir != "") {
 127                                         string path = hasPath(maskfile);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       maskfile = inputDir + maskfile;         }
 130                                 }
 131
 132                                 ifstream in;
 133                                 int     ableToOpen = openInputFile(maskfile, in);
 134                                 if (ableToOpen == 1) { abort = true; }
 135                                 in.close();
 136                         }
 137
 138                         string temp;
 139                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
 140                         filter = isTrue(temp);
 141
 142                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
 143                         convert(temp, processors);
 144
 145                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
 146                         convert(temp, window);
 147
 148                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
 149                         convert(temp, numwanted);
 150
 151                 }
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159
 160 void ChimeraCcodeCommand::help(){
 161         try {
 162
 163                 m->mothurOut("The chimera.ccode command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 164                 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");
 165                 m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n");
 166                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 167                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 168                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 169                 m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
 170                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 171                 #ifdef USE_MPI
 172                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 173                 #endif
 174                 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");
 175                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n");
 176                 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
 177                 m->mothurOut("The chimera.ccode command should be in the following format: \n");
 178                 m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n");
 179                 m->mothurOut("Example: chimera.ccode(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n");
 180                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "ChimeraCcodeCommand", "help");
 184                 exit(1);
 185         }
 186 }
 187
 188 //***************************************************************************************************************
 189
 190 ChimeraCcodeCommand::~ChimeraCcodeCommand(){    /*      do nothing      */      }
 191
 192 //***************************************************************************************************************
 193
 194 int ChimeraCcodeCommand::execute(){
 195         try{
 196
 197                 if (abort == true) { return 0; }
 198
 199                 for (int s = 0; s < fastaFileNames.size(); s++) {
 200
 201                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 202
 203                         int start = time(NULL);
 204
 205                         //set user options
 206                         if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }
 207
 208                         chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir);
 209
 210                         //is your template aligned?
 211                         if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
 212                         templateSeqsLength = chimera->getLength();
 213
 214                         string outputFileName, accnosFileName;
 215                         if (maskfile != "") {
 216                                 outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
 217                                 accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
 218                         }else {
 219                                 outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s]))  + "ccode.chimeras";
 220                                 accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s]))  + "ccode.accnos";
 221                         }
 222
 223                         string mapInfo = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "mapinfo";
 224
 225                         if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
 226
 227                 #ifdef USE_MPI
 228
 229                                 int pid, end, numSeqsPerProcessor;
 230                                 int tag = 2001;
 231                                 vector<long> MPIPos;
 232
 233                                 MPI_Status status;
 234                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 235                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 236
 237                                 MPI_File inMPI;
 238                                 MPI_File outMPI;
 239                                 MPI_File outMPIAccnos;
 240
 241                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 242                                 int inMode=MPI_MODE_RDONLY;
 243
 244                                 char outFilename[1024];
 245                                 strcpy(outFilename, outputFileName.c_str());
 246
 247                                 char outAccnosFilename[1024];
 248                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 249
 250                                 char inFileName[1024];
 251                                 strcpy(inFileName, fastaFileNames[s].c_str());
 252
 253                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 254                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 255                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 256
 257                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 258
 259                                 if (pid == 0) { //you are the root process
 260                                         string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
 261
 262                                         //print header
 263                                         int length = outTemp.length();
 264                                         char* buf2 = new char[length];
 265                                         memcpy(buf2, outTemp.c_str(), length);
 266
 267                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 268                                         delete buf2;
 269
 270                                         MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 271
 272                                         //send file positions to all processes
 273                                         for(int i = 1; i < processors; i++) {
 274                                                 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 275                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 276                                         }
 277
 278                                         //figure out how many sequences you have to align
 279                                         numSeqsPerProcessor = numSeqs / processors;
 280                                         int startIndex =  pid * numSeqsPerProcessor;
 281                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 282
 283
 284                                         //align your part
 285                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 286
 287                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 288
 289                                 }else{ //you are a child process
 290                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 291                                         MPIPos.resize(numSeqs+1);
 292                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 293
 294                                         //figure out how many sequences you have to align
 295                                         numSeqsPerProcessor = numSeqs / processors;
 296                                         int startIndex =  pid * numSeqsPerProcessor;
 297                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 298
 299
 300                                         //align your part
 301                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 302
 303                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 304                                 }
 305
 306                                 //close files
 307                                 MPI_File_close(&inMPI);
 308                                 MPI_File_close(&outMPI);
 309                                 MPI_File_close(&outMPIAccnos);
 310
 311                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 312
 313                 #else
 314                         ofstream outHeader;
 315                         string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader";
 316                         openOutputFile(tempHeader, outHeader);
 317
 318                         outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
 319
 320                         outHeader.close();
 321
 322                         //break up file
 323                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 324                                 if(processors == 1){
 325                                         ifstream inFASTA;
 326                                         openInputFile(fastaFileNames[s], inFASTA);
 327                                         getNumSeqs(inFASTA, numSeqs);
 328                                         inFASTA.close();
 329
 330                                         lines.push_back(new linePair(0, numSeqs));
 331
 332                                         driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 333
 334                                         if (m->control_pressed) {
 335                                                 remove(outputFileName.c_str());
 336                                                 remove(tempHeader.c_str());
 337                                                 remove(accnosFileName.c_str());
 338                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 339                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 340                                                 delete chimera;
 341                                                 return 0;
 342                                         }
 343
 344                                 }else{
 345                                         vector<unsigned long int> positions;
 346                                         processIDS.resize(0);
 347
 348                                         ifstream inFASTA;
