chimeracheckcommand.cpp

   1 /*
   2  *  chimeracheckcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeracheckcommand.h"
  11 #include "referencedb.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ChimeraCheckCommand::setParameters(){
  15         try {
  16                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
  18                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
  19                 CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
  20                 CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
  21                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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                 CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "ChimeraCheckCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string ChimeraCheckCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  41                 helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
  42                 helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n";
  43                 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";
  44                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
  45                 helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \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 increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n";
  51                 helpString += "The ksize parameter allows you to input kmersize, default is 7. \n";
  52                 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";
  53                 helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n";
  54                 helpString += "You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n";
  55                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  56                 helpString += "The chimera.check command should be in the following format: \n";
  57                 helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n";
  58                 helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n";
  59                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "ChimeraCheckCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 string ChimeraCheckCommand::getOutputPattern(string type) {
  69     try {
  70         string pattern = "";
  71
  72         if (type == "chimera") {  pattern = "[filename],chimeracheck.chimeras"; }
  73         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  74
  75         return pattern;
  76     }
  77     catch(exception& e) {
  78         m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
  79         exit(1);
  80     }
  81 }
  82 //**********************************************************************************************************************
  83 ChimeraCheckCommand::ChimeraCheckCommand(){
  84         try {
  85                 abort = true; calledHelp = true;
  86                 setParameters();
  87                 vector<string> tempOutNames;
  88                 outputTypes["chimera"] = tempOutNames;
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
  92                 exit(1);
  93         }
  94 }
  95 //***************************************************************************************************************
  96 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  97         try {
  98                 abort = false; calledHelp = false;
  99                 ReferenceDB* rdb = ReferenceDB::getInstance();
 100
 101                 //allow user to run help
 102                 if(option == "help") { help(); abort = true; calledHelp = true; }
 103                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 104
 105                 else {
 106                         vector<string> myArray = setParameters();
 107
 108                         OptionParser parser(option);
 109                         map<string,string> parameters = parser.getParameters();
 110
 111                         ValidParameters validParameter("chimera.check");
 112                         map<string,string>::iterator it;
 113
 114                         //check to make sure all parameters are valid for command
 115                         for (it = parameters.begin(); it != parameters.end(); it++) {
 116                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 117                         }
 118
 119                         vector<string> tempOutNames;
 120                         outputTypes["chimera"] = tempOutNames;
 121
 122                         //if the user changes the input directory command factory will send this info to us in the output parameter
 123                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 124                         if (inputDir == "not found"){   inputDir = "";          }
 125                         else {
 126                                 it = parameters.find("reference");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         string path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 132                                 }
 133                         }
 134
 135                         //check for required parameters
 136                         fastafile = validParameter.validFile(parameters, "fasta", false);
 137                         if (fastafile == "not found") {
 138                                 //if there is a current fasta file, use it
 139                                 string filename = m->getFastaFile();
 140                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 141                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 142                         }else {
 143                                 m->splitAtDash(fastafile, fastaFileNames);
 144
 145                                 //go through files and make sure they are good, if not, then disregard them
 146                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 147
 148                                         bool ignore = false;
 149                                         if (fastaFileNames[i] == "current") {
 150                                                 fastaFileNames[i] = m->getFastaFile();
 151                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 152                                                 else {
 153                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 154                                                         //erase from file list
 155                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 156                                                         i--;
 157                                                 }
 158                                         }
 159
 160                                         if (!ignore) {
 161
 162
 163                                                 if (inputDir != "") {
 164                                                         string path = m->hasPath(fastaFileNames[i]);
 165                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 166                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 167                                                 }
 168
 169                                                 int ableToOpen;
 170                                                 ifstream in;
 171
 172                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 173
 174                                                 //if you can't open it, try default location
 175                                                 if (ableToOpen == 1) {
 176                                                         if (m->getDefaultPath() != "") { //default path is set
 177                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 178                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 179                                                                 ifstream in2;
 180                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 181                                                                 in2.close();
 182                                                                 fastaFileNames[i] = tryPath;
 183                                                         }
 184                                                 }
