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::setParameters(){
  14         try {
  15                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
  19                 CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
  20                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
  21                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "ChimeraCheckCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string ChimeraCheckCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  39                 helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
  40                 helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n";
  41                 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";
  42                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
  43                 helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \n";
  44                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  45 #ifdef USE_MPI
  46                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  47 #endif
  48                 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n";
  49                 helpString += "The ksize parameter allows you to input kmersize, default is 7. \n";
  50                 helpString += "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";
  51                 helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n";
  52                 helpString += "You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n";
  53                 helpString += "The chimera.check command should be in the following format: \n";
  54                 helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n";
  55                 helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n";
  56                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  57                 return helpString;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "ChimeraCheckCommand", "getHelpString");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 ChimeraCheckCommand::ChimeraCheckCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 setParameters();
  69                 vector<string> tempOutNames;
  70                 outputTypes["chimera"] = tempOutNames;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
  74                 exit(1);
  75         }
  76 }
  77 //***************************************************************************************************************
  78 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; calledHelp = true; }
  84                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  85
  86                 else {
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter("chimera.check");
  93                         map<string,string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         vector<string> tempOutNames;
 101                         outputTypes["chimera"] = tempOutNames;
 102
 103                         //if the user changes the input directory command factory will send this info to us in the output parameter
 104                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 105                         if (inputDir == "not found"){   inputDir = "";          }
 106                         else {
 107                                 it = parameters.find("reference");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         string path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 113                                 }
 114                         }
 115
 116                         //check for required parameters
 117                         fastafile = validParameter.validFile(parameters, "fasta", false);
 118                         if (fastafile == "not found") {
 119                                 //if there is a current fasta file, use it
 120                                 string filename = m->getFastaFile();
 121                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 122                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 123                         }else {
 124                                 m->splitAtDash(fastafile, fastaFileNames);
 125
 126                                 //go through files and make sure they are good, if not, then disregard them
 127                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 128
 129                                         bool ignore = false;
 130                                         if (fastaFileNames[i] == "current") {
 131                                                 fastaFileNames[i] = m->getFastaFile();
 132                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 133                                                 else {
 134                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 135                                                         //erase from file list
 136                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 137                                                         i--;
 138                                                 }
 139                                         }
 140
 141                                         if (!ignore) {
 142
 143
 144                                                 if (inputDir != "") {
 145                                                         string path = m->hasPath(fastaFileNames[i]);
 146                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 148                                                 }
 149
 150                                                 int ableToOpen;
 151                                                 ifstream in;
 152
 153                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 154
 155                                                 //if you can't open it, try default location
 156                                                 if (ableToOpen == 1) {
 157                                                         if (m->getDefaultPath() != "") { //default path is set
 158                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 159                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 160                                                                 ifstream in2;
 161                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 162                                                                 in2.close();
 163                                                                 fastaFileNames[i] = tryPath;
 164                                                         }
 165                                                 }
 166
 167                                                 //if you can't open it, try default location
 168                                                 if (ableToOpen == 1) {
 169                                                         if (m->getOutputDir() != "") { //default path is set
 170                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 171                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 172                                                                 ifstream in2;
 173                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 174                                                                 in2.close();
 175                                                                 fastaFileNames[i] = tryPath;
 176                                                         }
 177                                                 }
 178
 179                                                 in.close();
 180
 181                                                 if (ableToOpen == 1) {
 182                                                         m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
 183                                                         //erase from file list
 184                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 185                                                         i--;
 186                                                 }
 187                                         }
 188                                 }
 189
 190                                 //make sure there is at least one valid file left
 191                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 192                         }
 193
 194                         //if the user changes the output directory command factory will send this info to us in the output parameter
 195                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 196
 197                         templatefile = validParameter.validFile(parameters, "reference", true);
 198                         if (templatefile == "not open") { abort = true; }
 199                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 200
 201                         namefile = validParameter.validFile(parameters, "name", false);
 202                         if (namefile == "not found") { namefile = ""; }
 203                         else {
 204                                 m->splitAtDash(namefile, nameFileNames);
 205
 206                                 //go through files and make sure they are good, if not, then disregard them
 207                                 for (int i = 0; i < nameFileNames.size(); i++) {
 208
 209                                         bool ignore = false;
