filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 /**************************************************************************************/
  14
  15 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 filterFileName = "";
  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", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter("filter.seqs");
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = m->hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("hard");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = m->hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
  58                                 }
  59                         }
  60
  61                         //check for required parameters
  62                         fasta = validParameter.validFile(parameters, "fasta", false);
  63                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
  64                         else {
  65                                 m->splitAtDash(fasta, fastafileNames);
  66
  67                                 //go through files and make sure they are good, if not, then disregard them
  68                                 for (int i = 0; i < fastafileNames.size(); i++) {
  69                                         if (inputDir != "") {
  70                                                 string path = m->hasPath(fastafileNames[i]);
  71                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  72                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
  73                                         }
  74
  75                                         ifstream in;
  76                                         int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
  77
  78                                         //if you can't open it, try default location
  79                                         if (ableToOpen == 1) {
  80                                                 if (m->getDefaultPath() != "") { //default path is set
  81                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
  82                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  83                                                         ableToOpen = m->openInputFile(tryPath, in, "noerror");
  84                                                         fastafileNames[i] = tryPath;
  85                                                 }
  86                                         }
  87                                         in.close();
  88
  89                                         if (ableToOpen == 1) {
  90                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
  91                                                 //erase from file list
  92                                                 fastafileNames.erase(fastafileNames.begin()+i);
  93                                                 i--;
  94                                         }else{
  95                                                 string simpleName = m->getSimpleName(fastafileNames[i]);
  96                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  97                                         }
  98                                         in.close();
  99                                 }
 100
 101                                 //make sure there is at least one valid file left
 102                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 103                         }
 104
 105                         if (!abort) {
 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 += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 110                                 }
 111                         }
 112                         //check for optional parameter and set defaults
 113                         // ...at some point should added some additional type checking...
 114
 115                         string temp;
 116                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 117                         else if (hard == "not open") { hard = ""; abort = true; }
 118
 119                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 120                         trump = temp[0];
 121
 122                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 123                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 124
 125                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 126                         convert(temp, processors);
 127
 128                         vertical = validParameter.validFile(parameters, "vertical", false);
 129                         if (vertical == "not found") {
 130                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 131                                 else { vertical = "F";  }
 132                         }
 133
 134                         numSeqs = 0;
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145
 146 void FilterSeqsCommand::help(){
 147         try {
 148
 149                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 150                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 151                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 152                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 153                 m->mothurOut("The trump parameter .... The default is ...\n");
 154                 m->mothurOut("The soft parameter .... The default is ....\n");
 155                 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
 156                 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
 157                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 158                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 159                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 160                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 161
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "FilterSeqsCommand", "help");
 165                 exit(1);
 166         }
 167 }
 168
 169 /**************************************************************************************/
 170
 171 int FilterSeqsCommand::execute() {
 172         try {
 173
 174                 if (abort == true) { return 0; }
 175
 176                 ifstream inFASTA;
 177                 m->openInputFile(fastafileNames[0], inFASTA);
 178
 179                 Sequence testSeq(inFASTA);
 180                 alignmentLength = testSeq.getAlignLength();
 181                 inFASTA.close();
 182
 183                 ////////////create filter/////////////////
 184                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 185
 186                 filter = createFilter();
 187
 188                 m->mothurOutEndLine();  m->mothurOutEndLine();
 189
 190                 if (m->control_pressed) { return 0; }
 191
 192                 #ifdef USE_MPI
 193                         int pid;
 194                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 195
 196                         if (pid == 0) { //only one process should output the filter
 197                 #endif
 198
 199                 ofstream outFilter;
 200
 201                 string filterFile = outputDir + filterFileName + ".filter";
 202                 m->openOutputFile(filterFile, outFilter);
 203                 outFilter << filter << endl;
 204                 outFilter.close();
 205                 outputNames.push_back(filterFile);
 206
 207                 #ifdef USE_MPI
 208                         }
 209                 #endif
 210
 211                 ////////////run filter/////////////////
 212
 213                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 214
 215                 filterSequences();
 216
 217                 m->mothurOutEndLine();  m->mothurOutEndLine();
 218
 219                 int filteredLength = 0;
 220                 for(int i=0;i<alignmentLength;i++){
 221                         if(filter[i] == '1'){   filteredLength++;       }
