chimeraslayercommand.cpp

   1 /*
   2  *  chimeraslayercommand.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 "chimeraslayercommand.h"
  11 #include "chimeraslayer.h"
  12
  13
  14 //***************************************************************************************************************
  15
  16 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
  17         try {
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch",
  26                         "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string,string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33                         map<string,string>::iterator it;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  42                         if (inputDir == "not found"){   inputDir = "";          }
  43                         else {
  44                                 string path;
  45                                 it = parameters.find("template");
  46                                 //user has given a template file
  47                                 if(it != parameters.end()){
  48                                         path = hasPath(it->second);
  49                                         //if the user has not given a path then, add inputdir. else leave path alone.
  50                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  51                                 }
  52                         }
  53
  54
  55                         //check for required parameters
  56                         fastafile = validParameter.validFile(parameters, "fasta", false);
  57                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
  58                         else {
  59                                 splitAtDash(fastafile, fastaFileNames);
  60
  61                                 //go through files and make sure they are good, if not, then disregard them
  62                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  63                                         if (inputDir != "") {
  64                                                 string path = hasPath(fastaFileNames[i]);
  65                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  66                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  67                                         }
  68
  69                                         int ableToOpen;
  70                                         ifstream in;
  71
  72                                         #ifdef USE_MPI
  73                                                 int pid;
  74                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
  75                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  76
  77                                                 if (pid == 0) {
  78                                         #endif
  79
  80                                         ableToOpen = openInputFile(fastaFileNames[i], in);
  81                                         in.close();
  82
  83                                         #ifdef USE_MPI
  84                                                         for (int j = 1; j < processors; j++) {
  85                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
  86                                                         }
  87                                                 }else{
  88                                                         MPI_Status status;
  89                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
  90                                                 }
  91
  92                                         #endif
  93
  94                                         if (ableToOpen == 1) {
  95                                                 m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  96                                                 //erase from file list
  97                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
  98                                                 i--;
  99                                         }
 100                                 }
 101
 102                                 //make sure there is at least one valid file left
 103                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 104                         }
 105
 106                         //if the user changes the output directory command factory will send this info to us in the output parameter
 107                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 108                                 outputDir = "";
 109                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
 110                         }
 111
 112                         templatefile = validParameter.validFile(parameters, "template", true);
 113                         if (templatefile == "not open") { abort = true; }
 114                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
 115
 116                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
 117                         convert(temp, processors);
 118
 119                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 120                         convert(temp, ksize);
 121
 122                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 123                         convert(temp, window);
 124
 125                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 126                         convert(temp, match);
 127
 128                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 129                         convert(temp, mismatch);
 130
 131                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 132                         convert(temp, divR);
 133
 134                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 135                         convert(temp, minSimilarity);
 136
 137                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 138                         convert(temp, minCoverage);
 139
 140                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 141                         convert(temp, minBS);
 142
 143                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
 144                         convert(temp, minSNP);
 145
 146                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 147                         convert(temp, parents);
 148
 149                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
 150                         realign = isTrue(temp);
 151
 152                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
 153
 154                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "100"; }
 155                         convert(temp, iters);
 156
 157                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 158                         convert(temp, increment);
 159
 160                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 161                         convert(temp, numwanted);
 162
 163                         if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 164                 }
 165         }
 166         catch(exception& e) {
 167                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 168                 exit(1);
 169         }
 170 }
 171 //**********************************************************************************************************************
 172
 173 void ChimeraSlayerCommand::help(){
 174         try {
 175
 176                 m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 177                 m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
 178                 m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
 179                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 180                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n");
 181                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 182                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 183                 #ifdef USE_MPI
 184                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 185                 #endif
 186                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
 187                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
 188                 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
 189                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
 190                 m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
 191                 m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n");
 192                 m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
 193                 m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
 194                 m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
 195                 m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
 196                 m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
 197                 m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
 198                 m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
 199                 m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
 200                 m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false.  \n");
 201                 m->mothurOut("The chimera.slayer command should be in the following format: \n");
