chimerauchimecommand.cpp

   1 /*
   2  *  chimerauchimecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/13/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimerauchimecommand.h"
  11 #include "deconvolutecommand.h"
  12 #include "uc.h"
  13 #include "sequence.hpp"
  14
  15
  16 //**********************************************************************************************************************
  17 vector<string> ChimeraUchimeCommand::setParameters(){
  18         try {
  19                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  20                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  21                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "ChimeraUchimeCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string ChimeraUchimeCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The chimera.uchime command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  40                 helpString += "This command is a wrapper for uchime written by Robert C. Edgar.\n";
  41                 helpString += "The chimera.uchime command parameters are fasta, name, reference and processors.\n";
  42                 helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
  43                 helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
  44                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  45                 helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
  46                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  47 #ifdef USE_MPI
  48                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  49 #endif
  50                 helpString += "The chimera.uchime command should be in the following format: \n";
  51                 helpString += "chimera.uchime(fasta=yourFastaFile, reference=yourTemplate) \n";
  52                 helpString += "Example: chimera.uchime(fasta=AD.align, reference=silva.gold.align) \n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "ChimeraUchimeCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 ChimeraUchimeCommand::ChimeraUchimeCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["chimera"] = tempOutNames;
  68                 outputTypes["accnos"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "ChimeraUchimeCommand", "ChimeraUchimeCommand");
  72                 exit(1);
  73         }
  74 }
  75 //***************************************************************************************************************
  76 ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
  77         try {
  78                 abort = false; calledHelp = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; calledHelp = true; }
  82                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  83
  84                 else {
  85                         vector<string> myArray = setParameters();
  86
  87                         OptionParser parser(option);
  88                         map<string,string> parameters = parser.getParameters();
  89
  90                         ValidParameters validParameter("chimera.uchime");
  91                         map<string,string>::iterator it;
  92
  93                         //check to make sure all parameters are valid for command
  94                         for (it = parameters.begin(); it != parameters.end(); it++) {
  95                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  96                         }
  97
  98                         vector<string> tempOutNames;
  99                         outputTypes["chimera"] = tempOutNames;
 100                         outputTypes["accnos"] = tempOutNames;
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105
 106                         //check for required parameters
 107                         fastafile = validParameter.validFile(parameters, "fasta", false);
 108                         if (fastafile == "not found") {
 109                                 //if there is a current fasta file, use it
 110                                 string filename = m->getFastaFile();
 111                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 112                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 113                         }else {
 114                                 m->splitAtDash(fastafile, fastaFileNames);
 115
 116                                 //go through files and make sure they are good, if not, then disregard them
 117                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 118
 119                                         bool ignore = false;
 120                                         if (fastaFileNames[i] == "current") {
 121                                                 fastaFileNames[i] = m->getFastaFile();
 122                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 123                                                 else {
 124                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 125                                                         //erase from file list
 126                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 127                                                         i--;
 128                                                 }
 129                                         }
 130
 131                                         if (!ignore) {
 132
 133                                                 if (inputDir != "") {
 134                                                         string path = m->hasPath(fastaFileNames[i]);
 135                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 137                                                 }
 138
 139                                                 int ableToOpen;
 140                                                 ifstream in;
 141
 142                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 143
 144                                                 //if you can't open it, try default location
 145                                                 if (ableToOpen == 1) {
 146                                                         if (m->getDefaultPath() != "") { //default path is set
 147                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 148                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 149                                                                 ifstream in2;
 150                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 151                                                                 in2.close();
 152                                                                 fastaFileNames[i] = tryPath;
 153                                                         }
 154                                                 }
 155
 156                                                 if (ableToOpen == 1) {
 157                                                         if (m->getOutputDir() != "") { //default path is set
 158                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 159                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 160                                                                 ifstream in2;
 161                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 162                                                                 in2.close();
 163                                                                 fastaFileNames[i] = tryPath;
 164                                                         }
