chimeraccodecommand.cpp

   1 /*
   2  *  chimeraccodecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/30/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraccodecommand.h"
  11 #include "ccode.h"
  12 #include "referencedb.h"
  13 //**********************************************************************************************************************
  14 vector<string> ChimeraCcodeCommand::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-mapinfo-accnos",false,true,true); parameters.push_back(pfasta);
  18                 CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
  19                 CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
  20                 CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pnumwanted);
  21                 CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
  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, "ChimeraCcodeCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string ChimeraCcodeCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  41                 helpString += "This command was created using the algorithms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
  42                 helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\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 filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n";
  47                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  48 #ifdef USE_MPI
  49                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  50 #endif
  51                 helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n";
  52                 helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n";
  53                 helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n";
  54                 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.";
  55                 helpString += "The chimera.ccode command should be in the following format: \n";
  56                 helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
  57                 helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
  58                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  59                 return helpString;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "ChimeraCcodeCommand", "getHelpString");
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67 string ChimeraCcodeCommand::getOutputPattern(string type) {
  68     try {
  69         string pattern = "";
  70
  71         if (type == "chimera") {  pattern = "[filename],[tag],ccode.chimeras-[filename],ccode.chimeras"; }
  72         else if (type == "accnos") {  pattern = "[filename],[tag],ccode.accnos-[filename],ccode.accnos"; }
  73         else if (type == "mapinfo") {  pattern =  "[filename],mapinfo"; }
  74         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  75
  76         return pattern;
  77     }
  78     catch(exception& e) {
  79         m->errorOut(e, "ChimeraCcodeCommand", "getOutputPattern");
  80         exit(1);
  81     }
  82 }
  83 //**********************************************************************************************************************
  84 ChimeraCcodeCommand::ChimeraCcodeCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["chimera"] = tempOutNames;
  90                 outputTypes["mapinfo"] = tempOutNames;
  91                 outputTypes["accnos"] = tempOutNames;
  92
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
  96                 exit(1);
  97         }
  98 }
  99 //***************************************************************************************************************
 100 ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
 101         try {
 102                 abort = false; calledHelp = false;
 103                 ReferenceDB* rdb = ReferenceDB::getInstance();
 104
 105                 //allow user to run help
 106                 if(option == "help") { help(); abort = true; calledHelp = true; }
 107                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 108
 109                 else {
 110                         vector<string> myArray = setParameters();
 111
 112                         OptionParser parser(option);
 113                         map<string,string> parameters = parser.getParameters();
 114
 115                         ValidParameters validParameter("chimera.ccode");
 116                         map<string,string>::iterator it;
 117
 118                         //check to make sure all parameters are valid for command
 119                         for (it = parameters.begin(); it != parameters.end(); it++) {
 120                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 121                         }
 122
 123                         vector<string> tempOutNames;
 124                         outputTypes["chimera"] = tempOutNames;
 125                         outputTypes["mapinfo"] = tempOutNames;
 126                         outputTypes["accnos"] = tempOutNames;
 127
 128
 129                         //if the user changes the input directory command factory will send this info to us in the output parameter
 130                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 131                         if (inputDir == "not found"){   inputDir = "";          }
 132                         else {
 133                                 string path;
 134                                 it = parameters.find("reference");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 140                                 }
 141                         }
 142
 143                         //check for required parameters
 144                         fastafile = validParameter.validFile(parameters, "fasta", false);
 145                         if (fastafile == "not found") {                                 //if there is a current fasta file, use it
 146                                 string filename = m->getFastaFile();
 147                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 148                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 149                         }else {
 150                                 m->splitAtDash(fastafile, fastaFileNames);
 151
 152                                 //go through files and make sure they are good, if not, then disregard them
 153                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 154
 155                                         bool ignore = false;
 156                                         if (fastaFileNames[i] == "current") {
 157                                                 fastaFileNames[i] = m->getFastaFile();
 158                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 159                                                 else {
 160                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 161                                                         //erase from file list
 162                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 163                                                         i--;
 164                                                 }
 165                                         }
 166
 167                                         if (!ignore) {
 168
