chimeracheckcommand.cpp

   1 /*
   2  *  chimeracheckcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeracheckcommand.h"
  11 #include "chimeracheckrdp.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraCheckCommand::ChimeraCheckCommand(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","processors","increment","template","ksize","svg", "name","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                                 it = parameters.find("template");
  43                                 //user has given a template file
  44                                 if(it != parameters.end()){
  45                                         string path = hasPath(it->second);
  46                                         //if the user has not given a path then, add inputdir. else leave path alone.
  47                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  48                                 }
  49                         }
  50
  51                         //check for required parameters
  52                         fastafile = validParameter.validFile(parameters, "fasta", false);
  53                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
  54                         else {
  55                                 splitAtDash(fastafile, fastaFileNames);
  56
  57                                 //go through files and make sure they are good, if not, then disregard them
  58                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  59                                         if (inputDir != "") {
  60                                                 string path = hasPath(fastaFileNames[i]);
  61                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  62                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  63                                         }
  64
  65                                         int ableToOpen;
  66                                         ifstream in;
  67
  68                                         #ifdef USE_MPI
  69                                                 int pid;
  70                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
  71                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  72
  73                                                 if (pid == 0) {
  74                                         #endif
  75
  76                                         ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
  77
  78                                         //if you can't open it, try default location
  79                                         if (ableToOpen == 1) {
  80                                                 if (m->getDefaultPath() != "") { //default path is set
  81                                                         string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
  82                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  83                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  84                                                         fastaFileNames[i] = tryPath;
  85                                                 }
  86                                         }
  87                                         in.close();
  88
  89                                         #ifdef USE_MPI
  90                                                         for (int j = 1; j < processors; j++) {
  91                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
  92                                                         }
  93                                                 }else{
  94                                                         MPI_Status status;
  95                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
  96                                                 }
  97
  98                                         #endif
  99
 100                                         if (ableToOpen == 1) {
 101                                                 m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
 102                                                 //erase from file list
 103                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 104                                                 i--;
 105                                         }
 106                                 }
 107
 108                                 //make sure there is at least one valid file left
 109                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 110                         }
 111
 112                         //if the user changes the output directory command factory will send this info to us in the output parameter
 113                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 114
 115                         templatefile = validParameter.validFile(parameters, "template", true);
 116                         if (templatefile == "not open") { abort = true; }
 117                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 118
 119                         namefile = validParameter.validFile(parameters, "name", false);
 120                         if (namefile == "not found") { namefile = ""; }
 121                         else {
 122                                 splitAtDash(namefile, nameFileNames);
 123
 124                                 //go through files and make sure they are good, if not, then disregard them
 125                                 for (int i = 0; i < nameFileNames.size(); i++) {
 126                                         if (inputDir != "") {
 127                                                 string path = hasPath(nameFileNames[i]);
 128                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 129                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 130                                         }
 131
 132                                         int ableToOpen;
 133                                         ifstream in;
 134
 135                                         #ifdef USE_MPI
 136                                                 int pid;
 137                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 138                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 139
 140                                                 if (pid == 0) {
 141                                         #endif
 142
 143                                         ableToOpen = openInputFile(nameFileNames[i], in, "noerror");
 144
 145                                         //if you can't open it, try default location
 146                                         if (ableToOpen == 1) {
 147                                                 if (m->getDefaultPath() != "") { //default path is set
 148                                                         string tryPath = m->getDefaultPath() + getSimpleName(nameFileNames[i]);
 149                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 150                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
 151                                                         nameFileNames[i] = tryPath;
 152                                                 }
 153                                         }
 154                                         in.close();
 155
 156                                         #ifdef USE_MPI
 157                                                         for (int j = 1; j < processors; j++) {
 158                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
 159                                                         }
 160                                                 }else{
 161                                                         MPI_Status status;
 162                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 163                                                 }
 164
 165                                         #endif
 166
 167                                         if (ableToOpen == 1) {
