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, processors 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 processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 158                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 159                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 160                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 161                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 162
 163         }
 164         catch(exception& e) {
 165                 m->errorOut(e, "FilterSeqsCommand", "help");
 166                 exit(1);
 167         }
 168 }
 169
 170 /**************************************************************************************/
 171
 172 int FilterSeqsCommand::execute() {
 173         try {
 174
 175                 if (abort == true) { return 0; }
 176
 177                 ifstream inFASTA;
 178                 m->openInputFile(fastafileNames[0], inFASTA);
 179
 180                 Sequence testSeq(inFASTA);
 181                 alignmentLength = testSeq.getAlignLength();
 182                 inFASTA.close();
 183
 184                 ////////////create filter/////////////////
 185                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 186
 187                 filter = createFilter();
 188
 189                 m->mothurOutEndLine();  m->mothurOutEndLine();
 190
 191                 if (m->control_pressed) { return 0; }
 192
 193                 #ifdef USE_MPI
 194                         int pid;
 195                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 196
 197                         if (pid == 0) { //only one process should output the filter
 198                 #endif
 199
 200                 ofstream outFilter;
 201
 202                 //prevent giantic file name
 203                 string filterFile;
 204                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 205                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 206
 207                 m->openOutputFile(filterFile, outFilter);
 208                 outFilter << filter << endl;
 209                 outFilter.close();
 210                 outputNames.push_back(filterFile);
 211
 212                 #ifdef USE_MPI
 213                         }
 214                 #endif
 215
 216                 ////////////run filter/////////////////
 217
 218                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 219
 220                 filterSequences();
 221
 222                 m->mothurOutEndLine();  m->mothurOutEndLine();
 223
 224                 int filteredLength = 0;
 225                 for(int i=0;i<alignmentLength;i++){
 226                         if(filter[i] == '1'){   filteredLength++;       }
 227                 }
 228
 229                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 230
 231
 232                 m->mothurOutEndLine();
 233                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 234                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 235                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 236                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 237
 238
 239                 m->mothurOutEndLine();
 240                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 241                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 242                 m->mothurOutEndLine();
 243
 244                 return 0;
 245
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "FilterSeqsCommand", "execute");
 249                 exit(1);
 250         }
 251 }
 252 /**************************************************************************************/
 253 int FilterSeqsCommand::filterSequences() {
 254         try {
 255
 256                 numSeqs = 0;
 257
 258                 for (int s = 0; s < fastafileNames.size(); s++) {
 259
 260                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 261
 262                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 263 #ifdef USE_MPI
 264                                 int pid, start, end, numSeqsPerProcessor, num;
 265                                 int tag = 2001;
 266                                 vector<unsigned long int>MPIPos;
 267
 268                                 MPI_Status status;
 269                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 270                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 271
 272                                 MPI_File outMPI;
 273                                 MPI_File tempMPI;
 274                                 MPI_File inMPI;
 275                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 276                                 int inMode=MPI_MODE_RDONLY;
 277
 278                                 char outFilename[1024];
 279                                 strcpy(outFilename, filteredFasta.c_str());
 280
 281                                 char inFileName[1024];
 282                                 strcpy(inFileName, fastafileNames[s].c_str());
 283
 284                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 285                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 286
 287                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 288
 289                                 if (pid == 0) { //you are the root process
 290
 291                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 292                                         numSeqs += num;
 293
 294                                         //send file positions to all processes
 295                                         for(int i = 1; i < processors; i++) {
 296                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 297                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 298                                         }
 299
 300                                         //figure out how many sequences you have to do
 301                                         numSeqsPerProcessor = num / processors;
 302                                         int startIndex =  pid * numSeqsPerProcessor;
 303                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 304
 305
 306                                         //do your part
 307                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 308
 309                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 310
 311                                         //wait on chidren
 312                                         for(int i = 1; i < processors; i++) {
 313                                                 char buf[5];
 314                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 315                                         }
 316
 317                                 }else { //you are a child process
 318                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 319                                         MPIPos.resize(num+1);
 320                                         numSeqs += num;
 321                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 322
 323                                         //figure out how many sequences you have to align
 324                                         numSeqsPerProcessor = num / processors;
 325                                         int startIndex =  pid * numSeqsPerProcessor;
 326                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 327
 328
 329                                         //align your part
 330                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 331
 332                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 333
 334                                         char buf[5];
 335                                         strcpy(buf, "done");
 336
 337                                         //tell parent you are done.