 169                                                 if (inputDir != "") {
 170                                                         string path = m->hasPath(fastaFileNames[i]);
 171                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 173                                                 }
 174
 175                                                 int ableToOpen;
 176                                                 ifstream in;
 177
 178                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 179
 180                                                 //if you can't open it, try default location
 181                                                 if (ableToOpen == 1) {
 182                                                         if (m->getDefaultPath() != "") { //default path is set
 183                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 184                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 185                                                                 ifstream in2;
 186                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 187                                                                 in2.close();
 188                                                                 fastaFileNames[i] = tryPath;
 189                                                         }
 190                                                 }
 191
 192                                                 //if you can't open it, try default location
 193                                                 if (ableToOpen == 1) {
 194                                                         if (m->getOutputDir() != "") { //default path is set
 195                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 196                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 197                                                                 ifstream in2;
 198                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 199                                                                 in2.close();
 200                                                                 fastaFileNames[i] = tryPath;
 201                                                         }
 202                                                 }
 203
 204                                                 in.close();
 205
 206                                                 if (ableToOpen == 1) {
 207                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 208                                                         //erase from file list
 209                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 210                                                         i--;
 211                                                 }else {
 212                                                         m->setFastaFile(fastaFileNames[i]);
 213                                                 }
 214                                         }
 215                                 }
 216
 217                                 //make sure there is at least one valid file left
 218                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 219                         }
 220
 221                         //if the user changes the output directory command factory will send this info to us in the output parameter
 222                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 223
 224                         maskfile = validParameter.validFile(parameters, "mask", false);
 225                         if (maskfile == "not found") { maskfile = "";  }
 226                         else if (maskfile != "default")  {
 227                                 if (inputDir != "") {
 228                                         string path = m->hasPath(maskfile);
 229                                         //if the user has not given a path then, add inputdir. else leave path alone.
 230                                         if (path == "") {       maskfile = inputDir + maskfile;         }
 231                                 }
 232
 233                                 ifstream in;
 234                                 int     ableToOpen = m->openInputFile(maskfile, in);
 235                                 if (ableToOpen == 1) { abort = true; }
 236                                 in.close();
 237                         }
 238
 239                         string temp;
 240                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
 241                         filter = m->isTrue(temp);
 242
 243                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 244                         m->setProcessors(temp);
 245                         m->mothurConvert(temp, processors);
 246
 247                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
 248                         m->mothurConvert(temp, window);
 249
 250                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
 251                         m->mothurConvert(temp, numwanted);
 252
 253                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 254                         save = m->isTrue(temp);
 255                         rdb->save = save;
 256                         if (save) { //clear out old references
 257                                 rdb->clearMemory();
 258                         }
 259
 260                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 261                         templatefile = validParameter.validFile(parameters, "reference", true);
 262                         if (templatefile == "not found") {
 263                                 //check for saved reference sequences
 264                                 if (rdb->referenceSeqs.size() != 0) {
 265                                         templatefile = "saved";
 266                                 }else {
 267                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 268                                         m->mothurOutEndLine();
 269                                         abort = true;
 270                                 }
 271                         }else if (templatefile == "not open") { abort = true; }
 272                         else {  if (save) {     rdb->setSavedReference(templatefile);   }       }
 273
 274
 275                 }
 276         }
 277         catch(exception& e) {
 278                 m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
 279                 exit(1);
 280         }
 281 }
 282 //***************************************************************************************************************
 283 int ChimeraCcodeCommand::execute(){
 284         try{
 285
 286                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 287
 288                 for (int s = 0; s < fastaFileNames.size(); s++) {
 289
 290                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 291
 292                         int start = time(NULL);
 293
 294                         //set user options
 295                         if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }
 296
 297                         chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir);
 298
 299                         //is your template aligned?
