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()];\r
 171                         memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 172
 173                         char* inFileName = new char[fastafile.length()];\r
 174                         memcpy(inFileName, fastafile.c_str(), fastafile.length());
 175
 176                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 177                         MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 178
 179                         delete outFilename;
 180                         delete inFileName;
 181
 182                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  delete chimera; return 0;  }
 183
 184                         if (pid == 0) { //you are the root process
 185                                 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 186
 187                                 //send file positions to all processes
 188                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 189                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 190
 191                                 //figure out how many sequences you have to align
 192                                 numSeqsPerProcessor = numSeqs / processors;
 193                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 194                                 int startIndex =  pid * numSeqsPerProcessor;
 195
 196                                 //align your part
 197                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 198
 199                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  remove(outputFileName.c_str());  delete chimera; return 0;  }
 200
 201                                 //wait on chidren
 202                                 for(int i = 1; i < processors; i++) {
 203                                         char buf[4];
 204                                         MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 205                                 }
 206                         }else{ //you are a child process
 207                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 208                                 MPIPos.resize(numSeqs+1);
 209                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 210
 211                                 //figure out how many sequences you have to align
 212                                 numSeqsPerProcessor = numSeqs / processors;
 213                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 214                                 int startIndex =  pid * numSeqsPerProcessor;
 215
 216                                 //align your part
 217                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 218
 219                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   delete chimera; return 0;  }
 220
 221                                 //tell parent you are done.
 222                                 char buf[4];
 223                                 strcpy(buf, "done");
 224                                 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 225                         }
 226
 227                         //close files
 228                         MPI_File_close(&inMPI);
 229                         MPI_File_close(&outMPI);
 230         #else
 231
 232                 //break up file
 233                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 234                         if(processors == 1){
 235                                 ifstream inFASTA;
 236                                 openInputFile(fastafile, inFASTA);
 237                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 238                                 inFASTA.close();
 239
 240                                 lines.push_back(new linePair(0, numSeqs));
 241
 242                                 driver(lines[0], outputFileName, fastafile);
 243
 244                                 if (m->control_pressed) {
 245                                         remove(outputFileName.c_str());
 246                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 247                                         delete chimera;
 248                                         return 0;
 249                                 }
 250
 251                         }else{
 252                                 vector<int> positions;
 253                                 processIDS.resize(0);
 254
 255                                 ifstream inFASTA;
 256                                 openInputFile(fastafile, inFASTA);
 257
 258                                 string input;
 259                                 while(!inFASTA.eof()){
 260                                         input = getline(inFASTA);
 261                                         if (input.length() != 0) {
 262                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 263                                         }
 264                                 }
 265                                 inFASTA.close();
 266
 267                                 numSeqs = positions.size();
 268
 269                                 int numSeqsPerProcessor = numSeqs / processors;
 270
 271                                 for (int i = 0; i < processors; i++) {
 272                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 273                                         if(i == processors - 1){
 274                                                 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
 275                                         }
 276                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 277                                 }
 278
 279
 280                                 createProcesses(outputFileName, fastafile);
 281
 282                                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 283
 284                                 //append output files
 285                                 for(int i=1;i<processors;i++){
 286                                         appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 287                                         remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 288                                 }
 289
 290                                 if (m->control_pressed) {
 291                                         remove(outputFileName.c_str());
 292                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 293                                         delete chimera;
 294                                         return 0;
 295                                 }
 296                         }
 297
 298                 #else
 299                         ifstream inFASTA;
 300                         openInputFile(fastafile, inFASTA);
 301                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 302                         inFASTA.close();
 303                         lines.push_back(new linePair(0, numSeqs));
 304
 305                         driver(lines[0], outputFileName, fastafile);
 306
 307                         if (m->control_pressed) {
 308                                         remove(outputFileName.c_str());
 309                                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 310                                         delete chimera;
 311                                         return 0;
 312                         }
 313                 #endif
 314         #endif
 315                 delete chimera;
 316                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 317
 318                 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();
 319
 320                 m->mothurOutEndLine();
 321                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 322                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 323                 m->mothurOutEndLine();
 324                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 325
 326                 return 0;
 327
 328         }
 329         catch(exception& e) {
 330                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 331                 exit(1);
 332         }
 333 }
 334 //**********************************************************************************************************************
 335
 336 int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filename){
 337         try {
 338                 ofstream out;
 339                 openOutputFile(outputFName, out);
 340
 341                 ofstream out2;
 342
 343                 ifstream inFASTA;
 344                 openInputFile(filename, inFASTA);
 345
 346                 inFASTA.seekg(line->start);
 347
 348                 for(int i=0;i<line->numSeqs;i++){
 349
 350                         if (m->control_pressed) {       return 1;       }
 351
 352                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 353
 354                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 355                                 //find chimeras
 356                                 chimera->getChimeras(candidateSeq);
 357
 358                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 359
 360                                 //print results
 361                                 chimera->print(out, out2);
 362                         }
 363                         delete candidateSeq;
 364
 365                         //report progress
 366                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 367                 }
 368                 //report progress
 369                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 370
 371                 out.close();
 372                 inFASTA.close();
 373
 374                 return 0;
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 378                 exit(1);
 379         }
 380 }
 381 //**********************************************************************************************************************
 382 #ifdef USE_MPI
 383 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
 384         try {
 385                 MPI_File outAccMPI;
 386                 MPI_Status status;
 387                 int pid;
 388                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 389
 390                 for(int i=0;i<num;i++){
 391
 392                         if (m->control_pressed) { return 0; }
 393
 394                         //read next sequence
 395                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 396
 397                         char* buf4 = new char[length];
 398                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 399
 400                         string tempBuf = buf4;
 401                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 402                         istringstream iss (tempBuf,istringstream::in);
 403                         delete buf4;
 404
 405                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 406
 407                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 408                                 //find chimeras
 409                                 chimera->getChimeras(candidateSeq);
 410
 411                                 //print results
 412                                 chimera->print(outMPI, outAccMPI);
 413                         }
 414                         delete candidateSeq;
 415
 416                         //report progress
 417                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 418                 }
 419                 //report progress
 420                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 421
 422                 return 0;
 423         }
 424         catch(exception& e) {
 425                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 426                 exit(1);
 427         }
 428 }
 429 #endif
 430
 431 /**************************************************************************************************/
 432
 433 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 434         try {
 435 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 436                 int process = 0;
 437                 //              processIDS.resize(0);
 438
 439                 //loop through and create all the processes you want
 440                 while (process != processors) {
 441                         int pid = fork();
 442
 443                         if (pid > 0) {
 444                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 445                                 process++;
 446                         }else if (pid == 0){
 447                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 448                                 exit(0);
 449                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 450                 }
 451
 452                 //force parent to wait until all the processes are done
 453                 for (int i=0;i<processors;i++) {
 454                         int temp = processIDS[i];
 455                         wait(&temp);
 456                 }
 457
 458                 return 0;
 459 #endif
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 463                 exit(1);
 464         }
 465 }
 466 /**************************************************************************************************/
 467
 468