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
  12 //**********************************************************************************************************************
  13 vector<string> ChimeraCheckCommand::getValidParameters(){
  14         try {
  15                 string AlignArray[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
  16                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "ChimeraCheckCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 vector<string> ChimeraCheckCommand::getRequiredParameters(){
  26         try {
  27                 string AlignArray[] =  {"template","fasta"};
  28                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "ChimeraCheckCommand", "getRequiredParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 vector<string> ChimeraCheckCommand::getRequiredFiles(){
  38         try {
  39                 vector<string> myArray;
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "ChimeraCheckCommand", "getRequiredFiles");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 ChimeraCheckCommand::ChimeraCheckCommand(){
  49         try {
  50                 vector<string> tempOutNames;
  51                 outputTypes["chimera"] = tempOutNames;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
  55                 exit(1);
  56         }
  57 }
  58 //***************************************************************************************************************
  59 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  60         try {
  61                 abort = false;
  62
  63                 //allow user to run help
  64                 if(option == "help") { help(); abort = true; }
  65
  66                 else {
  67                         //valid paramters for this command
  68                         string Array[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
  69                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  70
  71                         OptionParser parser(option);
  72                         map<string,string> parameters = parser.getParameters();
  73
  74                         ValidParameters validParameter("chimera.check");
  75                         map<string,string>::iterator it;
  76
  77                         //check to make sure all parameters are valid for command
  78                         for (it = parameters.begin(); it != parameters.end(); it++) {
  79                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  80                         }
  81
  82                         vector<string> tempOutNames;
  83                         outputTypes["chimera"] = tempOutNames;
  84
  85                         //if the user changes the input directory command factory will send this info to us in the output parameter
  86                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  87                         if (inputDir == "not found"){   inputDir = "";          }
  88                         else {
  89                                 it = parameters.find("template");
  90                                 //user has given a template file
  91                                 if(it != parameters.end()){
  92                                         string path = m->hasPath(it->second);
  93                                         //if the user has not given a path then, add inputdir. else leave path alone.
  94                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  95                                 }
  96                         }
  97
  98                         //check for required parameters
  99                         fastafile = validParameter.validFile(parameters, "fasta", false);
 100                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 101                         else {
 102                                 m->splitAtDash(fastafile, fastaFileNames);
 103
 104                                 //go through files and make sure they are good, if not, then disregard them
 105                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 106                                         if (inputDir != "") {
 107                                                 string path = m->hasPath(fastaFileNames[i]);
 108                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 109                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 110                                         }
 111
 112                                         int ableToOpen;
 113                                         ifstream in;
 114
 115                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 116
 117                                         //if you can't open it, try default location
 118                                         if (ableToOpen == 1) {
 119                                                 if (m->getDefaultPath() != "") { //default path is set
 120                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 121                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 122                                                         ifstream in2;
 123                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 124                                                         in2.close();
 125                                                         fastaFileNames[i] = tryPath;
 126                                                 }
 127                                         }
 128
 129                                         //if you can't open it, try default location
 130                                         if (ableToOpen == 1) {
 131                                                 if (m->getOutputDir() != "") { //default path is set
 132                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 133                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 134                                                         ifstream in2;
 135                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 136                                                         in2.close();
 137                                                         fastaFileNames[i] = tryPath;
 138                                                 }
 139                                         }
 140
 141                                         in.close();
 142
 143                                         if (ableToOpen == 1) {
 144                                                 m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
 145                                                 //erase from file list
 146                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 147                                                 i--;
 148                                         }
 149                                 }
 150
 151                                 //make sure there is at least one valid file left
 152                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 153                         }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 157
 158                         templatefile = validParameter.validFile(parameters, "template", true);
 159                         if (templatefile == "not open") { abort = true; }
 160                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 161
 162                         namefile = validParameter.validFile(parameters, "name", false);
 163                         if (namefile == "not found") { namefile = ""; }
 164                         else {
 165                                 m->splitAtDash(namefile, nameFileNames);
 166
 167                                 //go through files and make sure they are good, if not, then disregard them
 168                                 for (int i = 0; i < nameFileNames.size(); i++) {
 169                                         if (inputDir != "") {
 170                                                 string path = m->hasPath(nameFileNames[i]);
 171                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 172                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 173                                         }
 174
 175                                         int ableToOpen;
 176                                         ifstream in;
 177
 178                                         ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 179
 180                                         //if you can't open it, try default location
 181                                         if (ableToOpen == 1) {
 182                                                 if (m->getDefaultPath() != "") { //default path is set
 183                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 184                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 185                                                         ifstream in2;
 186                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 187                                                         in2.close();
 188                                                         nameFileNames[i] = tryPath;
 189                                                 }
 190                                         }
 191
 192                                         //if you can't open it, try default location