 338                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 339                                 }
 340
 341                                 MPI_File_close(&outMPI);
 342                                 MPI_File_close(&inMPI);
 343                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 344
 345 #else
 346                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 347
 348                         for (int i = 0; i < (positions.size()-1); i++) {
 349                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 350                         }
 351                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 352                                 if(processors == 1){
 353                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 354                                         numSeqs += numFastaSeqs;
 355                                 }else{
 356                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 357                                         numSeqs += numFastaSeqs;
 358
 359                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 360
 361                                         //append fasta files
 362                                         for(int i=1;i<processors;i++){
 363                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 364                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 365                                         }
 366                                 }
 367
 368                                 if (m->control_pressed) {  return 1; }
 369                 #else
 370                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 371                                 numSeqs += numFastaSeqs;
 372
 373                                 if (m->control_pressed) {  return 1; }
 374                 #endif
 375 #endif
 376                         outputNames.push_back(filteredFasta);
 377                 }
 378
 379                 return 0;
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 383                 exit(1);
 384         }
 385 }
 386 #ifdef USE_MPI
 387 /**************************************************************************************/
 388 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 389         try {
 390                 string outputString = "";
 391                 int count = 0;
 392                 MPI_Status status;
 393
 394                 for(int i=0;i<num;i++){
 395
 396                         if (m->control_pressed) { return 0; }
 397
 398                         //read next sequence
 399                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 400                         char* buf4 = new char[length];
 401                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 402
 403                         string tempBuf = buf4;
 404                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 405                         istringstream iss (tempBuf,istringstream::in);
 406                         delete buf4;
 407
 408                         Sequence seq(iss);  m->gobble(iss);
 409
 410                         if (seq.getName() != "") {
 411                                 string align = seq.getAligned();
 412                                 string filterSeq = "";
 413
 414                                 for(int j=0;j<alignmentLength;j++){
 415                                         if(filter[j] == '1'){
 416                                                 filterSeq += align[j];
 417                                         }
 418                                 }
 419
 420                                 count++;
 421                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 422
 423                                 if(count % 10 == 0){ //output to file
 424                                         //send results to parent
 425                                         int length = outputString.length();
 426                                         char* buf = new char[length];
 427                                         memcpy(buf, outputString.c_str(), length);
 428
 429                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 430                                         outputString = "";
 431                                         delete buf;
 432                                 }
 433
 434                         }
 435
 436                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 437                 }
 438
 439                 if(outputString != ""){ //output to file
 440                         //send results to parent
 441                         int length = outputString.length();
 442                         char* buf = new char[length];
 443                         memcpy(buf, outputString.c_str(), length);
 444
 445                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 446                         outputString = "";
 447                         delete buf;
 448                 }
 449
 450                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 451
 452                 return 0;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 456                 exit(1);
 457         }
 458 }
 459 #endif
 460 /**************************************************************************************/
 461 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 462         try {
 463                 ofstream out;
 464                 m->openOutputFile(outputFilename, out);
 465
 466                 ifstream in;
 467                 m->openInputFile(inputFilename, in);
 468
 469                 in.seekg(filePos->start);
 470
 471                 bool done = false;
 472                 int count = 0;
 473
 474                 while (!done) {
 475
 476                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 477
 478                                 Sequence seq(in); m->gobble(in);
 479                                 if (seq.getName() != "") {
 480                                         string align = seq.getAligned();
 481                                         string filterSeq = "";
 482
 483                                         for(int j=0;j<alignmentLength;j++){
 484                                                 if(filter[j] == '1'){
 485                                                         filterSeq += align[j];
 486                                                 }
 487                                         }
 488
 489                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 490                                 count++;
 491                         }
 492
 493                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 494                                 unsigned long int pos = in.tellg();
 495                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 496                         #else
 497                                 if (in.eof()) { break; }
 498                         #endif
 499
 500                         //report progress
 501                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 502                 }
 503                 //report progress
 504                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 505
 506
 507                 out.close();
 508                 in.close();
 509
 510                 return count;
 511         }
 512         catch(exception& e) {
 513                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 514                 exit(1);
 515         }
 516 }
 517 /**************************************************************************************************/
 518
 519 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 520         try {
 521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 522                 int process = 0;
 523                 int num = 0;
 524                 processIDS.clear();
 525
 526                 //loop through and create all the processes you want
 527                 while (process != processors) {
 528                         int pid = fork();
 529
 530                         if (pid > 0) {
 531                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 532                                 process++;
 533                         }else if (pid == 0){
 534                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 535                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 536
 537                                 //pass numSeqs to parent
 538                                 ofstream out;
 539                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 540                                 m->openOutputFile(tempFile, out);
 541                                 out << num << endl;
 542                                 out.close();
 543
 544                                 exit(0);
 545                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 546                 }
 547
 548                 //force parent to wait until all the processes are done
 549                 for (int i=0;i<processors;i++) {