 300                         if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
 301                         templateSeqsLength = chimera->getLength();
 302
 303                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 304                         string outputFileName, accnosFileName;
 305             map<string, string> variables;
 306             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
 307             string mapInfo = getOutputFileName("mapinfo", variables);
 308                         if (maskfile != "") { variables["[tag]"] = maskfile; }
 309             outputFileName = getOutputFileName("chimera", variables);
 310             accnosFileName = getOutputFileName("accnos", variables);
 311
 312                         if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear(); return 0;        }
 313
 314                 #ifdef USE_MPI
 315
 316                                 int pid, numSeqsPerProcessor;
 317                                 int tag = 2001;
 318                                 vector<unsigned long long> MPIPos;
 319
 320                                 MPI_Status status;
 321                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 322                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 323
 324                                 MPI_File inMPI;
 325                                 MPI_File outMPI;
 326                                 MPI_File outMPIAccnos;
 327
 328                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 329                                 int inMode=MPI_MODE_RDONLY;
 330
 331                                 char outFilename[1024];
 332                                 strcpy(outFilename, outputFileName.c_str());
 333
 334                                 char outAccnosFilename[1024];
 335                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 336
 337                                 char inFileName[1024];
 338                                 strcpy(inFileName, fastaFileNames[s].c_str());
 339
 340                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 341                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 342                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 343
 344                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        } outputTypes.clear();  delete chimera; return 0;  }
 345
 346                                 if (pid == 0) { //you are the root process
 347                                         string outTemp = "For full window mapping info refer to " + mapInfo + "\n";
 348
 349                                         //print header
 350                                         int length = outTemp.length();
 351                                         char* buf2 = new char[length];
 352                                         memcpy(buf2, outTemp.c_str(), length);
 353
 354                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 355                                         delete buf2;
 356
 357                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 358
 359                                         //send file positions to all processes
 360                                         for(int i = 1; i < processors; i++) {
 361                                                 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 362                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 363                                         }
 364
 365                                         //figure out how many sequences you have to align
 366                                         numSeqsPerProcessor = numSeqs / processors;
 367                                         int startIndex =  pid * numSeqsPerProcessor;
 368                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 369
 370
 371                                         //align your part
 372                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 373
 374                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear();  delete chimera; return 0;  }
 375
 376                                 }else{ //you are a child process
 377                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 378                                         MPIPos.resize(numSeqs+1);
 379                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 380
 381                                         //figure out how many sequences you have to align
 382                                         numSeqsPerProcessor = numSeqs / processors;
 383                                         int startIndex =  pid * numSeqsPerProcessor;
 384                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 385
 386
 387                                         //align your part
 388                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 389
 390                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  outputTypes.clear(); delete chimera; return 0;  }
 391                                 }
 392
 393                                 //close files
 394                                 MPI_File_close(&inMPI);
 395                                 MPI_File_close(&outMPI);
 396                                 MPI_File_close(&outMPIAccnos);
 397
 398                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 399
 400                 #else
 401                         ofstream outHeader;
 402                         string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader";
 403                         m->openOutputFile(tempHeader, outHeader);
 404
 405                         outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
 406
 407                         outHeader.close();
 408
 409
 410
 411                         //break up file
 412                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 413                                 vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
 414
 415                                 for (int i = 0; i < (positions.size()-1); i++) {
 416                                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 417                                 }
 418
 419                                 if(processors == 1){
 420
 421                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 422
 423                                         if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 424
 425                                 }else{
 426                                         processIDS.resize(0);
 427
 428                                         numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
 429
 430                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 431                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 432
 433                                         //append output files
 434                                         for(int i=1;i<processors;i++){
 435                                                 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 436                                                 m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
 437                                         }
 438
 439                                         //append output files
 440                                         for(int i=1;i<processors;i++){
 441                                                 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 442                                                 m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
 443                                         }
 444
 445                                         if (m->control_pressed) {
 446                                                 m->mothurRemove(outputFileName);
 447                                                 m->mothurRemove(accnosFileName);
 448                                                 for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } outputTypes.clear();
 449                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 450                                                 delete chimera;
 451                                                 return 0;
 452                                         }
 453
 454                                 }
 455
 456                         #else
 457                                 lines.push_back(new linePair(0, 1000));
 458                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 459
 460                                 if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 461
 462                         #endif
 463
 464                         m->appendFiles(outputFileName, tempHeader);
 465
 466                         m->mothurRemove(outputFileName);