 202                 m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
 203                 m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
 204                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "ChimeraSlayerCommand", "help");
 208                 exit(1);
 209         }
 210 }
 211
 212 //***************************************************************************************************************
 213
 214 ChimeraSlayerCommand::~ChimeraSlayerCommand(){  /*      do nothing      */      }
 215
 216 //***************************************************************************************************************
 217
 218 int ChimeraSlayerCommand::execute(){
 219         try{
 220
 221                 if (abort == true) { return 0; }
 222
 223                 for (int s = 0; s < fastaFileNames.size(); s++) {
 224
 225                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 226
 227                         int start = time(NULL);
 228
 229                         chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 230
 231                         string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
 232                         string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 233
 234                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
 235
 236                         if (chimera->getUnaligned()) {
 237                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 238                                 delete chimera;
 239                                 return 0;
 240                         }
 241                         templateSeqsLength = chimera->getLength();
 242
 243                 #ifdef USE_MPI
 244                         int pid, end, numSeqsPerProcessor;
 245                                 int tag = 2001;
 246                                 vector<long> MPIPos;
 247
 248                                 MPI_Status status;
 249                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 250                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 251
 252                                 MPI_File inMPI;
 253                                 MPI_File outMPI;
 254                                 MPI_File outMPIAccnos;
 255
 256                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 257                                 int inMode=MPI_MODE_RDONLY;
 258
 259                                 char outFilename[1024];
 260                                 strcpy(outFilename, outputFileName.c_str());
 261
 262                                 char outAccnosFilename[1024];
 263                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 264
 265                                 char inFileName[1024];
 266                                 strcpy(inFileName, fastaFileNames[s].c_str());
 267
 268                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 269                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 270                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 271
 272                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
 273
 274                                 if (pid == 0) { //you are the root process
 275                                         m->mothurOutEndLine();
 276                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 277                                         m->mothurOutEndLine();
 278
 279                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 280
 281                                         //print header
 282                                         int length = outTemp.length();
 283                                         char* buf2 = new char[length];
 284                                         memcpy(buf2, outTemp.c_str(), length);
 285
 286                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 287                                         delete buf2;
 288
 289                                         MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 290
 291                                         //send file positions to all processes
 292                                         for(int i = 1; i < processors; i++) {
 293                                                 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 294                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 295                                         }
 296
 297                                         //figure out how many sequences you have to align
 298                                         numSeqsPerProcessor = numSeqs / processors;
 299                                         int startIndex =  pid * numSeqsPerProcessor;
 300                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 301
 302                                         //do your part
 303                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 304
 305                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 306
 307                                 }else{ //you are a child process
 308                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 309                                         MPIPos.resize(numSeqs+1);
 310                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 311
 312                                         //figure out how many sequences you have to align
 313                                         numSeqsPerProcessor = numSeqs / processors;
 314                                         int startIndex =  pid * numSeqsPerProcessor;
 315                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 316
 317                                         //do your part
 318                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 319
 320                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 321                                 }
 322
 323                                 //close files
 324                                 MPI_File_close(&inMPI);
 325                                 MPI_File_close(&outMPI);
 326                                 MPI_File_close(&outMPIAccnos);
 327                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 328
 329                 #else
 330                         ofstream outHeader;
 331                         string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 332                         openOutputFile(tempHeader, outHeader);
 333
 334                         chimera->printHeader(outHeader);
 335                         outHeader.close();
 336
 337                         //break up file
 338                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 339                                 if(processors == 1){
 340                                         ifstream inFASTA;
 341                                         openInputFile(fastaFileNames[s], inFASTA);
 342                                         getNumSeqs(inFASTA, numSeqs);
 343                                         inFASTA.close();
 344
 345                                         lines.push_back(new linePair(0, numSeqs));
 346
 347                                         driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 348
 349                                         if (m->control_pressed) {
 350                                                 remove(outputFileName.c_str());
 351                                                 remove(tempHeader.c_str());
 352                                                 remove(accnosFileName.c_str());
 353                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 354                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 355                                                 delete chimera;
 356                                                 return 0;
 357                                         }
 358
 359                                 }else{
 360                                         vector<int> positions;
 361                                         processIDS.resize(0);
 362
 363                                         ifstream inFASTA;
 364                                         openInputFile(fastaFileNames[s], inFASTA);
 365
 366                                         string input;
 367                                         while(!inFASTA.eof()){
 368                                                 input = getline(inFASTA);
 369                                                 if (input.length() != 0) {
 370                                                         if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 371                                                 }
 372                                         }
 373                                         inFASTA.close();
 374
 375                                         numSeqs = positions.size();
 376
 377                                         int numSeqsPerProcessor = numSeqs / processors;
 378
 379                                         for (int i = 0; i < processors; i++) {
 380                                                 long int startPos = positions[ i * numSeqsPerProcessor ];
 381                                                 if(i == processors - 1){