 550                         int temp = processIDS[i];
 551                         wait(&temp);
 552                 }
 553
 554                 for (int i = 0; i < processIDS.size(); i++) {
 555                         ifstream in;
 556                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 557                         m->openInputFile(tempFile, in);
 558                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 559                         in.close(); remove(tempFile.c_str());
 560                 }
 561
 562
 563                 return num;
 564 #endif
 565         }
 566         catch(exception& e) {
 567                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 568                 exit(1);
 569         }
 570 }
 571 /**************************************************************************************/
 572 string FilterSeqsCommand::createFilter() {
 573         try {
 574                 string filterString = "";
 575                 Filters F;
 576
 577                 if (soft != 0)                  {  F.setSoft(soft);             }
 578                 if (trump != '*')               {  F.setTrump(trump);   }
 579
 580                 F.setLength(alignmentLength);
 581
 582                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 583                         F.initialize();
 584                 }
 585
 586                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 587                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 588
 589                 numSeqs = 0;
 590                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 591                         for (int s = 0; s < fastafileNames.size(); s++) {
 592
 593                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 594
 595 #ifdef USE_MPI
 596                                 int pid, numSeqsPerProcessor, num;
 597                                 int tag = 2001;
 598                                 vector<unsigned long int> MPIPos;
 599
 600                                 MPI_Status status;
 601                                 MPI_File inMPI;
 602                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 603                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 604
 605                                 //char* tempFileName = new char(fastafileNames[s].length());
 606                                 //tempFileName = &(fastafileNames[s][0]);
 607
 608                                 char tempFileName[1024];
 609                                 strcpy(tempFileName, fastafileNames[s].c_str());
 610
 611                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 612
 613                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 614
 615                                 if (pid == 0) { //you are the root process
 616                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 617                                                 numSeqs += num;
 618
 619                                                 //send file positions to all processes
 620                                                 for(int i = 1; i < processors; i++) {
 621                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 622                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 623                                                 }
 624
 625                                                 //figure out how many sequences you have to do
 626                                                 numSeqsPerProcessor = num / processors;
 627                                                 int startIndex =  pid * numSeqsPerProcessor;
 628                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 629
 630
 631                                                 //do your part
 632                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 633
 634                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 635
 636                                 }else { //i am the child process
 637                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 638                                         MPIPos.resize(num+1);
 639                                         numSeqs += num;
 640                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 641
 642                                         //figure out how many sequences you have to align
 643                                         numSeqsPerProcessor = num / processors;
 644                                         int startIndex =  pid * numSeqsPerProcessor;
 645                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 646
 647
 648                                         //do your part
 649                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 650
 651                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 652                                 }
 653
 654                                 MPI_File_close(&inMPI);
 655                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 656
 657 #else
 658                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 659
 660                 for (int i = 0; i < (positions.size()-1); i++) {
 661                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 662                 }
 663                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 664                                 if(processors == 1){
 665                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 666                                         numSeqs += numFastaSeqs;
 667                                 }else{
 668                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 669                                         numSeqs += numFastaSeqs;
 670                                 }
 671
 672                                 if (m->control_pressed) {  return filterString; }
 673                 #else
 674                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 675                                 numSeqs += numFastaSeqs;
 676                                 if (m->control_pressed) {  return filterString; }
 677                 #endif
 678 #endif
 679
 680                         }
 681                 }
 682
 683
 684 #ifdef USE_MPI
 685                 int pid;
 686                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 687                 MPI_Status status;
 688
 689                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 690
 691                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 692
 693                         if (pid == 0) { //only one process should output the filter
 694
 695                                 vector<int> temp; temp.resize(alignmentLength+1);
 696
 697                                 //get the frequencies from the child processes
 698                                 for(int i = 1; i < processors; i++) {
 699
 700                                         for (int j = 0; j < 5; j++) {
 701
 702                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 703                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 704
 705                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 706                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 707                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 708                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 709                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 710                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 711                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 712                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 713                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 714                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 715                                                 }
 716                                         }
 717                                 }
 718                         }else{
 719
 720                                 //send my fequency counts
 721                                 F.a.push_back(Atag);
 722                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 723                                 F.t.push_back(Ttag);
 724                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 725                                 F.c.push_back(Ctag);
 726                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 727                                 F.g.push_back(Gtag);
 728                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 729                                 F.gap.push_back(Gaptag);
 730                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 731                         }
 732
 733                 }
 734
 735                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 736
 737                 if (pid == 0) { //only one process should output the filter
 738 #endif
 739
 740                 F.setNumSeqs(numSeqs);