 193                                         if (ableToOpen == 1) {
 194                                                 if (m->getOutputDir() != "") { //default path is set
 195                                                         string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 196                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 197                                                         ifstream in2;
 198                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 199                                                         in2.close();
 200                                                         nameFileNames[i] = tryPath;
 201                                                 }
 202                                         }
 203
 204                                         in.close();
 205
 206                                         if (ableToOpen == 1) {
 207                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 208                                                 //erase from file list
 209                                                 nameFileNames.erase(nameFileNames.begin()+i);
 210                                                 i--;
 211                                         }
 212
 213                                 }
 214
 215                                 //make sure there is at least one valid file left
 216                                 if (nameFileNames.size() != 0) {
 217                                         if (nameFileNames.size() != fastaFileNames.size()) {
 218                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 219                                                  abort = true;
 220                                         }
 221                                 }
 222                         }
 223
 224                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
 225                         convert(temp, processors);
 226
 227                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 228                         convert(temp, ksize);
 229
 230                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 231                         svg = m->isTrue(temp);
 232                         if (nameFileNames.size() != 0) { svg = true; }
 233
 234                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 235                         convert(temp, increment);
 236                 }
 237         }
 238         catch(exception& e) {
 239                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 240                 exit(1);
 241         }
 242 }
 243 //**********************************************************************************************************************
 244
 245 void ChimeraCheckCommand::help(){
 246         try {
 247
 248                 m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 249                 m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
 250                 m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
 251                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 252                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 253                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 254                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 255                 #ifdef USE_MPI
 256                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 257                 #endif
 258                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n");
 259                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
 260                 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");
 261                 m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 262                 m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n");
 263                 m->mothurOut("The chimera.check command should be in the following format: \n");
 264                 m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
 265                 m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
 266                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 267         }
 268         catch(exception& e) {
 269                 m->errorOut(e, "ChimeraCheckCommand", "help");
 270                 exit(1);
 271         }
 272 }
 273
 274 //***************************************************************************************************************
 275
 276 ChimeraCheckCommand::~ChimeraCheckCommand(){    /*      do nothing      */      }
 277
 278 //***************************************************************************************************************
 279
 280 int ChimeraCheckCommand::execute(){
 281         try{
 282
 283                 if (abort == true) { return 0; }
 284
 285                 for (int i = 0; i < fastaFileNames.size(); i++) {
 286
 287                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 288
 289                         int start = time(NULL);
 290
 291                         string thisNameFile = "";
 292                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 293
 294                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 295
 296                         if (m->control_pressed) { delete chimera;       return 0;       }
 297
 298                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
 299                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 300                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 301
 302                 #ifdef USE_MPI
 303
 304                                 int pid, numSeqsPerProcessor;
 305                                 int tag = 2001;
 306                                 vector<unsigned long int> MPIPos;
 307
 308                                 MPI_Status status;
 309                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 310                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 311
 312                                 MPI_File inMPI;
 313                                 MPI_File outMPI;
 314
 315                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 316                                 int inMode=MPI_MODE_RDONLY;
 317
 318                                 char outFilename[1024];
 319                                 strcpy(outFilename, outputFileName.c_str());
 320
 321                                 char inFileName[1024];
 322                                 strcpy(inFileName, fastaFileNames[i].c_str());
 323
 324                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 325                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 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()); } outputTypes.clear(); delete chimera; return 0;  }
 328
 329                                 if (pid == 0) { //you are the root process
 330                                         MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 331
 332                                         //send file positions to all processes
 333                                         for(int j = 1; j < processors; j++) {
 334                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 335                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 336                                         }
 337
 338                                         //figure out how many sequences you have to align
 339                                         numSeqsPerProcessor = numSeqs / processors;
 340                                         int startIndex =  pid * numSeqsPerProcessor;
 341                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 342
 343
 344                                         //align your part
 345                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 346
 347                                         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()); }   outputTypes.clear(); delete chimera; return 0;  }
 348
 349                                         //wait on chidren
 350                                         for(int j = 1; j < processors; j++) {
 351                                                 char buf[5];
 352                                                 MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 353                                         }
 354                                 }else{ //you are a child process
 355                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 356                                         MPIPos.resize(numSeqs+1);
 357                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 358
 359                                         //figure out how many sequences you have to align
 360                                         numSeqsPerProcessor = numSeqs / processors;
 361                                         int startIndex =  pid * numSeqsPerProcessor;
 362                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 363
 364                                         //align your part
 365                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 366
 367                                         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()); }  outputTypes.clear(); delete chimera; return 0;  }
 368
 369                                         //tell parent you are done.
