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-amzon.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                         bool hasAccnos = true;
 234
 235                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
 236
 237                         if (chimera->getUnaligned()) {
 238                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 239                                 delete chimera;
 240                                 return 0;
 241                         }
 242                         templateSeqsLength = chimera->getLength();
 243
 244                 #ifdef USE_MPI
 245                         int pid, end, numSeqsPerProcessor;
 246                                 int tag = 2001;
 247                                 vector<long> MPIPos;
 248                                 MPIWroteAccnos = false;
 249
 250                                 MPI_Status status;
 251                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 252                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 253
 254                                 MPI_File inMPI;
 255                                 MPI_File outMPI;
 256                                 MPI_File outMPIAccnos;
 257
 258                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 259                                 int inMode=MPI_MODE_RDONLY;
 260
 261                                 char outFilename[1024];
 262                                 strcpy(outFilename, outputFileName.c_str());
 263
 264                                 char outAccnosFilename[1024];
 265                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 266
 267                                 char inFileName[1024];
 268                                 strcpy(inFileName, fastaFileNames[s].c_str());
 269
 270                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 271                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 272                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 273
 274                                 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;  }
 275
 276                                 if (pid == 0) { //you are the root process
 277                                         m->mothurOutEndLine();
 278                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 279                                         m->mothurOutEndLine();
 280
 281                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 282
 283                                         //print header
 284                                         int length = outTemp.length();
 285                                         char* buf2 = new char[length];
 286                                         memcpy(buf2, outTemp.c_str(), length);
 287
 288                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 289                                         delete buf2;
 290
 291                                         MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 292
 293                                         //send file positions to all processes
 294                                         for(int i = 1; i < processors; i++) {
 295                                                 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 296                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 297                                         }
 298
 299                                         //figure out how many sequences you have to align
 300                                         numSeqsPerProcessor = numSeqs / processors;
 301                                         int startIndex =  pid * numSeqsPerProcessor;
 302                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 303
 304                                         //do your part
 305                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 306
 307                                         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;  }
 308
 309                                         for (int i = 1; i < processors; i++) {
 310                                                 bool tempResult;
 311                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 312                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 313                                         }
 314                                 }else{ //you are a child process
 315                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 316                                         MPIPos.resize(numSeqs+1);
 317                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 318
 319                                         //figure out how many sequences you have to align
 320                                         numSeqsPerProcessor = numSeqs / processors;
 321                                         int startIndex =  pid * numSeqsPerProcessor;
 322                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 323
 324                                         //do your part
 325                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 326
 327                                         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;  }
 328
 329                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 330                                 }
 331
 332                                 //close files
 333                                 MPI_File_close(&inMPI);
 334                                 MPI_File_close(&outMPI);
 335                                 MPI_File_close(&outMPIAccnos);
 336                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 337
 338                                 //delete accnos file if blank
 339                                 if (pid == 0) {
 340                                         if (!MPIWroteAccnos) {
 341                                                 hasAccnos = false;
 342                                                 remove(accnosFileName.c_str());
 343                                         }
 344                                 }
 345
 346                 #else
 347                         ofstream outHeader;
 348                         string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 349                         openOutputFile(tempHeader, outHeader);
 350
 351                         chimera->printHeader(outHeader);
 352                         outHeader.close();
 353
 354                         //break up file
 355                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 356                                 if(processors == 1){
 357                                         ifstream inFASTA;
 358                                         openInputFile(fastaFileNames[s], inFASTA);
 359                                         getNumSeqs(inFASTA, numSeqs);
 360                                         inFASTA.close();
 361
 362                                         lines.push_back(new linePair(0, numSeqs));
 363
 364                                         driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 365
 366                                         if (m->control_pressed) {
 367                                                 remove(outputFileName.c_str());
 368                                                 remove(tempHeader.c_str());
 369                                                 remove(accnosFileName.c_str());
 370                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 371                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 372                                                 delete chimera;
 373                                                 return 0;
 374                                         }
 375
 376                                         //delete accnos file if its blank
 377                                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 378
 379                                 }else{
 380                                         vector<int> positions;
 381                                         processIDS.resize(0);
 382
 383                                         ifstream inFASTA;
 384                                         openInputFile(fastaFileNames[s], inFASTA);
 385
 386                                         string input;
 387                                         while(!inFASTA.eof()){
 388                                                 input = getline(inFASTA);
 389                                                 if (input.length() != 0) {
 390                                                         if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 391                                                 }
 392                                         }
 393                                         inFASTA.close();
 394
 395                                         numSeqs = positions.size();
 396
 397                                         int numSeqsPerProcessor = numSeqs / processors;
 398
 399                                         for (int i = 0; i < processors; i++) {
 400                                                 long int startPos = positions[ i * numSeqsPerProcessor ];
 401                                                 if(i == processors - 1){
 402                                                         numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 403                                                 }
 404                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 405                                         }
 406
 407                                         createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
 408
 409                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 410
 411                                         //append output files
 412                                         for(int i=1;i<processors;i++){
 413                                                 appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 414                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 415                                         }
 416
 417                                         vector<string> nonBlankAccnosFiles;