 185
 186                                                 //if you can't open it, try default location
 187                                                 if (ableToOpen == 1) {
 188                                                         if (m->getOutputDir() != "") { //default path is set
 189                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 190                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 191                                                                 ifstream in2;
 192                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 193                                                                 in2.close();
 194                                                                 fastaFileNames[i] = tryPath;
 195                                                         }
 196                                                 }
 197
 198                                                 in.close();
 199
 200                                                 if (ableToOpen == 1) {
 201                                                         m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
 202                                                         //erase from file list
 203                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 204                                                         i--;
 205                                                 }else {
 206                                                         m->setFastaFile(fastaFileNames[i]);
 207                                                 }
 208                                         }
 209                                 }
 210
 211                                 //make sure there is at least one valid file left
 212                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 213                         }
 214
 215                         //if the user changes the output directory command factory will send this info to us in the output parameter
 216                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 217
 218                         namefile = validParameter.validFile(parameters, "name", false);
 219                         if (namefile == "not found") { namefile = ""; }
 220                         else {
 221                                 m->splitAtDash(namefile, nameFileNames);
 222
 223                                 //go through files and make sure they are good, if not, then disregard them
 224                                 for (int i = 0; i < nameFileNames.size(); i++) {
 225
 226                                         bool ignore = false;
 227                                         if (nameFileNames[i] == "current") {
 228                                                 nameFileNames[i] = m->getNameFile();
 229                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 230                                                 else {
 231                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 232                                                         //erase from file list
 233                                                         nameFileNames.erase(nameFileNames.begin()+i);
 234                                                         i--;
 235                                                 }
 236                                         }
 237
 238                                         if (!ignore) {
 239
 240                                                 if (inputDir != "") {
 241                                                         string path = m->hasPath(nameFileNames[i]);
 242                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 243                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 244                                                 }
 245
 246                                                 int ableToOpen;
 247                                                 ifstream in;
 248
 249                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 250
 251                                                 //if you can't open it, try default location
 252                                                 if (ableToOpen == 1) {
 253                                                         if (m->getDefaultPath() != "") { //default path is set
 254                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 255                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 256                                                                 ifstream in2;
 257                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 258                                                                 in2.close();
 259                                                                 nameFileNames[i] = tryPath;
 260                                                         }
 261                                                 }
 262
 263                                                 //if you can't open it, try default location
 264                                                 if (ableToOpen == 1) {
 265                                                         if (m->getOutputDir() != "") { //default path is set
 266                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 267                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 268                                                                 ifstream in2;
 269                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 270                                                                 in2.close();
 271                                                                 nameFileNames[i] = tryPath;
 272                                                         }
 273                                                 }
 274
 275                                                 in.close();
 276
 277                                                 if (ableToOpen == 1) {
 278                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 279                                                         //erase from file list
 280                                                         nameFileNames.erase(nameFileNames.begin()+i);
 281                                                         i--;
 282                                                 }else {
 283                                                         m->setNameFile(nameFileNames[i]);
 284                                                 }
 285                                         }
 286                                 }
 287
 288                                 //make sure there is at least one valid file left
 289                                 if (nameFileNames.size() != 0) {
 290                                         if (nameFileNames.size() != fastaFileNames.size()) {
 291                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 292                                                  abort = true;
 293                                         }
 294                                 }
 295                         }
 296
 297                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 298                         m->setProcessors(temp);
 299                         m->mothurConvert(temp, processors);
 300
 301                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 302                         save = m->isTrue(temp);
 303                         rdb->save = save;
 304                         if (save) { //clear out old references
 305                                 rdb->clearMemory();
 306                         }
 307
 308                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 309                         templatefile = validParameter.validFile(parameters, "reference", true);
 310                         if (templatefile == "not found") {
 311                                 //check for saved reference sequences
 312                                 if (rdb->referenceSeqs.size() != 0) {
 313                                         templatefile = "saved";
 314                                 }else {
 315                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 316                                         m->mothurOutEndLine();