 168                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 169                                                 //erase from file list
 170                                                 nameFileNames.erase(nameFileNames.begin()+i);
 171                                                 i--;
 172                                         }
 173
 174                                 }
 175
 176                                 //make sure there is at least one valid file left
 177                                 if (nameFileNames.size() != 0) {
 178                                         if (nameFileNames.size() != fastaFileNames.size()) {
 179                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 180                                                  abort = true;
 181                                         }
 182                                 }
 183                         }
 184
 185                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
 186                         convert(temp, processors);
 187
 188                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 189                         convert(temp, ksize);
 190
 191                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 192                         svg = isTrue(temp);
 193                         if (nameFileNames.size() != 0) { svg = true; }
 194
 195                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 196                         convert(temp, increment);
 197                 }
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 201                 exit(1);
 202         }
 203 }
 204 //**********************************************************************************************************************
 205
 206 void ChimeraCheckCommand::help(){
 207         try {
 208
 209                 m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 210                 m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
 211                 m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
 212                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 213                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 214                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 215                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 216                 #ifdef USE_MPI
 217                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 218                 #endif
 219                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n");
 220                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
 221                 m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n");
 222                 m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 223                 m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n");
 224                 m->mothurOut("The chimera.check command should be in the following format: \n");
 225                 m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
 226                 m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
 227                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "ChimeraCheckCommand", "help");
 231                 exit(1);
 232         }
 233 }
 234
 235 //***************************************************************************************************************
 236
 237 ChimeraCheckCommand::~ChimeraCheckCommand(){    /*      do nothing      */      }
 238
 239 //***************************************************************************************************************
 240
 241 int ChimeraCheckCommand::execute(){
 242         try{
 243
 244                 if (abort == true) { return 0; }
 245
 246                 for (int i = 0; i < fastaFileNames.size(); i++) {
 247
 248                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 249
 250                         int start = time(NULL);
 251
 252                         string thisNameFile = "";
 253                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 254
 255                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 256
 257                         if (m->control_pressed) { delete chimera;       return 0;       }
 258
 259                         string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 260                         outputNames.push_back(outputFileName);
 261
 262                 #ifdef USE_MPI
 263
 264                                 int pid, end, numSeqsPerProcessor;
 265                                 int tag = 2001;
 266                                 vector<long> MPIPos;
 267
 268                                 MPI_Status status;
 269                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 270                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 271
 272                                 MPI_File inMPI;
 273                                 MPI_File outMPI;
 274
 275                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 276                                 int inMode=MPI_MODE_RDONLY;
 277
 278                                 char outFilename[1024];
 279                                 strcpy(outFilename, outputFileName.c_str());
 280
 281                                 char inFileName[1024];
 282                                 strcpy(inFileName, fastaFileNames[i].c_str());
 283
 284                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 285                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 286
 287                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } delete chimera; return 0;  }
 288
 289                                 if (pid == 0) { //you are the root process
 290                                         MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 291
 292                                         //send file positions to all processes
 293                                         for(int j = 1; j < processors; j++) {
 294                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 295                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 296                                         }
 297
 298                                         //figure out how many sequences you have to align
 299                                         numSeqsPerProcessor = numSeqs / processors;
 300                                         int startIndex =  pid * numSeqsPerProcessor;
 301                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 302
 303
 304                                         //align your part
 305                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 306
 307                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
 308
 309                                         //wait on chidren
 310                                         for(int j = 1; j < processors; j++) {
 311                                                 char buf[4];
 312                                                 MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 313                                         }
 314                                 }else{ //you are a child process
 315                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 316                                         MPIPos.resize(numSeqs+1);
 317                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 318
 319                                         //figure out how many sequences you have to align
 320                                         numSeqsPerProcessor = numSeqs / processors;
 321                                         int startIndex =  pid * numSeqsPerProcessor;
 322                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 323
 324                                         //align your part
 325                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 326
 327                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 328
 329                                         //tell parent you are done.