 210                                         if (nameFileNames[i] == "current") {
 211                                                 nameFileNames[i] = m->getNameFile();
 212                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 213                                                 else {
 214                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 215                                                         //erase from file list
 216                                                         nameFileNames.erase(nameFileNames.begin()+i);
 217                                                         i--;
 218                                                 }
 219                                         }
 220
 221                                         if (!ignore) {
 222
 223                                                 if (inputDir != "") {
 224                                                         string path = m->hasPath(nameFileNames[i]);
 225                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 226                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 227                                                 }
 228
 229                                                 int ableToOpen;
 230                                                 ifstream in;
 231
 232                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 233
 234                                                 //if you can't open it, try default location
 235                                                 if (ableToOpen == 1) {
 236                                                         if (m->getDefaultPath() != "") { //default path is set
 237                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 238                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 239                                                                 ifstream in2;
 240                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 241                                                                 in2.close();
 242                                                                 nameFileNames[i] = tryPath;
 243                                                         }
 244                                                 }
 245
 246                                                 //if you can't open it, try default location
 247                                                 if (ableToOpen == 1) {
 248                                                         if (m->getOutputDir() != "") { //default path is set
 249                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 250                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 251                                                                 ifstream in2;
 252                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 253                                                                 in2.close();
 254                                                                 nameFileNames[i] = tryPath;
 255                                                         }
 256                                                 }
 257
 258                                                 in.close();
 259
 260                                                 if (ableToOpen == 1) {
 261                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 262                                                         //erase from file list
 263                                                         nameFileNames.erase(nameFileNames.begin()+i);
 264                                                         i--;
 265                                                 }
 266                                         }
 267                                 }
 268
 269                                 //make sure there is at least one valid file left
 270                                 if (nameFileNames.size() != 0) {
 271                                         if (nameFileNames.size() != fastaFileNames.size()) {
 272                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 273                                                  abort = true;
 274                                         }
 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                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 283                         convert(temp, ksize);
 284
 285                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 286                         svg = m->isTrue(temp);
 287                         if (nameFileNames.size() != 0) { svg = true; }
 288
 289                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 290                         convert(temp, increment);
 291                 }
 292         }
 293         catch(exception& e) {
 294                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 295                 exit(1);
 296         }
 297 }
 298 //***************************************************************************************************************
 299
 300 int ChimeraCheckCommand::execute(){
 301         try{
 302
 303                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 304
 305                 for (int i = 0; i < fastaFileNames.size(); i++) {
 306
 307                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 308
 309                         int start = time(NULL);
 310
 311                         string thisNameFile = "";
 312                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 313
 314                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 315
 316                         if (m->control_pressed) { delete chimera;       return 0;       }
 317
 318                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
 319                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 320                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 321
 322                 #ifdef USE_MPI
 323
 324                                 int pid, numSeqsPerProcessor;
 325                                 int tag = 2001;
 326                                 vector<unsigned long int> MPIPos;
 327
 328                                 MPI_Status status;
 329                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 330                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 331
 332                                 MPI_File inMPI;
 333                                 MPI_File outMPI;
 334
 335                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 336                                 int inMode=MPI_MODE_RDONLY;
 337
 338                                 char outFilename[1024];
 339                                 strcpy(outFilename, outputFileName.c_str());
 340
 341                                 char inFileName[1024];
 342                                 strcpy(inFileName, fastaFileNames[i].c_str());
 343
 344                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 345                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 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                                 if (pid == 0) { //you are the root process
 350                                         MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 351
 352                                         //send file positions to all processes
 353                                         for(int j = 1; j < processors; j++) {
 354                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 355                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 356                                         }
 357
 358                                         //figure out how many sequences you have to align
 359                                         numSeqsPerProcessor = numSeqs / processors;
 360                                         int startIndex =  pid * numSeqsPerProcessor;
 361                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 362
 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                                         //wait on chidren
 370                                         for(int j = 1; j < processors; j++) {
 371                                                 char buf[5];
 372                                                 MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 373                                         }
 374                                 }else{ //you are a child process
 375                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 376                                         MPIPos.resize(numSeqs+1);
 377                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 378
 379                                         //figure out how many sequences you have to align
 380                                         numSeqsPerProcessor = numSeqs / processors;
 381                                         int startIndex =  pid * numSeqsPerProcessor;
 382                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 383
 384                                         //align your part
 385                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 386
 387                                         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;  }
 388
 389                                         //tell parent you are done.