 317                                         abort = true;
 318                                 }
 319                         }else if (templatefile == "not open") { abort = true; }
 320                         else {  if (save) {     rdb->setSavedReference(templatefile);   }       }
 321
 322
 323                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 324                         m->mothurConvert(temp, ksize);
 325
 326                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 327                         svg = m->isTrue(temp);
 328                         if (nameFileNames.size() != 0) { svg = true; }
 329
 330                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 331                         m->mothurConvert(temp, increment);
 332                 }
 333         }
 334         catch(exception& e) {
 335                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 336                 exit(1);
 337         }
 338 }
 339 //***************************************************************************************************************
 340
 341 int ChimeraCheckCommand::execute(){
 342         try{
 343
 344                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 345
 346                 for (int i = 0; i < fastaFileNames.size(); i++) {
 347
 348                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 349
 350                         int start = time(NULL);
 351
 352                         string thisNameFile = "";
 353                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 354
 355                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 356
 357                         if (m->control_pressed) { delete chimera;       return 0;       }
 358
 359                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
 360             map<string, string> variables;
 361             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
 362                         string outputFileName = getOutputFileName("chimera", variables);
 363                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 364
 365                 #ifdef USE_MPI
 366
 367                                 int pid, numSeqsPerProcessor;
 368                                 int tag = 2001;
 369                                 vector<unsigned long long> MPIPos;
 370
 371                                 MPI_Status status;
 372                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 373                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 374
 375                                 MPI_File inMPI;
 376                                 MPI_File outMPI;
 377
 378                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 379                                 int inMode=MPI_MODE_RDONLY;
 380
 381                                 char outFilename[1024];
 382                                 strcpy(outFilename, outputFileName.c_str());
 383
 384                                 char inFileName[1024];
 385                                 strcpy(inFileName, fastaFileNames[i].c_str());
 386
 387                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 388                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 389
 390                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    m->mothurRemove(outputNames[j]);        } outputTypes.clear(); delete chimera; return 0;  }
 391
 392                                 if (pid == 0) { //you are the root process
 393                                         MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 394
 395                                         //send file positions to all processes
 396                                         for(int j = 1; j < processors; j++) {
 397                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 398                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 399                                         }
 400
 401                                         //figure out how many sequences you have to align
 402                                         numSeqsPerProcessor = numSeqs / processors;
 403                                         int startIndex =  pid * numSeqsPerProcessor;
 404                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 405
 406
 407                                         //align your part
 408                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 409
 410                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    m->mothurRemove(outputNames[j]);        }   outputTypes.clear(); delete chimera; return 0;  }
 411
 412                                         //wait on chidren
 413                                         for(int j = 1; j < processors; j++) {
 414                                                 char buf[5];
 415                                                 MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 416                                         }
 417                                 }else{ //you are a child process
 418                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 419                                         MPIPos.resize(numSeqs+1);
 420                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 421
 422                                         //figure out how many sequences you have to align
 423                                         numSeqsPerProcessor = numSeqs / processors;
 424                                         int startIndex =  pid * numSeqsPerProcessor;
 425                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 426
 427                                         //align your part
 428                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 429
 430                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  outputTypes.clear(); delete chimera; return 0;  }
 431
 432                                         //tell parent you are done.
 433                                         char buf[5];
 434                                         strcpy(buf, "done");
 435                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 436                                 }
 437
 438                                 //close files
 439                                 MPI_File_close(&inMPI);
 440                                 MPI_File_close(&outMPI);
 441                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 442                 #else
 443
 444
 445
 446                         //break up file
 447                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 448                                 vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
 449
 450                                 for (int s = 0; s < (positions.size()-1); s++) {
 451                                         lines.push_back(new linePair(positions[s], positions[(s+1)]));
 452                                 }
 453
 454                                 if(processors == 1){
 455                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 456
 457                                         if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        } for (int j = 0; j < lines.size(); j++) {  delete lines[j];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 458
 459                                 }else{
 460                                         processIDS.resize(0);
 461
 462                                         numSeqs = createProcesses(outputFileName, fastaFileNames[i]);
 463
 464                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 465
 466                                         //append output files
 467                                         for(int j=1;j<processors;j++){
 468                                                 m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 469                                                 m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp"));
 470                                         }
 471
 472                                         if (m->control_pressed) {
 473                                                 for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } outputTypes.clear();