 418                                         //delete blank accnos files generated with multiple processes
 419                                         for(int i=0;i<processors;i++){
 420                                                 if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 421                                                         nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 422                                                 }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 423                                         }
 424
 425                                         //append accnos files
 426                                         if (nonBlankAccnosFiles.size() != 0) {
 427                                                 rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 428
 429                                                 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 430                                                         appendFiles(nonBlankAccnosFiles[h], accnosFileName);
 431                                                         remove(nonBlankAccnosFiles[h].c_str());
 432                                                 }
 433                                         }else{ hasAccnos = false;  }
 434
 435                                         if (m->control_pressed) {
 436                                                 remove(outputFileName.c_str());
 437                                                 remove(accnosFileName.c_str());
 438                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 439                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 440                                                 delete chimera;
 441                                                 return 0;
 442                                         }
 443
 444                                 }
 445
 446                         #else
 447                                 ifstream inFASTA;
 448                                 openInputFile(fastaFileNames[s], inFASTA);
 449                                 getNumSeqs(inFASTA, numSeqs);
 450                                 inFASTA.close();
 451                                 lines.push_back(new linePair(0, numSeqs));
 452
 453                                 driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 454
 455                                 if (m->control_pressed) {
 456                                                 remove(outputFileName.c_str());
 457                                                 remove(tempHeader.c_str());
 458                                                 remove(accnosFileName.c_str());
 459                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 460                                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 461                                                 delete chimera;
 462                                                 return 0;
 463                                 }
 464
 465                                 //delete accnos file if its blank
 466                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 467                         #endif
 468
 469                         appendFiles(outputFileName, tempHeader);
 470
 471                         remove(outputFileName.c_str());
 472                         rename(tempHeader.c_str(), outputFileName.c_str());
 473
 474                 #endif
 475                         delete chimera;
 476
 477
 478                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 479
 480                         outputNames.push_back(outputFileName);
 481                         if (hasAccnos) { outputNames.push_back(accnosFileName); }
 482
 483                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 484                         }
 485
 486                 m->mothurOutEndLine();
 487                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 488                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 489                 m->mothurOutEndLine();
 490
 491                 return 0;
 492
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 496                 exit(1);
 497         }
 498 }
 499 //**********************************************************************************************************************
 500
 501 int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
 502         try {
 503                 ofstream out;
 504                 openOutputFile(outputFName, out);
 505
 506                 ofstream out2;
 507                 openOutputFile(accnos, out2);
 508
 509                 ifstream inFASTA;
 510                 openInputFile(filename, inFASTA);
 511
 512                 inFASTA.seekg(line->start);
 513
 514                 for(int i=0;i<line->numSeqs;i++){
 515
 516                         if (m->control_pressed) {       return 1;       }
 517
 518                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 519
 520                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 521
 522                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 523                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 524                                 }else{
 525                                         //find chimeras
 526                                         chimera->getChimeras(candidateSeq);
 527
 528                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 529
 530                                         //print results
 531                                         chimera->print(out, out2);
 532                                 }
 533                         }
 534                         delete candidateSeq;
 535
 536                         //report progress
 537                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 538                 }
 539                 //report progress
 540                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 541
 542                 out.close();
 543                 out2.close();
 544                 inFASTA.close();
 545
 546                 return 0;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 550                 exit(1);
 551         }
 552 }
 553 //**********************************************************************************************************************
 554 #ifdef USE_MPI
 555 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
 556         try {
 557                 MPI_Status status;
 558                 int pid;
 559                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 560
 561                 for(int i=0;i<num;i++){
 562
 563                         if (m->control_pressed) {       return 1;       }
 564
 565                         //read next sequence
 566                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 567
 568                         char* buf4 = new char[length];
 569                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 570
 571                         string tempBuf = buf4;
 572                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 573                         istringstream iss (tempBuf,istringstream::in);
 574
 575                         delete buf4;
 576
 577                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 578
 579                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 580
 581                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 582                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 583                                 }else{
 584
 585                                         //find chimeras
 586                                         chimera->getChimeras(candidateSeq);
 587
 588                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 589                 //cout << "about to print" << endl;
 590                                         //print results
 591                                         bool isChimeric = chimera->print(outMPI, outAccMPI);
 592                                         if (isChimeric) { MPIWroteAccnos = true;  }
 593
 594                                 }
 595                         }
 596                         delete candidateSeq;
 597
 598                         //report progress
 599                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 600                 }
 601                 //report progress
 602                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 603
 604
 605                 return 0;
 606         }
 607         catch(exception& e) {
 608                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 609                 exit(1);
 610         }
 611 }
 612 #endif
 613
 614 /**************************************************************************************************/
 615
 616 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
 617         try {
 618 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 619                 int process = 0;
 620                 //              processIDS.resize(0);
 621
 622                 //loop through and create all the processes you want
 623                 while (process != processors) {
 624                         int pid = fork();
 625
 626                         if (pid > 0) {
 627                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 628                                 process++;
 629                         }else if (pid == 0){
 630                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
 631                                 exit(0);
 632                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 633                 }
 634
 635                 //force parent to wait until all the processes are done
 636                 for (int i=0;i<processors;i++) {
 637                         int temp = processIDS[i];
 638                         wait(&temp);
 639                 }
 640
 641                 return 0;
 642 #endif
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 646                 exit(1);
 647         }
 648 }
 649
 650 /**************************************************************************************************/
 651
 652