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                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 489                                 unsigned long int pos = in.tellg();
 490                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 491                         #else
 492                                 if (in.eof()) { break; }
 493                         #endif
 494
 495                         //report progress
 496                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 497                 }
 498                 //report progress
 499                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 500
 501
 502                 out.close();
 503                 in.close();
 504
 505                 return count;
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 509                 exit(1);
 510         }
 511 }
 512 /**************************************************************************************************/
 513
 514 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 515         try {
 516 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 517                 int process = 0;
 518                 int num = 0;
 519                 processIDS.clear();
 520
 521                 //loop through and create all the processes you want
 522                 while (process != processors) {
 523                         int pid = fork();
 524
 525                         if (pid > 0) {
 526                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 527                                 process++;
 528                         }else if (pid == 0){
 529                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 530                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 531
 532                                 //pass numSeqs to parent
 533                                 ofstream out;
 534                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 535                                 m->openOutputFile(tempFile, out);
 536                                 out << num << endl;
 537                                 out.close();
 538
 539                                 exit(0);
 540                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 541                 }
 542
 543                 //force parent to wait until all the processes are done
 544                 for (int i=0;i<processors;i++) {
 545                         int temp = processIDS[i];
 546                         wait(&temp);
 547                 }
 548
 549                 for (int i = 0; i < processIDS.size(); i++) {
 550                         ifstream in;
 551                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 552                         m->openInputFile(tempFile, in);
 553                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 554                         in.close(); remove(tempFile.c_str());
 555                 }
 556
 557
 558                 return num;
 559 #endif
 560         }
 561         catch(exception& e) {
 562                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 563                 exit(1);
 564         }
 565 }
 566 /**************************************************************************************/
 567 string FilterSeqsCommand::createFilter() {
 568         try {
 569                 string filterString = "";
 570                 Filters F;
 571
 572                 if (soft != 0)                  {  F.setSoft(soft);             }
 573                 if (trump != '*')               {  F.setTrump(trump);   }
 574
 575                 F.setLength(alignmentLength);
 576
 577                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 578                         F.initialize();
 579                 }
 580
 581                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 582                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 583
 584                 numSeqs = 0;
 585                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 586                         for (int s = 0; s < fastafileNames.size(); s++) {
 587
 588                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 589
 590 #ifdef USE_MPI
 591                                 int pid, numSeqsPerProcessor, num;
 592                                 int tag = 2001;
 593                                 vector<unsigned long int> MPIPos;
 594
 595                                 MPI_Status status;
 596                                 MPI_File inMPI;
 597                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 598                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 599
 600                                 //char* tempFileName = new char(fastafileNames[s].length());
 601                                 //tempFileName = &(fastafileNames[s][0]);
 602
 603                                 char tempFileName[1024];
 604                                 strcpy(tempFileName, fastafileNames[s].c_str());
 605
 606                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 607
 608                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 609
 610                                 if (pid == 0) { //you are the root process
 611                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 612                                                 numSeqs += num;
 613
 614                                                 //send file positions to all processes
 615                                                 for(int i = 1; i < processors; i++) {
 616                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 617                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 618                                                 }
 619
 620                                                 //figure out how many sequences you have to do
 621                                                 numSeqsPerProcessor = num / processors;
 622                                                 int startIndex =  pid * numSeqsPerProcessor;
 623                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 624
 625
 626                                                 //do your part
 627                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 628
 629                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 630
 631                                 }else { //i am the child process
 632                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 633                                         MPIPos.resize(num+1);
 634                                         numSeqs += num;
 635                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 636
 637                                         //figure out how many sequences you have to align
 638                                         numSeqsPerProcessor = num / processors;
 639                                         int startIndex =  pid * numSeqsPerProcessor;
 640                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 641
 642
 643                                         //do your part
 644                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 645
 646                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 647                                 }
 648
 649                                 MPI_File_close(&inMPI);
 650                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 651
 652 #else
 653                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 654
 655                 for (int i = 0; i < (positions.size()-1); i++) {
 656                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 657                 }
 658                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 659                                 if(processors == 1){
 660                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 661                                         numSeqs += numFastaSeqs;
 662                                 }else{
 663                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 664                                         numSeqs += numFastaSeqs;
 665                                 }
 666
 667                                 if (m->control_pressed) {  return filterString; }
 668                 #else
 669                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 670                                 numSeqs += numFastaSeqs;
 671                                 if (m->control_pressed) {  return filterString; }
 672                 #endif
 673 #endif
 674
 675                         }
 676                 }
 677
 678
 679 #ifdef USE_MPI
 680                 int pid;
 681                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 682                 MPI_Status status;
 683
 684                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 685
 686                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 687
 688                         if (pid == 0) { //only one process should output the filter
 689
 690                                 vector<int> temp; temp.resize(alignmentLength+1);
 691
 692                                 //get the frequencies from the child processes
 693                                 for(int i = 1; i < processors; i++) {
 694
 695                                         for (int j = 0; j < 5; j++) {
 696
 697                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 698                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 699
 700                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 701                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 702                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 703                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 704                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 705                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 706                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 707                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 708                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 709                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 710                                                 }