 474                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 475                                                 delete chimera;
 476                                                 return 0;
 477                                         }
 478                                 }
 479
 480                         #else
 481                                 lines.push_back(new linePair(0, 1000));
 482                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 483
 484                                 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++) {  m->mothurRemove(outputNames[j]);        } outputTypes.clear(); delete chimera; return 0; }
 485                         #endif
 486                 #endif
 487                         delete chimera;
 488                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 489
 490                         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();
 491                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 492
 493                 }
 494
 495                 m->mothurOutEndLine();
 496                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 497                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 498                 m->mothurOutEndLine();
 499
 500                 return 0;
 501
 502         }
 503         catch(exception& e) {
 504                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 505                 exit(1);
 506         }
 507 }
 508 //**********************************************************************************************************************
 509
 510 int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){
 511         try {
 512                 ofstream out;
 513                 m->openOutputFile(outputFName, out);
 514
 515                 ofstream out2;
 516
 517                 ifstream inFASTA;
 518                 m->openInputFile(filename, inFASTA);
 519
 520                 inFASTA.seekg(filePos->start);
 521
 522                 bool done = false;
 523                 int count = 0;
 524
 525                 while (!done) {
 526
 527                         if (m->control_pressed) {       return 1;       }
 528
 529                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 530
 531                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 532                                 //find chimeras
 533                                 chimera->getChimeras(candidateSeq);
 534
 535                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 536
 537                                 //print results
 538                                 chimera->print(out, out2);
 539                         }
 540                         delete candidateSeq;
 541
 542                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 543                                 unsigned long long pos = inFASTA.tellg();
 544                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 545                         #else
 546                                 if (inFASTA.eof()) { break; }
 547                         #endif
 548
 549                         //report progress
 550                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 551             count++;
 552                 }
 553                 //report progress
 554                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 555
 556                 out.close();
 557                 inFASTA.close();
 558
 559                 return count;
 560         }
 561         catch(exception& e) {
 562                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 563                 exit(1);
 564         }
 565 }
 566 //**********************************************************************************************************************
 567 #ifdef USE_MPI
 568 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos){
 569         try {
 570                 MPI_File outAccMPI;
 571                 MPI_Status status;
 572                 int pid;
 573                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 574
 575                 for(int i=0;i<num;i++){
 576
 577                         if (m->control_pressed) { return 0; }
 578
 579                         //read next sequence
 580                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 581
 582                         char* buf4 = new char[length];
 583                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 584
 585                         string tempBuf = buf4;
 586                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 587                         istringstream iss (tempBuf,istringstream::in);
 588                         delete buf4;
 589
 590                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 591
 592                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 593                                 //find chimeras
 594                                 chimera->getChimeras(candidateSeq);
 595
 596                                 //print results
 597                                 chimera->print(outMPI, outAccMPI);
 598                         }
 599                         delete candidateSeq;
 600
 601                         //report progress
 602                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 603                 }
 604                 //report progress
 605                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 606
 607                 return 0;
 608         }
 609         catch(exception& e) {
 610                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 611                 exit(1);
 612         }
 613 }
 614 #endif
 615
 616 /**************************************************************************************************/
 617
 618 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 619         try {
 620 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 621                 int process = 0;
 622                 int num = 0;
 623
 624                 //loop through and create all the processes you want
 625                 while (process != processors) {
 626                         int pid = fork();
 627
 628                         if (pid > 0) {
 629                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 630                                 process++;
 631                         }else if (pid == 0){
 632                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 633
 634                                 //pass numSeqs to parent
 635                                 ofstream out;
 636                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 637                                 m->openOutputFile(tempFile, out);
 638                                 out << num << endl;
 639                                 out.close();
 640
 641                                 exit(0);
 642                         }else {
 643                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 644                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 645                                 exit(0);
 646                         }
 647                 }
 648
 649                 //force parent to wait until all the processes are done
 650                 for (int i=0;i<processors;i++) {
 651                         int temp = processIDS[i];
 652                         wait(&temp);
 653                 }
 654
 655                 for (int i = 0; i < processIDS.size(); i++) {
 656                         ifstream in;
 657                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 658                         m->openInputFile(tempFile, in);
 659                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 660                         in.close(); m->mothurRemove(tempFile);
 661                 }
 662
 663                 return num;
 664 #endif
 665         }
 666         catch(exception& e) {
 667                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 668                 exit(1);
 669         }
 670 }
 671 /**************************************************************************************************/
 672
 673