 467                         rename(tempHeader.c_str(), outputFileName.c_str());
 468                 #endif
 469
 470                         delete chimera;
 471
 472                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 473                         outputNames.push_back(mapInfo); outputTypes["mapinfo"].push_back(mapInfo);
 474                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 475
 476                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 477
 478                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 479                 }
 480
 481
 482                 //set accnos file as new current accnosfile
 483                 string current = "";
 484                 itTypes = outputTypes.find("accnos");
 485                 if (itTypes != outputTypes.end()) {
 486                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 487                 }
 488
 489                 m->mothurOutEndLine();
 490                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 491                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 492                 m->mothurOutEndLine();
 493
 494                 return 0;
 495
 496         }
 497         catch(exception& e) {
 498                 m->errorOut(e, "ChimeraCcodeCommand", "execute");
 499                 exit(1);
 500         }
 501 }
 502 //**********************************************************************************************************************
 503
 504 int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){
 505         try {
 506                 ofstream out;
 507                 m->openOutputFile(outputFName, out);
 508
 509                 ofstream out2;
 510                 m->openOutputFile(accnos, out2);
 511
 512                 ifstream inFASTA;
 513                 m->openInputFile(filename, inFASTA);
 514
 515                 inFASTA.seekg(filePos->start);
 516
 517                 bool done = false;
 518                 int count = 0;
 519
 520                 while (!done) {
 521
 522                         if (m->control_pressed) {       return 1;       }
 523
 524                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 525
 526                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 527
 528                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 529                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 530                                 }else{
 531                                         //find chimeras
 532                                         chimera->getChimeras(candidateSeq);
 533
 534                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 535
 536                                         //print results
 537                                         chimera->print(out, out2);
 538                                 }
 539                                 count++;
 540                         }
 541                         delete candidateSeq;
 542
 543                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 544                                 unsigned long long pos = inFASTA.tellg();
 545                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 546                         #else
 547                                 if (inFASTA.eof()) { break; }
 548                         #endif
 549
 550                         //report progress
 551                         if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
 552                 }
 553                 //report progress
 554                 if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");     }
 555
 556                 out.close();
 557                 out2.close();
 558                 inFASTA.close();
 559
 560                 return count;
 561         }
 562         catch(exception& e) {
 563                 m->errorOut(e, "ChimeraCcodeCommand", "driver");
 564                 exit(1);
 565         }
 566 }
 567 //**********************************************************************************************************************
 568 #ifdef USE_MPI
 569 int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
 570         try {
 571
 572                 MPI_Status status;
 573                 int pid;
 574                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 575
 576                 for(int i=0;i<num;i++){
 577
 578                         if (m->control_pressed) { return 0; }
 579
 580                         //read next sequence
 581                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 582
 583                         char* buf4 = new char[length];
 584
 585                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 586
 587                         string tempBuf = buf4;
 588                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 589                         istringstream iss (tempBuf,istringstream::in);
 590                         delete buf4;
 591
 592                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 593
 594                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 595
 596                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 597                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 598                                 }else{
 599                                         //find chimeras
 600                                         chimera->getChimeras(candidateSeq);
 601
 602                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 603
 604                                         //print results
 605                                         chimera->print(outMPI, outAccMPI);
 606                                 }
 607                         }
 608                         delete candidateSeq;
 609
 610                         //report progress
 611                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 612                 }
 613                 //report progress
 614                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 615
 616
 617                 return 0;
 618         }
 619         catch(exception& e) {
 620                 m->errorOut(e, "ChimeraCcodeCommand", "driverMPI");
 621                 exit(1);
 622         }
 623 }
 624 #endif
 625
 626 /**************************************************************************************************/
 627
 628 int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 629         try {
 630 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 631                 int process = 0;
 632                 int num = 0;
 633
 634                 //loop through and create all the processes you want
 635                 while (process != processors) {
 636                         int pid = fork();
 637
 638                         if (pid > 0) {
 639                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 640                                 process++;
 641                         }else if (pid == 0){
 642                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 643
 644                                 //pass numSeqs to parent
 645                                 ofstream out;
 646                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 647                                 m->openOutputFile(tempFile, out);
 648                                 out << num << endl;
 649                                 out.close();
 650
 651                                 exit(0);
 652                         }else {
 653                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 654                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 655                                 exit(0);
 656                         }
 657                 }
 658
 659                 //force parent to wait until all the processes are done
 660                 for (int i=0;i<processors;i++) {
 661                         int temp = processIDS[i];
 662                         wait(&temp);
 663                 }
 664
 665                 for (int i = 0; i < processIDS.size(); i++) {
 666                         ifstream in;
 667                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 668                         m->openInputFile(tempFile, in);
 669                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 670                         in.close(); m->mothurRemove(tempFile);
 671                 }
 672
 673                 return num;
 674 #endif
 675         }
 676         catch(exception& e) {
 677                 m->errorOut(e, "ChimeraCcodeCommand", "createProcesses");
 678                 exit(1);
 679         }
 680 }
 681 //**********************************************************************************************************************
 682