 349                                         openInputFile(fastaFileNames[s], inFASTA);
 350
 351                                         string input;
 352                                         while(!inFASTA.eof()){
 353                                                 input = getline(inFASTA);
 354                                                 if (input.length() != 0) {
 355                                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 356                                                 }
 357                                         }
 358                                         inFASTA.close();
 359
 360                                         numSeqs = positions.size();
 361
 362                                         int numSeqsPerProcessor = numSeqs / processors;
 363
 364                                         for (int i = 0; i < processors; i++) {
 365                                                 unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 366                                                 if(i == processors - 1){
 367                                                         numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 368                                                 }
 369                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 370                                         }
 371
 372
 373                                         createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
 374
 375                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 376                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 377
 378                                         //append output files
 379                                         for(int i=1;i<processors;i++){
 380                                                 appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 381                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 382                                         }
 383
 384                                         //append output files
 385                                         for(int i=1;i<processors;i++){
 386                                                 appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 387                                                 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
 388                                         }
 389
 390                                         if (m->control_pressed) {
 391                                                 remove(outputFileName.c_str());
 392                                                 remove(accnosFileName.c_str());
 393                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 394                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 395                                                 delete chimera;
 396                                                 return 0;
 397                                         }
 398
 399                                 }
 400
 401                         #else
 402                                 ifstream inFASTA;
 403                                 openInputFile(fastaFileNames[s], inFASTA);
 404                                 getNumSeqs(inFASTA, numSeqs);
 405                                 inFASTA.close();
 406                                 lines.push_back(new linePair(0, numSeqs));
 407
 408                                 driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 409
 410                                 if (m->control_pressed) {
 411                                                 remove(outputFileName.c_str());
 412                                                 remove(tempHeader.c_str());
 413                                                 remove(accnosFileName.c_str());
 414                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 415                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 416                                                 delete chimera;
 417                                                 return 0;
 418                                 }
 419
 420                         #endif
 421
 422                         appendFiles(outputFileName, tempHeader);
 423
 424                         remove(outputFileName.c_str());
 425                         rename(tempHeader.c_str(), outputFileName.c_str());
 426                 #endif
 427
 428                         delete chimera;
 429
 430                         outputNames.push_back(outputFileName);
 431                         outputNames.push_back(mapInfo);
 432                         outputNames.push_back(accnosFileName);
 433
 434                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 435
 436                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 437                 }
 438
 439                 m->mothurOutEndLine();
 440                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 441                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 442                 m->mothurOutEndLine();
 443
 444                 return 0;
 445
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "ChimeraCcodeCommand", "execute");
 449                 exit(1);
 450         }
 451 }
 452 //**********************************************************************************************************************
 453
 454 int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 455         try {
 456                 ofstream out;
 457                 openOutputFile(outputFName, out);
 458
 459                 ofstream out2;
 460                 openOutputFile(accnos, out2);
 461
 462                 ifstream inFASTA;
 463                 openInputFile(filename, inFASTA);
 464
 465                 inFASTA.seekg(line->start);
 466
 467                 for(int i=0;i<line->numSeqs;i++){
 468
 469                         if (m->control_pressed) {       return 1;       }
 470
 471                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 472
 473                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 474
 475                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 476                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 477                                 }else{
 478                                         //find chimeras
 479                                         chimera->getChimeras(candidateSeq);
 480
 481                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 482
 483                                         //print results
 484                                         chimera->print(out, out2);
 485                                 }
 486                         }
 487                         delete candidateSeq;
 488
 489                         //report progress
 490                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 491                 }
 492                 //report progress
 493                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 494
 495                 out.close();
 496                 out2.close();
 497                 inFASTA.close();
 498
 499                 return 0;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "ChimeraCcodeCommand", "driver");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507 #ifdef USE_MPI
 508 int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 509         try {
 510
 511                 MPI_Status status;
 512                 int pid;
 513                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 514
 515                 for(int i=0;i<num;i++){
 516
 517                         if (m->control_pressed) { return 0; }
 518
 519                         //read next sequence
 520                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 521
 522                         char* buf4 = new char[length];
 523
 524                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 525
 526                         string tempBuf = buf4;
 527                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 528                         istringstream iss (tempBuf,istringstream::in);
 529                         delete buf4;
 530
 531                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 532
 533                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 534
 535                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 536                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 537                                 }else{
 538                                         //find chimeras
 539                                         chimera->getChimeras(candidateSeq);
 540
 541                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 542
 543                                         //print results
 544                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 545                                 }
 546                         }
 547                         delete candidateSeq;
 548
 549                         //report progress
 550                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 551                 }
 552                 //report progress
 553                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 554
 555
 556                 return 0;
 557         }
 558         catch(exception& e) {
 559                 m->errorOut(e, "ChimeraCcodeCommand", "driverMPI");
 560                 exit(1);
 561         }
 562 }
 563 #endif
 564
 565 /**************************************************************************************************/
 566
 567 int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 568         try {
 569 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 570                 int process = 0;
 571                 //              processIDS.resize(0);
 572
 573                 //loop through and create all the processes you want
 574                 while (process != processors) {
 575                         int pid = fork();
 576
 577                         if (pid > 0) {
 578                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 579                                 process++;
 580                         }else if (pid == 0){
 581                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 582                                 exit(0);
 583                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 584                 }
 585
 586                 //force parent to wait until all the processes are done
 587                 for (int i=0;i<processors;i++) {
 588                         int temp = processIDS[i];
 589                         wait(&temp);
 590                 }
 591
 592                 return 0;
 593 #endif
 594         }
 595         catch(exception& e) {
 596                 m->errorOut(e, "ChimeraCcodeCommand", "createProcesses");
 597                 exit(1);
 598         }
 599 }
 600 //**********************************************************************************************************************
 601