 370                                         char buf[5];
 371                                         strcpy(buf, "done");
 372                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 373                                 }
 374
 375                                 //close files
 376                                 MPI_File_close(&inMPI);
 377                                 MPI_File_close(&outMPI);
 378                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 379                 #else
 380
 381                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[i], processors);
 382
 383                         for (int s = 0; s < (positions.size()-1); s++) {
 384                                 lines.push_back(new linePair(positions[s], positions[(s+1)]));
 385                         }
 386
 387                         //break up file
 388                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 389                                 if(processors == 1){
 390                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 391
 392                                         if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) {  delete lines[j];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 393
 394                                 }else{
 395                                         processIDS.resize(0);
 396
 397                                         numSeqs = createProcesses(outputFileName, fastaFileNames[i]);
 398
 399                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 400
 401                                         //append output files
 402                                         for(int j=1;j<processors;j++){
 403                                                 m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 404                                                 remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
 405                                         }
 406
 407                                         if (m->control_pressed) {
 408                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear();
 409                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 410                                                 delete chimera;
 411                                                 return 0;
 412                                         }
 413                                 }
 414
 415                         #else
 416                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 417
 418                                 if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; }
 419                         #endif
 420                 #endif
 421                         delete chimera;
 422                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 423
 424                         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();
 425                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 426
 427                 }
 428
 429                 m->mothurOutEndLine();
 430                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 431                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 432                 m->mothurOutEndLine();
 433
 434                 return 0;
 435
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 439                 exit(1);
 440         }
 441 }
 442 //**********************************************************************************************************************
 443
 444 int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){
 445         try {
 446                 ofstream out;
 447                 m->openOutputFile(outputFName, out);
 448
 449                 ofstream out2;
 450
 451                 ifstream inFASTA;
 452                 m->openInputFile(filename, inFASTA);
 453
 454                 inFASTA.seekg(filePos->start);
 455
 456                 bool done = false;
 457                 int count = 0;
 458
 459                 while (!done) {
 460
 461                         if (m->control_pressed) {       return 1;       }
 462
 463                         Sequence* candidateSeq = new Sequence(inFASTA);  m->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                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 477                                 unsigned long int pos = inFASTA.tellg();
 478                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 479                         #else
 480                                 if (inFASTA.eof()) { break; }
 481                         #endif
 482
 483                         //report progress
 484                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 485                 }
 486                 //report progress
 487                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 488
 489                 out.close();
 490                 inFASTA.close();
 491
 492                 return count;
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 496                 exit(1);
 497         }
 498 }
 499 //**********************************************************************************************************************
 500 #ifdef USE_MPI
 501 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos){
 502         try {
 503                 MPI_File outAccMPI;
 504                 MPI_Status status;
 505                 int pid;
 506                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 507
 508                 for(int i=0;i<num;i++){
 509
 510                         if (m->control_pressed) { return 0; }
 511
 512                         //read next sequence
 513                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 514
 515                         char* buf4 = new char[length];
 516                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 517
 518                         string tempBuf = buf4;
 519                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 520                         istringstream iss (tempBuf,istringstream::in);
 521                         delete buf4;
 522
 523                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 524
 525                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 526                                 //find chimeras
 527                                 chimera->getChimeras(candidateSeq);
 528
 529                                 //print results
 530                                 chimera->print(outMPI, outAccMPI);
 531                         }
 532                         delete candidateSeq;
 533
 534                         //report progress
 535                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 536                 }
 537                 //report progress
 538                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 539
 540                 return 0;
 541         }
 542         catch(exception& e) {
 543                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 544                 exit(1);
 545         }
 546 }
 547 #endif
 548
 549 /**************************************************************************************************/
 550
 551 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 552         try {
 553 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 554                 int process = 0;
 555                 int num = 0;
 556
 557                 //loop through and create all the processes you want
 558                 while (process != processors) {
 559                         int pid = fork();
 560
 561                         if (pid > 0) {
 562                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 563                                 process++;
 564                         }else if (pid == 0){
 565                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 566
 567                                 //pass numSeqs to parent
 568                                 ofstream out;
 569                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 570                                 m->openOutputFile(tempFile, out);
 571                                 out << num << endl;
 572                                 out.close();
 573
 574                                 exit(0);
 575                         }else {
 576                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 577                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 578                                 exit(0);
 579                         }
 580                 }
 581
 582                 //force parent to wait until all the processes are done
 583                 for (int i=0;i<processors;i++) {
 584                         int temp = processIDS[i];
 585                         wait(&temp);
 586                 }
 587
 588                 for (int i = 0; i < processIDS.size(); i++) {
 589                         ifstream in;
 590                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 591                         m->openInputFile(tempFile, in);
 592                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 593                         in.close(); remove(tempFile.c_str());
 594                 }
 595
 596                 return num;
 597 #endif
 598         }
 599         catch(exception& e) {
 600                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 601                 exit(1);
 602         }
 603 }
 604 /**************************************************************************************************/
 605
 606