 165                                                 }
 166
 167                                                 in.close();
 168
 169                                                 if (ableToOpen == 1) {
 170                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 171                                                         //erase from file list
 172                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 173                                                         i--;
 174                                                 }
 175                                         }
 176                                 }
 177
 178                                 //make sure there is at least one valid file left
 179                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 180                         }
 181
 182
 183                         //check for required parameters
 184                         bool hasName = true;
 185                         namefile = validParameter.validFile(parameters, "name", false);
 186                         if (namefile == "not found") { namefile = "";  hasName = false; }
 187                         else {
 188                                 m->splitAtDash(namefile, nameFileNames);
 189
 190                                 //go through files and make sure they are good, if not, then disregard them
 191                                 for (int i = 0; i < nameFileNames.size(); i++) {
 192
 193                                         bool ignore = false;
 194                                         if (nameFileNames[i] == "current") {
 195                                                 nameFileNames[i] = m->getNameFile();
 196                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 197                                                 else {
 198                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 199                                                         //erase from file list
 200                                                         nameFileNames.erase(nameFileNames.begin()+i);
 201                                                         i--;
 202                                                 }
 203                                         }
 204
 205                                         if (!ignore) {
 206
 207                                                 if (inputDir != "") {
 208                                                         string path = m->hasPath(nameFileNames[i]);
 209                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 210                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 211                                                 }
 212
 213                                                 int ableToOpen;
 214                                                 ifstream in;
 215
 216                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 217
 218                                                 //if you can't open it, try default location
 219                                                 if (ableToOpen == 1) {
 220                                                         if (m->getDefaultPath() != "") { //default path is set
 221                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 222                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 223                                                                 ifstream in2;
 224                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 225                                                                 in2.close();
 226                                                                 nameFileNames[i] = tryPath;
 227                                                         }
 228                                                 }
 229
 230                                                 if (ableToOpen == 1) {
 231                                                         if (m->getOutputDir() != "") { //default path is set
 232                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 233                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 234                                                                 ifstream in2;
 235                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 236                                                                 in2.close();
 237                                                                 nameFileNames[i] = tryPath;
 238                                                         }
 239                                                 }
 240
 241                                                 in.close();
 242
 243                                                 if (ableToOpen == 1) {
 244                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 245                                                         //erase from file list
 246                                                         nameFileNames.erase(nameFileNames.begin()+i);
 247                                                         i--;
 248                                                 }
 249                                         }
 250                                 }
 251
 252                                 //make sure there is at least one valid file left
 253                                 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
 254                         }
 255
 256                         if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
 257
 258                         //if the user changes the output directory command factory will send this info to us in the output parameter
 259                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 260
 261
 262                         string path;
 263                         it = parameters.find("reference");
 264                         //user has given a template file
 265                         if(it != parameters.end()){
 266                                 if (it->second == "self") { templatefile = "self"; }
 267                                 else {
 268                                         path = m->hasPath(it->second);
 269                                         //if the user has not given a path then, add inputdir. else leave path alone.
 270                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 271
 272                                         templatefile = validParameter.validFile(parameters, "reference", true);
 273                                         if (templatefile == "not open") { abort = true; }
 274                                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
 275                                 }
 276                         }
 277
 278                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 279                         m->setProcessors(temp);
 280                         convert(temp, processors);
 281                 }
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 285                 exit(1);
 286         }
 287 }
 288 //***************************************************************************************************************
 289
 290 int ChimeraUchimeCommand::execute(){
 291         try{
 292                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 293
 294                 for (int s = 0; s < fastaFileNames.size(); s++) {
 295
 296                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 297
 298                         int start = time(NULL);
 299                         string nameFile = "";
