chimeracheckcommand.cpp

   1 /*
   2  *  chimeracheckcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeracheckcommand.h"
  11 #include "chimeracheckrdp.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 string path;
  43                                 it = parameters.find("fasta");
  44                                 //user has given a template file
  45                                 if(it != parameters.end()){
  46                                         path = hasPath(it->second);
  47                                         //if the user has not given a path then, add inputdir. else leave path alone.
  48                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  49                                 }
  50
  51                                 it = parameters.find("template");
  52                                 //user has given a template file
  53                                 if(it != parameters.end()){
  54                                         path = hasPath(it->second);
  55                                         //if the user has not given a path then, add inputdir. else leave path alone.
  56                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  57                                 }
  58
  59                                 it = parameters.find("name");
  60                                 //user has given a template file
  61                                 if(it != parameters.end()){
  62                                         path = hasPath(it->second);
  63                                         //if the user has not given a path then, add inputdir. else leave path alone.
  64                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  65                                 }
  66                         }
  67
  68
  69                         //check for required parameters
  70                         fastafile = validParameter.validFile(parameters, "fasta", true);
  71                         if (fastafile == "not open") { abort = true; }
  72                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
  73
  74                         //if the user changes the output directory command factory will send this info to us in the output parameter
  75                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  76                                 outputDir = "";
  77                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  78                         }
  79
  80                         templatefile = validParameter.validFile(parameters, "template", true);
  81                         if (templatefile == "not open") { abort = true; }
  82                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
  83
  84                         namefile = validParameter.validFile(parameters, "name", true);
  85                         if (namefile == "not open") { abort = true; }
  86                         else if (namefile == "not found") { namefile = "";  }
  87
  88                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
  89                         convert(temp, processors);
  90
  91                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
  92                         convert(temp, ksize);
  93
  94                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
  95                         svg = isTrue(temp);
  96
  97                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
  98                         convert(temp, increment);
  99                 }
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108 void ChimeraCheckCommand::help(){
 109         try {
 110
 111                 m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 112                 m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
 113                 m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
 114                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 115                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 116                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 117                 #ifdef USE_MPI
 118                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 119                 #endif
 120                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n");
 121                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
 122                 m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n");
 123                 m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 124                 m->mothurOut("The chimera.check command should be in the following format: \n");
 125                 m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
 126                 m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
 127                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 128         }
 129         catch(exception& e) {
 130                 m->errorOut(e, "ChimeraCheckCommand", "help");
 131                 exit(1);
 132         }
 133 }
 134
 135 //***************************************************************************************************************
 136
 137 ChimeraCheckCommand::~ChimeraCheckCommand(){    /*      do nothing      */      }
 138
 139 //***************************************************************************************************************
 140
 141 int ChimeraCheckCommand::execute(){
 142         try{
 143
 144                 if (abort == true) { return 0; }
 145
 146                 int start = time(NULL);
 147
 148                 chimera = new ChimeraCheckRDP(fastafile, templatefile, namefile, svg, increment, ksize, outputDir);
 149
 150                 if (m->control_pressed) { delete chimera;       return 0;       }
 151
 152                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile))  + "chimeracheck.chimeras";
 153
 154         #ifdef USE_MPI
 155
 156                         int pid, end, numSeqsPerProcessor;
 157                         int tag = 2001;
 158                         vector<long> MPIPos;
 159
 160                         MPI_Status status;
 161                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 162                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 163
 164                         MPI_File inMPI;
 165                         MPI_File outMPI;
 166
 167                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 168                         int inMode=MPI_MODE_RDONLY;
 169
 170                         //char* outFilename = new char[outputFileName.length()];
 171                         //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 172
 173                         char outFilename[1024];
 174                         strcpy(outFilename, outputFileName.c_str());
 175
 176                         //char* inFileName = new char[fastafile.length()];
 177                         //memcpy(inFileName, fastafile.c_str(), fastafile.length());
 178
 179                         char inFileName[1024];
 180                         strcpy(inFileName, fastafile.c_str());
 181
 182                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 183                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 184
 185                         //delete outFilename;
 186                         //delete inFileName;
 187
 188                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  delete chimera; return 0;  }
 189
 190                         if (pid == 0) { //you are the root process
 191                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 192
 193                                 //send file positions to all processes
 194                                 for(int i = 1; i < processors; i++) {
 195                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 196                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 197                                 }
 198
 199                                 //figure out how many sequences you have to align
 200                                 numSeqsPerProcessor = numSeqs / processors;
 201                                 int startIndex =  pid * numSeqsPerProcessor;
 202                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 203
 204
 205                                 //align your part
 206                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 207
 208                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  remove(outputFileName.c_str());  delete chimera; return 0;  }
 209
 210                                 //wait on chidren
 211                                 for(int i = 1; i < processors; i++) {
 212                                         char buf[4];
 213                                         MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 214                                 }
 215                         }else{ //you are a child process
 216                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 217                                 MPIPos.resize(numSeqs+1);
 218                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 219
 220                                 //figure out how many sequences you have to align
 221                                 numSeqsPerProcessor = numSeqs / processors;
 222                                 int startIndex =  pid * numSeqsPerProcessor;
 223                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 224
 225
 226                                 //align your part
 227                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 228
 229                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   delete chimera; return 0;  }
 230
 231                                 //tell parent you are done.
