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