 330                                         char buf[4];
 331                                         strcpy(buf, "done");
 332                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 333                                 }
 334
 335                                 //close files
 336                                 MPI_File_close(&inMPI);
 337                                 MPI_File_close(&outMPI);
 338                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 339                 #else
 340
 341                         //break up file
 342                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 343                                 if(processors == 1){
 344                                         ifstream inFASTA;
 345                                         openInputFile(fastaFileNames[i], inFASTA);
 346                                         getNumSeqs(inFASTA, numSeqs);
 347                                         inFASTA.close();
 348
 349                                         lines.push_back(new linePair(0, numSeqs));
 350
 351                                         driver(lines[0], outputFileName, fastaFileNames[i]);
 352
 353                                         if (m->control_pressed) {
 354                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 355                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 356                                                 delete chimera;
 357                                                 return 0;
 358                                         }
 359
 360                                 }else{
 361                                         vector<unsigned long int> positions;
 362                                         processIDS.resize(0);
 363
 364                                         ifstream inFASTA;
 365                                         openInputFile(fastaFileNames[i], inFASTA);
 366
 367                                         string input;
 368                                         while(!inFASTA.eof()){
 369                                                 input = getline(inFASTA);
 370                                                 if (input.length() != 0) {
 371                                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 372                                                 }
 373                                         }
 374                                         inFASTA.close();
 375
 376                                         numSeqs = positions.size();
 377
 378                                         int numSeqsPerProcessor = numSeqs / processors;
 379
 380                                         for (int j = 0; j < processors; j++) {
 381                                                 unsigned long int startPos = positions[ j * numSeqsPerProcessor ];
 382                                                 if(j == processors - 1){
 383                                                         numSeqsPerProcessor = numSeqs - j * numSeqsPerProcessor;
 384                                                 }
 385                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 386                                         }
 387
 388
 389                                         createProcesses(outputFileName, fastaFileNames[i]);
 390
 391                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 392
 393                                         //append output files
 394                                         for(int j=1;j<processors;j++){
 395                                                 appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 396                                                 remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
 397                                         }
 398
 399                                         if (m->control_pressed) {
 400                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 401                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 402                                                 delete chimera;
 403                                                 return 0;
 404                                         }
 405                                 }
 406
 407                         #else
 408                                 ifstream inFASTA;
 409                                 openInputFile(fastaFileNames[i], inFASTA);
 410                                 getNumSeqs(inFASTA, numSeqs);
 411                                 inFASTA.close();
 412                                 lines.push_back(new linePair(0, numSeqs));
 413
 414                                 driver(lines[0], outputFileName, fastaFileNames[i]);
 415
 416                                 if (m->control_pressed) {
 417                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 418                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 419                                                 delete chimera;
 420                                                 return 0;
 421                                 }
 422                         #endif
 423                 #endif
 424                         delete chimera;
 425                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 426
 427                         m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
 428                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 429
 430                 }
 431
 432                 m->mothurOutEndLine();
 433                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 434                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 435                 m->mothurOutEndLine();
 436
 437                 return 0;
 438
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 442                 exit(1);
 443         }
 444 }
 445 //**********************************************************************************************************************
 446
 447 int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filename){
 448         try {
 449                 ofstream out;
 450                 openOutputFile(outputFName, out);
 451
 452                 ofstream out2;
 453
 454                 ifstream inFASTA;
 455                 openInputFile(filename, inFASTA);
 456
 457                 inFASTA.seekg(line->start);
 458
 459                 for(int i=0;i<line->numSeqs;i++){
 460
 461                         if (m->control_pressed) {       return 1;       }
 462
 463                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 464
 465                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 466                                 //find chimeras
 467                                 chimera->getChimeras(candidateSeq);
 468
 469                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 470
 471                                 //print results
 472                                 chimera->print(out, out2);
 473                         }
 474                         delete candidateSeq;
 475
 476                         //report progress
 477                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 478                 }
 479                 //report progress
 480                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 481
 482                 out.close();
 483                 inFASTA.close();
 484
 485                 return 0;
 486         }
 487         catch(exception& e) {
 488                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 489                 exit(1);
 490         }
 491 }
 492 //**********************************************************************************************************************
 493 #ifdef USE_MPI
 494 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
 495         try {
 496                 MPI_File outAccMPI;
 497                 MPI_Status status;
 498                 int pid;
 499                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 500
 501                 for(int i=0;i<num;i++){
 502
 503                         if (m->control_pressed) { return 0; }
 504
 505                         //read next sequence
 506                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 507
 508                         char* buf4 = new char[length];
 509                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 510
 511                         string tempBuf = buf4;
 512                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 513                         istringstream iss (tempBuf,istringstream::in);
 514                         delete buf4;
 515
 516                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 517
 518                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 519                                 //find chimeras
 520                                 chimera->getChimeras(candidateSeq);
 521
 522                                 //print results
 523                                 chimera->print(outMPI, outAccMPI);
 524                         }
 525                         delete candidateSeq;
 526
 527                         //report progress
 528                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 529                 }
 530                 //report progress
 531                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 532
 533                 return 0;
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 537                 exit(1);
 538         }
 539 }
 540 #endif
 541
 542 /**************************************************************************************************/
 543
 544 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 545         try {
 546 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 547                 int process = 0;
 548                 //              processIDS.resize(0);
 549
 550                 //loop through and create all the processes you want
 551                 while (process != processors) {
 552                         int pid = fork();
 553
 554                         if (pid > 0) {
 555                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 556                                 process++;
 557                         }else if (pid == 0){
 558                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 559                                 exit(0);
 560                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 561                 }
 562
 563                 //force parent to wait until all the processes are done
 564                 for (int i=0;i<processors;i++) {
 565                         int temp = processIDS[i];
 566                         wait(&temp);
 567                 }
 568
 569                 return 0;
 570 #endif
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 574                 exit(1);
 575         }
 576 }
 577 /**************************************************************************************************/
 578
 579