 232                                 char buf[4];
 233                                 strcpy(buf, "done");
 234                                 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 235                         }
 236
 237                         //close files
 238                         MPI_File_close(&inMPI);
 239                         MPI_File_close(&outMPI);
 240                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 241         #else
 242
 243                 //break up file
 244                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 245                         if(processors == 1){
 246                                 ifstream inFASTA;
 247                                 openInputFile(fastafile, inFASTA);
 248                                 getNumSeqs(inFASTA, numSeqs);
 249                                 inFASTA.close();
 250
 251                                 lines.push_back(new linePair(0, numSeqs));
 252
 253                                 driver(lines[0], outputFileName, fastafile);
 254
 255                                 if (m->control_pressed) {
 256                                         remove(outputFileName.c_str());
 257                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 258                                         delete chimera;
 259                                         return 0;
 260                                 }
 261
 262                         }else{
 263                                 vector<int> positions;
 264                                 processIDS.resize(0);
 265
 266                                 ifstream inFASTA;
 267                                 openInputFile(fastafile, inFASTA);
 268
 269                                 string input;
 270                                 while(!inFASTA.eof()){
 271                                         input = getline(inFASTA);
 272                                         if (input.length() != 0) {
 273                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 274                                         }
 275                                 }
 276                                 inFASTA.close();
 277
 278                                 numSeqs = positions.size();
 279
 280                                 int numSeqsPerProcessor = numSeqs / processors;
 281
 282                                 for (int i = 0; i < processors; i++) {
 283                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 284                                         if(i == processors - 1){
 285                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 286                                         }
 287                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 288                                 }
 289
 290
 291                                 createProcesses(outputFileName, fastafile);
 292
 293                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 294
 295                                 //append output files
 296                                 for(int i=1;i<processors;i++){
 297                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 298                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 299                                 }
 300
 301                                 if (m->control_pressed) {
 302                                         remove(outputFileName.c_str());
 303                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 304                                         delete chimera;
 305                                         return 0;
 306                                 }
 307                         }
 308
 309                 #else
 310                         ifstream inFASTA;
 311                         openInputFile(fastafile, inFASTA);
 312                         getNumSeqs(inFASTA, numSeqs);
 313                         inFASTA.close();
 314                         lines.push_back(new linePair(0, numSeqs));
 315
 316                         driver(lines[0], outputFileName, fastafile);
 317
 318                         if (m->control_pressed) {
 319                                         remove(outputFileName.c_str());
 320                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 321                                         delete chimera;
 322                                         return 0;
 323                         }
 324                 #endif
 325         #endif
 326                 delete chimera;
 327                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 328
 329                 m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
 330
 331                 m->mothurOutEndLine();
 332                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 333                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 334                 m->mothurOutEndLine();
 335                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 336
 337                 return 0;
 338
 339         }
 340         catch(exception& e) {
 341                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 342                 exit(1);
 343         }
 344 }
 345 //**********************************************************************************************************************
 346
 347 int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filename){
 348         try {
 349                 ofstream out;
 350                 openOutputFile(outputFName, out);
 351
 352                 ofstream out2;
 353
 354                 ifstream inFASTA;
 355                 openInputFile(filename, inFASTA);
 356
 357                 inFASTA.seekg(line->start);
 358
 359                 for(int i=0;i<line->numSeqs;i++){
 360
 361                         if (m->control_pressed) {       return 1;       }
 362
 363                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 364
 365                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 366                                 //find chimeras
 367                                 chimera->getChimeras(candidateSeq);
 368
 369                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 370
 371                                 //print results
 372                                 chimera->print(out, out2);
 373                         }
 374                         delete candidateSeq;
 375
 376                         //report progress
 377                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 378                 }
 379                 //report progress
 380                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 381
 382                 out.close();
 383                 inFASTA.close();
 384
 385                 return 0;
 386         }
 387         catch(exception& e) {
 388                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 389                 exit(1);
 390         }
 391 }
 392 //**********************************************************************************************************************
 393 #ifdef USE_MPI
 394 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
 395         try {
 396                 MPI_File outAccMPI;
 397                 MPI_Status status;
 398                 int pid;
 399                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 400
 401                 for(int i=0;i<num;i++){
 402
 403                         if (m->control_pressed) { return 0; }
 404
 405                         //read next sequence
 406                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 407
 408                         char* buf4 = new char[length];
 409                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 410
 411                         string tempBuf = buf4;
 412                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 413                         istringstream iss (tempBuf,istringstream::in);
 414                         delete buf4;
 415
 416                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 417
 418                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 419                                 //find chimeras
 420                                 chimera->getChimeras(candidateSeq);
 421
 422                                 //print results
 423                                 chimera->print(outMPI, outAccMPI);
 424                         }
 425                         delete candidateSeq;
 426
 427                         //report progress
 428                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 429                 }
 430                 //report progress
 431                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 432
 433                 return 0;
 434         }
 435         catch(exception& e) {
 436                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 437                 exit(1);
 438         }
 439 }
 440 #endif
 441
 442 /**************************************************************************************************/
 443
 444 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 445         try {
 446 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 447                 int process = 0;
 448                 //              processIDS.resize(0);
 449
 450                 //loop through and create all the processes you want
 451                 while (process != processors) {
 452                         int pid = fork();
 453
 454                         if (pid > 0) {
 455                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 456                                 process++;
 457                         }else if (pid == 0){
 458                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 459                                 exit(0);
 460                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 461                 }
 462
 463                 //force parent to wait until all the processes are done
 464                 for (int i=0;i<processors;i++) {
 465                         int temp = processIDS[i];
 466                         wait(&temp);
 467                 }
 468
 469                 return 0;
 470 #endif
 471         }
 472         catch(exception& e) {
 473                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 474                 exit(1);
 475         }
 476 }
 477 /**************************************************************************************************/
 478
 479