 222                 }
 223
 224                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 225
 226
 227                 m->mothurOutEndLine();
 228                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 229                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 230                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 231                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 232
 233
 234                 m->mothurOutEndLine();
 235                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 236                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 237                 m->mothurOutEndLine();
 238
 239                 return 0;
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "FilterSeqsCommand", "execute");
 244                 exit(1);
 245         }
 246 }
 247 /**************************************************************************************/
 248 int FilterSeqsCommand::filterSequences() {
 249         try {
 250
 251                 numSeqs = 0;
 252
 253                 for (int s = 0; s < fastafileNames.size(); s++) {
 254
 255                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 256
 257                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 258 #ifdef USE_MPI
 259                                 int pid, start, end, numSeqsPerProcessor, num;
 260                                 int tag = 2001;
 261                                 vector<unsigned long int>MPIPos;
 262
 263                                 MPI_Status status;
 264                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 265                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 266
 267                                 MPI_File outMPI;
 268                                 MPI_File tempMPI;
 269                                 MPI_File inMPI;
 270                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 271                                 int inMode=MPI_MODE_RDONLY;
 272
 273                                 char outFilename[1024];
 274                                 strcpy(outFilename, filteredFasta.c_str());
 275
 276                                 char inFileName[1024];
 277                                 strcpy(inFileName, fastafileNames[s].c_str());
 278
 279                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 280                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 281
 282                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 283
 284                                 if (pid == 0) { //you are the root process
 285
 286                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 287                                         numSeqs += num;
 288
 289                                         //send file positions to all processes
 290                                         for(int i = 1; i < processors; i++) {
 291                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 292                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 293                                         }
 294
 295                                         //figure out how many sequences you have to do
 296                                         numSeqsPerProcessor = num / processors;
 297                                         int startIndex =  pid * numSeqsPerProcessor;
 298                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 299
 300
 301                                         //do your part
 302                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 303
 304                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 305
 306                                         //wait on chidren
 307                                         for(int i = 1; i < processors; i++) {
 308                                                 char buf[4];
 309                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 310                                         }
 311
 312                                 }else { //you are a child process
 313                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 314                                         MPIPos.resize(num+1);
 315                                         numSeqs += num;
 316                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 317
 318                                         //figure out how many sequences you have to align
 319                                         numSeqsPerProcessor = num / processors;
 320                                         int startIndex =  pid * numSeqsPerProcessor;
 321                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 322
 323
 324                                         //align your part
 325                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 326
 327                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 328
 329                                         char buf[4];
 330                                         strcpy(buf, "done");
 331
 332                                         //tell parent you are done.
 333                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 334                                 }
 335
 336                                 MPI_File_close(&outMPI);
 337                                 MPI_File_close(&inMPI);
 338                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 339
 340 #else
 341                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 342
 343                         for (int i = 0; i < (positions.size()-1); i++) {
 344                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 345                         }
 346                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 347                                 if(processors == 1){
 348                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 349                                         numSeqs += numFastaSeqs;
 350                                 }else{
 351                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 352                                         numSeqs += numFastaSeqs;
 353
 354                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 355
 356                                         //append fasta files
 357                                         for(int i=1;i<processors;i++){
 358                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 359                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 360                                         }
 361                                 }
 362
 363                                 if (m->control_pressed) {  return 1; }
 364                 #else
 365                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 366                                 numSeqs += numFastaSeqs;
 367
 368                                 if (m->control_pressed) {  return 1; }
 369                 #endif
 370 #endif
 371                         outputNames.push_back(filteredFasta);
 372                 }
 373
 374                 return 0;
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 378                 exit(1);
 379         }
 380 }
 381 #ifdef USE_MPI
 382 /**************************************************************************************/
 383 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 384         try {
 385                 string outputString = "";
 386                 int count = 0;
 387                 MPI_Status status;
 388
 389                 for(int i=0;i<num;i++){
 390
 391                         if (m->control_pressed) { return 0; }
 392
 393                         //read next sequence
 394                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 395                         char* buf4 = new char[length];
 396                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 397