 741                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 742                 if(soft != 0)                           {       F.doSoft();             }
 743                 filterString = F.getFilter();
 744
 745 #ifdef USE_MPI
 746                 //send filter string to kids
 747                 //for(int i = 1; i < processors; i++) {
 748                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 749                 //}
 750                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 751         }else{
 752                 //recieve filterString
 753                 char* tempBuf = new char[alignmentLength];
 754                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 755                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 756
 757                 filterString = tempBuf;
 758                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 759                 delete tempBuf;
 760         }
 761
 762         MPI_Barrier(MPI_COMM_WORLD);
 763 #endif
 764
 765                 return filterString;
 766         }
 767         catch(exception& e) {
 768                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 769                 exit(1);
 770         }
 771 }
 772 /**************************************************************************************/
 773 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 774         try {
 775
 776                 ifstream in;
 777                 m->openInputFile(filename, in);
 778
 779                 in.seekg(filePos->start);
 780
 781                 bool done = false;
 782                 int count = 0;
 783
 784                 while (!done) {
 785
 786                         if (m->control_pressed) { in.close(); return 1; }
 787
 788                         Sequence seq(in); m->gobble(in);
 789                         if (seq.getName() != "") {
 790                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 791
 792                                         if(trump != '*')                        {       F.doTrump(seq);         }
 793                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 794                                         cout.flush();
 795                                         count++;
 796                         }
 797
 798                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 799                                 unsigned long int pos = in.tellg();
 800                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 801                         #else
 802                                 if (in.eof()) { break; }
 803                         #endif
 804
 805                         //report progress
 806                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 807                 }
 808                 //report progress
 809                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 810                 in.close();
 811
 812                 return count;
 813         }
 814         catch(exception& e) {
 815                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 816                 exit(1);
 817         }
 818 }
 819 #ifdef USE_MPI
 820 /**************************************************************************************/
 821 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 822         try {
 823
 824                 MPI_Status status;
 825                 int pid;
 826                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 827
 828                 for(int i=0;i<num;i++){
 829
 830                         if (m->control_pressed) { return 0; }
 831
 832                         //read next sequence
 833                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 834
 835                         char* buf4 = new char[length];
 836                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 837
 838                         string tempBuf = buf4;
 839                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 840                         istringstream iss (tempBuf,istringstream::in);
 841                         delete buf4;
 842
 843                         Sequence seq(iss);
 844
 845                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 846
 847                         if(trump != '*'){       F.doTrump(seq); }
 848                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 849                         cout.flush();
 850
 851                         //report progress
 852                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 853                 }
 854
 855                 //report progress
 856                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 857
 858                 return 0;
 859         }
 860         catch(exception& e) {
 861                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 862                 exit(1);
 863         }
 864 }
 865 #endif
 866 /**************************************************************************************************/
 867
 868 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 869         try {
 870 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 871                 int process = 1;
 872                 int num = 0;
 873                 processIDS.clear();
 874
 875                 //loop through and create all the processes you want
 876                 while (process != processors) {
 877                         int pid = fork();
 878
 879                         if (pid > 0) {
 880                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 881                                 process++;
 882                         }else if (pid == 0){
 883                                 //reset child's filter counts to 0;
 884                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 885                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 886                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 887                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 888                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 889
 890                                 num = driverCreateFilter(F, filename, lines[process]);
 891
 892                                 //write out filter counts to file
 893                                 filename += toString(getpid()) + "filterValues.temp";
 894                                 ofstream out;
 895                                 m->openOutputFile(filename, out);
 896
 897                                 out << num << endl;
 898                                 out << F.getFilter() << endl;
 899                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 900                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 901                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 902                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 903                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 904
 905                                 //cout << F.getFilter() << endl;
 906                                 out.close();
 907
 908                                 exit(0);
 909                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 910                 }
 911
 912                 //parent do your part
 913                 num = driverCreateFilter(F, filename, lines[0]);
 914
 915                 //force parent to wait until all the processes are done
 916                 for (int i=0;i<(processors-1);i++) {
 917                         int temp = processIDS[i];
 918                         wait(&temp);
 919                 }
 920
 921                 //parent reads in and combines Filter info
 922                 for (int i = 0; i < processIDS.size(); i++) {
 923                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 924                         ifstream in;
 925                         m->openInputFile(tempFilename, in);
 926
 927                         int temp, tempNum;
 928                         string tempFilterString;
 929
 930                         in >> tempNum; m->gobble(in); num += tempNum;
 931
 932                         in >> tempFilterString;
 933                         F.mergeFilter(tempFilterString);
 934
 935                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
 936                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
 937                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
 938                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
 939                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
 940
 941                         in.close();
 942                         remove(tempFilename.c_str());
 943                 }
 944
 945                 return num;
 946 #endif
 947         }
 948         catch(exception& e) {
 949                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 950                 exit(1);
 951         }
 952 }
 953 /**************************************************************************************/