 390                                         char buf[5];
 391                                         strcpy(buf, "done");
 392                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 393                                 }
 394
 395                                 //close files
 396                                 MPI_File_close(&inMPI);
 397                                 MPI_File_close(&outMPI);
 398                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 399                 #else
 400
 401                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[i], processors);
 402
 403                         for (int s = 0; s < (positions.size()-1); s++) {
 404                                 lines.push_back(new linePair(positions[s], positions[(s+1)]));
 405                         }
 406
 407                         //break up file
 408                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 409                                 if(processors == 1){
 410                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 411
 412                                         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; }
 413
 414                                 }else{
 415                                         processIDS.resize(0);
 416
 417                                         numSeqs = createProcesses(outputFileName, fastaFileNames[i]);
 418
 419                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 420
 421                                         //append output files
 422                                         for(int j=1;j<processors;j++){
 423                                                 m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 424                                                 remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
 425                                         }
 426
 427                                         if (m->control_pressed) {
 428                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear();
 429                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 430                                                 delete chimera;
 431                                                 return 0;
 432                                         }
 433                                 }
 434
 435                         #else
 436                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 437
 438                                 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; }
 439                         #endif
 440                 #endif
 441                         delete chimera;
 442                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 443
 444                         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();
 445                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 446
 447                 }
 448
 449                 m->mothurOutEndLine();
 450                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 451                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 452                 m->mothurOutEndLine();
 453
 454                 return 0;
 455
 456         }
 457         catch(exception& e) {
 458                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 459                 exit(1);
 460         }
 461 }
 462 //**********************************************************************************************************************
 463
 464 int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){
 465         try {
 466                 ofstream out;
 467                 m->openOutputFile(outputFName, out);
 468
 469                 ofstream out2;
 470
 471                 ifstream inFASTA;
 472                 m->openInputFile(filename, inFASTA);
 473
 474                 inFASTA.seekg(filePos->start);
 475
 476                 bool done = false;
 477                 int count = 0;
 478
 479                 while (!done) {
 480
 481                         if (m->control_pressed) {       return 1;       }
 482
 483                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 484
 485                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 486                                 //find chimeras
 487                                 chimera->getChimeras(candidateSeq);
 488
 489                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 490
 491                                 //print results
 492                                 chimera->print(out, out2);
 493                         }
 494                         delete candidateSeq;
 495
 496                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 497                                 unsigned long int pos = inFASTA.tellg();
 498                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 499                         #else
 500                                 if (inFASTA.eof()) { break; }
 501                         #endif
 502
 503                         //report progress
 504                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 505                 }
 506                 //report progress
 507                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 508
 509                 out.close();
 510                 inFASTA.close();
 511
 512                 return count;
 513         }
 514         catch(exception& e) {
 515                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 516                 exit(1);
 517         }
 518 }
 519 //**********************************************************************************************************************
 520 #ifdef USE_MPI
 521 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos){
 522         try {
 523                 MPI_File outAccMPI;
 524                 MPI_Status status;
 525                 int pid;
 526                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 527
 528                 for(int i=0;i<num;i++){
 529
 530                         if (m->control_pressed) { return 0; }
 531
 532                         //read next sequence
 533                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 534
 535                         char* buf4 = new char[length];
 536                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 537
 538                         string tempBuf = buf4;
 539                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 540                         istringstream iss (tempBuf,istringstream::in);
 541                         delete buf4;
 542
 543                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 544
 545                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 546                                 //find chimeras
 547                                 chimera->getChimeras(candidateSeq);
 548
 549                                 //print results
 550                                 chimera->print(outMPI, outAccMPI);
 551                         }
 552                         delete candidateSeq;
 553
 554                         //report progress
 555                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 556                 }
 557                 //report progress
 558                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 559
 560                 return 0;
 561         }
 562         catch(exception& e) {
 563                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 564                 exit(1);
 565         }
 566 }
 567 #endif
 568
 569 /**************************************************************************************************/
 570
 571 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 572         try {
 573 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 574                 int process = 0;
 575                 int num = 0;
 576
 577                 //loop through and create all the processes you want
 578                 while (process != processors) {
 579                         int pid = fork();
 580
 581                         if (pid > 0) {
 582                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 583                                 process++;
 584                         }else if (pid == 0){
 585                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 586
 587                                 //pass numSeqs to parent
 588                                 ofstream out;
 589                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 590                                 m->openOutputFile(tempFile, out);
 591                                 out << num << endl;
 592                                 out.close();
 593
 594                                 exit(0);
 595                         }else {
 596                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 597                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 598                                 exit(0);
 599                         }
 600                 }
 601
 602                 //force parent to wait until all the processes are done
 603                 for (int i=0;i<processors;i++) {
 604                         int temp = processIDS[i];
 605                         wait(&temp);
 606                 }
 607
 608                 for (int i = 0; i < processIDS.size(); i++) {
 609                         ifstream in;
 610                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 611                         m->openInputFile(tempFile, in);
 612                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 613                         in.close(); remove(tempFile.c_str());
 614                 }
 615
 616                 return num;
 617 #endif
 618         }
 619         catch(exception& e) {
 620                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 621                 exit(1);
 622         }
 623 }
 624 /**************************************************************************************************/
 625
 626