 398                         string tempBuf = buf4;
 399                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 400                         istringstream iss (tempBuf,istringstream::in);
 401                         delete buf4;
 402
 403                         Sequence seq(iss);  m->gobble(iss);
 404
 405                         if (seq.getName() != "") {
 406                                 string align = seq.getAligned();
 407                                 string filterSeq = "";
 408
 409                                 for(int j=0;j<alignmentLength;j++){
 410                                         if(filter[j] == '1'){
 411                                                 filterSeq += align[j];
 412                                         }
 413                                 }
 414
 415                                 count++;
 416                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 417
 418                                 if(count % 10 == 0){ //output to file
 419                                         //send results to parent
 420                                         int length = outputString.length();
 421                                         char* buf = new char[length];
 422                                         memcpy(buf, outputString.c_str(), length);
 423
 424                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 425                                         outputString = "";
 426                                         delete buf;
 427                                 }
 428
 429                         }
 430
 431                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 432                 }
 433
 434                 if(outputString != ""){ //output to file
 435                         //send results to parent
 436                         int length = outputString.length();
 437                         char* buf = new char[length];
 438                         memcpy(buf, outputString.c_str(), length);
 439
 440                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 441                         outputString = "";
 442                         delete buf;
 443                 }
 444
 445                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 446
 447                 return 0;
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 451                 exit(1);
 452         }
 453 }
 454 #endif
 455 /**************************************************************************************/
 456 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 457         try {
 458                 ofstream out;
 459                 m->openOutputFile(outputFilename, out);
 460
 461                 ifstream in;
 462                 m->openInputFile(inputFilename, in);
 463
 464                 in.seekg(filePos->start);
 465
 466                 bool done = false;
 467                 int count = 0;
 468
 469                 while (!done) {
 470
 471                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 472
 473                                 Sequence seq(in); m->gobble(in);
 474                                 if (seq.getName() != "") {
 475                                         string align = seq.getAligned();
 476                                         string filterSeq = "";
 477
 478                                         for(int j=0;j<alignmentLength;j++){
 479                                                 if(filter[j] == '1'){
 480                                                         filterSeq += align[j];
 481                                                 }
 482                                         }
 483
 484                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 485                                 count++;
 486                         }
 487
 488                         unsigned long int pos = in.tellg();
 489                         if ((pos == -1) || (pos >= filePos->end)) { break; }
 490
 491                         //report progress
 492                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 493                 }
 494                 //report progress
 495                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 496
 497
 498                 out.close();
 499                 in.close();
 500
 501                 return count;
 502         }
 503         catch(exception& e) {
 504                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 505                 exit(1);
 506         }
 507 }
 508 /**************************************************************************************************/
 509
 510 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 511         try {
 512 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 513                 int process = 0;
 514                 int num = 0;
 515                 processIDS.clear();
 516
 517                 //loop through and create all the processes you want
 518                 while (process != processors) {
 519                         int pid = fork();
 520
 521                         if (pid > 0) {
 522                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 523                                 process++;
 524                         }else if (pid == 0){
 525                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 526                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 527
 528                                 //pass numSeqs to parent
 529                                 ofstream out;
 530                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 531                                 m->openOutputFile(tempFile, out);
 532                                 out << num << endl;
 533                                 out.close();
 534
 535                                 exit(0);
 536                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 537                 }
 538
 539                 //force parent to wait until all the processes are done
 540                 for (int i=0;i<processors;i++) {
 541                         int temp = processIDS[i];
 542                         wait(&temp);
 543                 }
 544
 545                 for (int i = 0; i < processIDS.size(); i++) {
 546                         ifstream in;
 547                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 548                         m->openInputFile(tempFile, in);
 549                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 550                         in.close(); remove(tempFile.c_str());
 551                 }
 552
 553
 554                 return num;
 555 #endif
 556         }
 557         catch(exception& e) {
 558                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 559                 exit(1);
 560         }
 561 }
 562 /**************************************************************************************/
 563 string FilterSeqsCommand::createFilter() {
 564         try {
 565                 string filterString = "";
 566                 Filters F;
 567
 568                 if (soft != 0)                  {  F.setSoft(soft);             }
 569                 if (trump != '*')               {  F.setTrump(trump);   }
 570
 571                 F.setLength(alignmentLength);
 572
 573                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 574                         F.initialize();
 575                 }
 576
 577                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 578                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 579
 580                 numSeqs = 0;
 581                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 582                         for (int s = 0; s < fastafileNames.size(); s++) {
 583
 584                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 585
 586 #ifdef USE_MPI
 587                                 int pid, numSeqsPerProcessor, num;