 300
 301                         if (templatefile == "self") { //you want to run slayer with a refernce template
 302
 303                                 #ifdef USE_MPI
 304                                         int pid;
 305                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 306                                         if (pid == 0) { //you are the root process
 307                                 #endif
 308
 309                                 if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 310                                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 311                                         nameFile = nameFileNames[s];
 312                                 }else {
 313                                         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 314
 315                                         //use unique.seqs to create new name and fastafile
 316                                         string inputString = "fasta=" + fastaFileNames[s];
 317                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 318                                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 319
 320                                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 321                                         uniqueCommand->execute();
 322
 323                                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 324
 325                                         delete uniqueCommand;
 326
 327                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 328
 329                                         nameFile = filenames["name"][0];
 330                                         fastaFileNames[s] = filenames["fasta"][0];
 331                                 }
 332
 333                                 //create input file for uchime
 334                                 //read through fastafile and store info
 335                                 map<string, string> seqs;
 336                                 ifstream in;
 337                                 m->openInputFile(fastaFileNames[s], in);
 338
 339                                 while (!in.eof()) {
 340
 341                                         if (m->control_pressed) { in.close(); for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }  return 0; }
 342
 343                                         Sequence seq(in); m->gobble(in);
 344                                         seqs[seq.getName()] = seq.getAligned();
 345                                 }
 346                                 in.close();
 347
 348                                 //read namefile
 349                                 vector<seqPriorityNode> nameMapCount;
 350                                 int error = m->readNames(nameFile, nameMapCount, seqs);
 351
 352                                 if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0; }
 353
 354                                 if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0; }
 355                                 if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }  return 0; }
 356
 357                                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
 358
 359                                 string newFasta = fastaFileNames[s] + ".temp";
 360                                 ofstream out;
 361                                 m->openOutputFile(newFasta, out);
 362
 363                                 //print new file in order of
 364                                 for (int i = 0; i < nameMapCount.size(); i++) {
 365                                         out << ">" << nameMapCount[i].name  << "/ab=" << nameMapCount[i].numIdentical << "/" << endl << nameMapCount[i].seq << endl;
 366                                 }
 367                                 out.close();
 368
 369                                 fastaFileNames[s] = newFasta;
 370
 371                                 #ifdef USE_MPI
 372                                         }
 373                                 #endif
 374                                 if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
 375                         }
 376
 377                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 378                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
 379                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 380
 381                         if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
 382
 383 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 384                         if(processors == 1){ driver(outputFileName, fastaFileNames[s], accnosFileName); }
 385                         else{   createProcesses(outputFileName, fastaFileNames[s], accnosFileName); }
 386 #else
 387                         driver(outputFileName, fastaFileNames[s], accnosFileName);
 388 #endif
 389                         if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } return 0; }
 390
 391
 392                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 393                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 394
 395                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check your sequences.");      m->mothurOutEndLine();
 396                 }
 397
 398                 //set accnos file as new current accnosfile
 399                 string current = "";
 400                 itTypes = outputTypes.find("accnos");
 401                 if (itTypes != outputTypes.end()) {
 402                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 403                 }
 404
 405                 m->mothurOutEndLine();
 406                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 407                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 408                 m->mothurOutEndLine();
 409
 410                 return 0;
 411
 412         }
 413         catch(exception& e) {
 414                 m->errorOut(e, "ChimeraUchimeCommand", "execute");
 415                 exit(1);
 416         }
 417 }
 418 //**********************************************************************************************************************
 419
 420 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos){
 421         try {
 422
 423                 vector<char*> cPara;
 424
 425                 char* tempUchime = new char[8];
 426                 strcpy(tempUchime, "./uchime ");
 427                 cPara.push_back(tempUchime);
 428
 429                 char* tempIn = new char[7];
 430                 strcpy(tempIn, "--input");
 431                 cPara.push_back(tempIn);
 432                 char* temp = new char[filename.length()];
 433                 strcpy(temp, filename.c_str());
 434                 cPara.push_back(temp);
 435
 436                 //are you using a reference file
 437                 if (templatefile != "self") {
 438
 439                         //add reference file
 440                         char* tempRef = new char[4];
 441                         strcpy(tempRef, "--db");
 442                         cPara.push_back(tempRef);
 443                         char* tempR = new char[templatefile.length()];
 444                         strcpy(tempR, templatefile.c_str());
 445                         cPara.push_back(tempR);
 446                 }
 447
 448                 char* tempO = new char[11];
 449                 strcpy(tempO, "--uchimeout");
 450                 cPara.push_back(tempO);