 711                                         }
 712                                 }
 713                         }else{
 714
 715                                 //send my fequency counts
 716                                 F.a.push_back(Atag);
 717                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 718                                 F.t.push_back(Ttag);
 719                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 720                                 F.c.push_back(Ctag);
 721                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 722                                 F.g.push_back(Gtag);
 723                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 724                                 F.gap.push_back(Gaptag);
 725                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 726                         }
 727
 728                 }
 729
 730                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 731
 732                 if (pid == 0) { //only one process should output the filter
 733 #endif
 734
 735                 F.setNumSeqs(numSeqs);
 736                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 737                 if(soft != 0)                           {       F.doSoft();             }
 738                 filterString = F.getFilter();
 739
 740 #ifdef USE_MPI
 741                 //send filter string to kids
 742                 //for(int i = 1; i < processors; i++) {
 743                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 744                 //}
 745                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 746         }else{
 747                 //recieve filterString
 748                 char* tempBuf = new char[alignmentLength];
 749                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 750                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 751
 752                 filterString = tempBuf;
 753                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 754                 delete tempBuf;
 755         }
 756
 757         MPI_Barrier(MPI_COMM_WORLD);
 758 #endif
 759
 760                 return filterString;
 761         }
 762         catch(exception& e) {
 763                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 764                 exit(1);
 765         }
 766 }
 767 /**************************************************************************************/
 768 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 769         try {
 770
 771                 ifstream in;
 772                 m->openInputFile(filename, in);
 773
 774                 in.seekg(filePos->start);
 775
 776                 bool done = false;
 777                 int count = 0;
 778
 779                 while (!done) {
 780
 781                         if (m->control_pressed) { in.close(); return 1; }
 782
 783                         Sequence seq(in); m->gobble(in);
 784                         if (seq.getName() != "") {
 785                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 786
 787                                         if(trump != '*')                        {       F.doTrump(seq);         }
 788                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 789                                         cout.flush();
 790                                         count++;
 791                         }
 792
 793                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 794                                 unsigned long int pos = in.tellg();
 795                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 796                         #else
 797                                 if (in.eof()) { break; }
 798                         #endif
 799
 800                         //report progress
 801                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 802                 }
 803                 //report progress
 804                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 805                 in.close();
 806
 807                 return count;
 808         }
 809         catch(exception& e) {
 810                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 811                 exit(1);
 812         }
 813 }
 814 #ifdef USE_MPI
 815 /**************************************************************************************/
 816 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 817         try {
 818
 819                 MPI_Status status;
 820                 int pid;
 821                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 822
 823                 for(int i=0;i<num;i++){
 824
 825                         if (m->control_pressed) { return 0; }
 826
 827                         //read next sequence
 828                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 829
 830                         char* buf4 = new char[length];
 831                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 832
 833                         string tempBuf = buf4;
 834                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 835                         istringstream iss (tempBuf,istringstream::in);
 836                         delete buf4;
 837
 838                         Sequence seq(iss);
 839
 840                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 841
 842                         if(trump != '*'){       F.doTrump(seq); }
 843                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 844                         cout.flush();
 845
 846                         //report progress
 847                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 848                 }
 849
 850                 //report progress
 851                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 852
 853                 return 0;
 854         }
 855         catch(exception& e) {
 856                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 857                 exit(1);
 858         }
 859 }
 860 #endif
 861 /**************************************************************************************************/
 862
 863 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 864         try {
 865 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 866                 int process = 0;
 867                 int num = 0;
 868                 processIDS.clear();
 869
 870                 //loop through and create all the processes you want
 871                 while (process != processors) {
 872                         int pid = fork();
 873
 874                         if (pid > 0) {
 875                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 876                                 process++;
 877                         }else if (pid == 0){
 878                                 //reset child's filter counts to 0;
 879                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 880                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 881                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 882                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 883                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 884
 885                                 num = driverCreateFilter(F, filename, lines[process]);
 886
 887                                 //write out filter counts to file
 888                                 filename += toString(getpid()) + "filterValues.temp";
 889                                 ofstream out;
 890                                 m->openOutputFile(filename, out);
 891
 892                                 out << num << endl;
 893                                 out << F.getFilter() << endl;
 894                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 895                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 896                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 897                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 898                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 899
 900                                 //cout << F.getFilter() << endl;
 901                                 out.close();
 902
 903                                 exit(0);
 904                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 905                 }
 906
 907                 //force parent to wait until all the processes are done
 908                 for (int i=0;i<processors;i++) {
 909                         int temp = processIDS[i];
 910                         wait(&temp);
 911                 }
 912
 913                 //parent reads in and combine Filter info
 914                 for (int i = 0; i < processIDS.size(); i++) {
 915                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 916                         ifstream in;
 917                         m->openInputFile(tempFilename, in);
 918
 919                         int temp, tempNum;
 920                         string tempFilterString;
 921
 922                         in >> tempNum; m->gobble(in); num += tempNum;
 923
 924                         in >> tempFilterString;
 925                         F.mergeFilter(tempFilterString);
 926
 927                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
 928                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
 929                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
 930                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
 931                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
 932
 933                         in.close();
 934                         remove(tempFilename.c_str());
 935                 }
 936
 937                 return num;
 938 #endif
 939         }
 940         catch(exception& e) {
 941                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 942                 exit(1);
 943         }
 944 }
 945 /**************************************************************************************/