 588                                 int tag = 2001;
 589                                 vector<unsigned long int> MPIPos;
 590
 591                                 MPI_Status status;
 592                                 MPI_File inMPI;
 593                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 594                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 595
 596                                 //char* tempFileName = new char(fastafileNames[s].length());
 597                                 //tempFileName = &(fastafileNames[s][0]);
 598
 599                                 char tempFileName[1024];
 600                                 strcpy(tempFileName, fastafileNames[s].c_str());
 601
 602                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 603
 604                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 605
 606                                 if (pid == 0) { //you are the root process
 607                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 608                                                 numSeqs += num;
 609
 610                                                 //send file positions to all processes
 611                                                 for(int i = 1; i < processors; i++) {
 612                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 613                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 614                                                 }
 615
 616                                                 //figure out how many sequences you have to do
 617                                                 numSeqsPerProcessor = num / processors;
 618                                                 int startIndex =  pid * numSeqsPerProcessor;
 619                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 620
 621
 622                                                 //do your part
 623                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 624
 625                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 626
 627                                 }else { //i am the child process
 628                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 629                                         MPIPos.resize(num+1);
 630                                         numSeqs += num;
 631                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 632
 633                                         //figure out how many sequences you have to align
 634                                         numSeqsPerProcessor = num / processors;
 635                                         int startIndex =  pid * numSeqsPerProcessor;
 636                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 637
 638
 639                                         //do your part
 640                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 641
 642                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 643                                 }
 644
 645                                 MPI_File_close(&inMPI);
 646                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 647
 648 #else
 649                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 650
 651                 for (int i = 0; i < (positions.size()-1); i++) {
 652                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 653                 }
 654                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 655                                 if(processors == 1){
 656                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 657                                         numSeqs += numFastaSeqs;
 658                                 }else{
 659                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 660                                         numSeqs += numFastaSeqs;
 661                                 }
 662
 663                                 if (m->control_pressed) {  return filterString; }
 664                 #else
 665                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 666                                 numSeqs += numFastaSeqs;
 667                                 if (m->control_pressed) {  return filterString; }
 668                 #endif
 669 #endif
 670
 671                         }
 672                 }
 673
 674
 675 #ifdef USE_MPI
 676                 int pid;
 677                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 678                 MPI_Status status;
 679
 680                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 681
 682                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 683
 684                         if (pid == 0) { //only one process should output the filter
 685
 686                                 vector<int> temp; temp.resize(alignmentLength+1);
 687
 688                                 //get the frequencies from the child processes
 689                                 for(int i = 1; i < processors; i++) {
 690
 691                                         for (int j = 0; j < 5; j++) {
 692
 693                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 694                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 695
 696                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 697                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 698                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 699                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 700                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 701                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 702                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 703                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 704                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 705                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 706                                                 }
 707                                         }
 708                                 }
 709                         }else{
 710
 711                                 //send my fequency counts
 712                                 F.a.push_back(Atag);
 713                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 714                                 F.t.push_back(Ttag);
 715                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 716                                 F.c.push_back(Ctag);
 717                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 718                                 F.g.push_back(Gtag);
 719                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 720                                 F.gap.push_back(Gaptag);
 721                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 722                         }
 723
 724                 }
 725
 726                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 727
 728                 if (pid == 0) { //only one process should output the filter
 729 #endif
 730
 731                 F.setNumSeqs(numSeqs);
 732                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 733                 if(soft != 0)                           {       F.doSoft();             }
 734                 filterString = F.getFilter();
 735
 736 #ifdef USE_MPI
 737                 //send filter string to kids
 738                 //for(int i = 1; i < processors; i++) {
 739                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 740                 //}
 741                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 742         }else{
 743                 //recieve filterString
 744                 char* tempBuf = new char[alignmentLength];
 745                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 746                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 747