 451                 char* tempout = new char[outputFName.length()];
 452                 strcpy(tempout, outputFName.c_str());
 453                 cPara.push_back(tempout);
 454
 455                 char** uchimeParameters;
 456                 uchimeParameters = new char*[cPara.size()];
 457                 for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i]; cout << cPara[i]; } cout << endl;
 458                 int numArgs = cPara.size();
 459
 460                 uchime_main(numArgs, uchimeParameters);
 461
 462                 //free memory
 463                 for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
 464                 delete[] uchimeParameters;
 465
 466                 //create accnos file from uchime results
 467                 ifstream in;
 468                 m->openInputFile(outputFName, in);
 469
 470                 ofstream out;
 471                 m->openOutputFile(accnos, out);
 472
 473                 int num = 0;
 474                 while(!in.eof()) {
 475
 476                         if (m->control_pressed) { break; }
 477
 478                         string name = "";
 479                         string chimeraFlag = "";
 480                         in >> chimeraFlag >> name;
 481
 482                         //fix name if needed
 483                         if (templatefile != "self") {
 484                                 name = name.substr(0, name.length()-1); //rip off last /
 485                                 name = name.substr(0, name.find_last_of('/'));
 486                         }
 487
 488                         for (int i = 0; i < 15; i++) {  in >> chimeraFlag; }
 489                         m->gobble(in);
 490
 491                         if (chimeraFlag == "Y") {  out << name << endl; }
 492                         num++;
 493                 }
 494                 in.close();
 495                 out.close();
 496
 497                 return num;
 498         }
 499         catch(exception& e) {
 500                 m->errorOut(e, "ChimeraUchimeCommand", "driver");
 501                 exit(1);
 502         }
 503 }
 504 /**************************************************************************************************/
 505
 506 int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 507         try {
 508
 509                 processIDS.clear();
 510                 int process = 1;
 511                 int num = 0;
 512
 513                 //break up file into multiple files
 514                 vector<string> files;
 515                 m->divideFile(filename, processors, files);
 516
 517                 if (m->control_pressed) {  return 0;  }
 518
 519 #ifdef USE_MPI
 520                 int pid, numSeqsPerProcessor;
 521                 int tag = 2001;
 522
 523                 MPI_Status status;
 524                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 525                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 526
 527                 if (pid == 0) { //you are the root process
 528                         num = driver(outputFileName, files[0], accnos);
 529
 530                         if (templatefile != "self") {
 531                                 //wait on chidren
 532                                 for(int j = 1; j < processors; j++) {
 533                                         int temp;
 534                                         MPI_Recv(&temp, 1, MPI_INT, j, tag, MPI_COMM_WORLD, &status);
 535                                         num += temp;
 536
 537                                         m->appendFiles((outputFileName + toString(j) + ".temp"), outputFileName);
 538                                         remove((outputFileName + toString(j) + ".temp").c_str());
 539
 540                                         m->appendFiles((accnos + toString(j) + ".temp"), accnos);
 541                                         remove((accnos + toString(j) + ".temp").c_str());
 542                                 }
 543                         }
 544                 }else{ //you are a child process
 545                         if (templatefile != "self") { //if template=self we can only use 1 processor
 546                                 num = driver(outputFileName+toString(pid) + ".temp", files[pid], accnos+toString(pid) + ".temp");
 547
 548                                 //send numSeqs to parent
 549                                 MPI_Send(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 550                         }
 551                 }
 552
 553                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 554 #else
 555
 556                 //loop through and create all the processes you want
 557                 while (process != processors) {
 558                         int pid = fork();
 559
 560                         if (pid > 0) {
 561                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 562                                 process++;
 563                         }else if (pid == 0){
 564                                 num = driver(outputFileName + toString(getpid()) + ".temp", files[process], accnos + toString(getpid()) + ".temp");
 565
 566                                 //pass numSeqs to parent
 567                                 ofstream out;
 568                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 569                                 m->openOutputFile(tempFile, out);
 570                                 out << num << endl;
 571                                 out.close();
 572
 573                                 exit(0);
 574                         }else {
 575                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 576                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 577                                 exit(0);
 578                         }
 579                 }
 580
 581                 //do my part
 582                 num = driver(outputFileName, files[0], accnos);
 583
 584                 //force parent to wait until all the processes are done
 585                 for (int i=0;i<processIDS.size();i++) {
 586                         int temp = processIDS[i];
 587                         wait(&temp);
 588                 }
 589
 590                 for (int i = 0; i < processIDS.size(); i++) {
 591                         ifstream in;
 592                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 593                         m->openInputFile(tempFile, in);
 594                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 595                         in.close(); remove(tempFile.c_str());
 596                 }
 597
 598
 599                 //append output files
 600                 for(int i=0;i<processIDS[i];i++){
 601                         m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 602                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 603
 604                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
 605                         remove((accnos + toString(processIDS[i]) + ".temp").c_str());
 606                 }
 607 #endif
 608                 //get rid of the file pieces.
 609                 for (int i = 0; i < files.size(); i++) { remove(files[i].c_str()); }
 610
 611                 return num;
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "ChimeraUchimeCommand", "createProcesses");
 615                 exit(1);
 616         }
 617 }
 618
 619 /**************************************************************************************************/
 620