 382                                                         numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 383                                                 }
 384                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 385                                         }
 386
 387                                         createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
 388
 389                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 390                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 391
 392                                         //append output files
 393                                         for(int i=1;i<processors;i++){
 394                                                 appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 395                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 396                                         }
 397
 398                                         //append output files
 399                                         for(int i=1;i<processors;i++){
 400                                                 appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 401                                                 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
 402                                         }
 403
 404                                         if (m->control_pressed) {
 405                                                 remove(outputFileName.c_str());
 406                                                 remove(accnosFileName.c_str());
 407                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 408                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 409                                                 delete chimera;
 410                                                 return 0;
 411                                         }
 412
 413                                 }
 414
 415                         #else
 416                                 ifstream inFASTA;
 417                                 openInputFile(fastaFileNames[s], inFASTA);
 418                                 getNumSeqs(inFASTA, numSeqs);
 419                                 inFASTA.close();
 420                                 lines.push_back(new linePair(0, numSeqs));
 421
 422                                 driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 423
 424                                 if (m->control_pressed) {
 425                                                 remove(outputFileName.c_str());
 426                                                 remove(tempHeader.c_str());
 427                                                 remove(accnosFileName.c_str());
 428                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 429                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 430                                                 delete chimera;
 431                                                 return 0;
 432                                 }
 433
 434                         #endif
 435
 436                         appendFiles(outputFileName, tempHeader);
 437
 438                         remove(outputFileName.c_str());
 439                         rename(tempHeader.c_str(), outputFileName.c_str());
 440
 441                 #endif
 442                         delete chimera;
 443
 444
 445                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 446
 447                         outputNames.push_back(outputFileName);
 448                         outputNames.push_back(accnosFileName);
 449
 450                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 451                 }
 452
 453                 m->mothurOutEndLine();
 454                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 455                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 456                 m->mothurOutEndLine();
 457
 458                 return 0;
 459
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 463                 exit(1);
 464         }
 465 }
 466 //**********************************************************************************************************************
 467
 468 int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 469         try {
 470                 ofstream out;
 471                 openOutputFile(outputFName, out);
 472
 473                 ofstream out2;
 474                 openOutputFile(accnos, out2);
 475
 476                 ifstream inFASTA;
 477                 openInputFile(filename, inFASTA);
 478
 479                 inFASTA.seekg(line->start);
 480
 481                 for(int i=0;i<line->numSeqs;i++){
 482
 483                         if (m->control_pressed) {       return 1;       }
 484
 485                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 486
 487                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 488
 489                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 490                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 491                                 }else{
 492                                         //find chimeras
 493                                         chimera->getChimeras(candidateSeq);
 494
 495                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 496
 497                                         //print results
 498                                         chimera->print(out, out2);
 499                                 }
 500                         }
 501                         delete candidateSeq;
 502
 503                         //report progress
 504                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 505                 }
 506                 //report progress
 507                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 508
 509                 out.close();
 510                 out2.close();
 511                 inFASTA.close();
 512
 513                 return 0;
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 517                 exit(1);
 518         }
 519 }
 520 //**********************************************************************************************************************
 521 #ifdef USE_MPI
 522 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 523         try {
 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 1;       }
 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
 542                         delete buf4;
 543
 544                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 545
 546                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 547
 548                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 549                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 550                                 }else{
 551
 552                                         //find chimeras
 553                                         chimera->getChimeras(candidateSeq);
 554
 555                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 556                 //cout << "about to print" << endl;
 557                                         //print results
 558                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 559                                 }
 560                         }
 561                         delete candidateSeq;
 562
 563                         //report progress
 564                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 565                 }
 566                 //report progress
 567                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 568
 569
 570                 return 0;
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 574                 exit(1);
 575         }
 576 }
 577 #endif
 578
 579 /**************************************************************************************************/
 580
 581 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
 582         try {
 583 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 584                 int process = 0;
 585                 //              processIDS.resize(0);
 586
 587                 //loop through and create all the processes you want
 588                 while (process != processors) {
 589                         int pid = fork();
 590
 591                         if (pid > 0) {
 592                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 593                                 process++;
 594                         }else if (pid == 0){
 595                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 596                                 exit(0);
 597                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 598                 }
 599
 600                 //force parent to wait until all the processes are done
 601                 for (int i=0;i<processors;i++) {
 602                         int temp = processIDS[i];
 603                         wait(&temp);
 604                 }
 605
 606                 return 0;
 607 #endif
 608         }
 609         catch(exception& e) {
 610                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 611                 exit(1);
 612         }
 613 }
 614
 615 /**************************************************************************************************/
 616
 617