 748                 filterString = tempBuf;
 749                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 750                 delete tempBuf;
 751         }
 752
 753         MPI_Barrier(MPI_COMM_WORLD);
 754 #endif
 755
 756                 return filterString;
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 760                 exit(1);
 761         }
 762 }
 763 /**************************************************************************************/
 764 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 765         try {
 766
 767                 ifstream in;
 768                 m->openInputFile(filename, in);
 769
 770                 in.seekg(filePos->start);
 771
 772                 bool done = false;
 773                 int count = 0;
 774
 775                 while (!done) {
 776
 777                         if (m->control_pressed) { in.close(); return 1; }
 778
 779                         Sequence seq(in); m->gobble(in);
 780                         if (seq.getName() != "") {
 781                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 782
 783                                         if(trump != '*')                        {       F.doTrump(seq);         }
 784                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 785                                         cout.flush();
 786                                         count++;
 787                         }
 788
 789                         unsigned long int pos = in.tellg();
 790                         if ((pos == -1) || (pos >= filePos->end)) { break; }
 791
 792                         //report progress
 793                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 794                 }
 795                 //report progress
 796                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 797                 in.close();
 798
 799                 return count;
 800         }
 801         catch(exception& e) {
 802                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 803                 exit(1);
 804         }
 805 }
 806 #ifdef USE_MPI
 807 /**************************************************************************************/
 808 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 809         try {
 810
 811                 MPI_Status status;
 812                 int pid;
 813                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 814
 815                 for(int i=0;i<num;i++){
 816
 817                         if (m->control_pressed) { return 0; }
 818
 819                         //read next sequence
 820                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 821
 822                         char* buf4 = new char[length];
 823                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 824
 825                         string tempBuf = buf4;
 826                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 827                         istringstream iss (tempBuf,istringstream::in);
 828                         delete buf4;
 829
 830                         Sequence seq(iss);
 831
 832                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 833
 834                         if(trump != '*'){       F.doTrump(seq); }
 835                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 836                         cout.flush();
 837
 838                         //report progress
 839                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 840                 }
 841
 842                 //report progress
 843                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 844
 845                 return 0;
 846         }
 847         catch(exception& e) {
 848                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 849                 exit(1);
 850         }
 851 }
 852 #endif
 853 /**************************************************************************************************/
 854
 855 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 856         try {
 857 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 858                 int process = 0;
 859                 int num = 0;
 860                 processIDS.clear();
 861
 862                 //loop through and create all the processes you want
 863                 while (process != processors) {
 864                         int pid = fork();
 865
 866                         if (pid > 0) {
 867                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 868                                 process++;
 869                         }else if (pid == 0){
 870                                 //reset child's filter counts to 0;
 871                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 872                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 873                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 874                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 875                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 876
 877                                 num = driverCreateFilter(F, filename, lines[process]);
 878
 879                                 //write out filter counts to file
 880                                 filename += toString(getpid()) + "filterValues.temp";
 881                                 ofstream out;
 882                                 m->openOutputFile(filename, out);
 883
 884                                 out << num << endl;
 885                                 out << F.getFilter() << endl;
 886                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 887                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 888                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 889                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 890                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 891
 892                                 //cout << F.getFilter() << endl;
 893                                 out.close();
 894
 895                                 exit(0);
 896                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 897                 }
 898
 899                 //force parent to wait until all the processes are done
 900                 for (int i=0;i<processors;i++) {
 901                         int temp = processIDS[i];
 902                         wait(&temp);
 903                 }
 904
 905                 //parent reads in and combine Filter info
 906                 for (int i = 0; i < processIDS.size(); i++) {
 907                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 908                         ifstream in;
 909                         m->openInputFile(tempFilename, in);
 910
 911                         int temp, tempNum;
 912                         string tempFilterString;
 913
 914                         in >> tempNum; m->gobble(in); num += tempNum;
 915
 916                         in >> tempFilterString;
 917                         F.mergeFilter(tempFilterString);
 918
 919                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
 920                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
 921                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
 922                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
 923                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
 924
 925                         in.close();
 926                         remove(tempFilename.c_str());
 927                 }
 928
 929                 return num;
 930 #endif
 931         }
 932         catch(exception& e) {
 933                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 934                 exit(1);
 935         }
 936 }
 937 /**************************************************************************************/