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;
  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 = 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 = 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                                 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 = 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                                         int ableToOpen;
  76                                         ifstream in;
  77                                         ableToOpen = openInputFile(fastafileNames[i], in);
  78                                         if (ableToOpen == 1) {
  79                                                 m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  80                                                 //erase from file list
  81                                                 fastafileNames.erase(fastafileNames.begin()+i);
  82                                                 i--;
  83                                         }else{
  84                                                 string simpleName = getSimpleName(fastafileNames[i]);
  85                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  86                                         }
  87                                         in.close();
  88                                 }
  89
  90                                 //make sure there is at least one valid file left
  91                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  92                         }
  93
  94                         if (!abort) {
  95                                 //if the user changes the output directory command factory will send this info to us in the output parameter
  96                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                         outputDir = "";
  98                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
  99                                 }
 100                         }
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103
 104                         string temp;
 105                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 106                         trump = temp[0];
 107
 108                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 109                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 110
 111                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 112                         convert(temp, processors);
 113
 114                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 115                         else if (hard == "not open") { abort = true; }
 116
 117                         vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
 118
 119                         numSeqs = 0;
 120
 121                 }
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 126                 exit(1);
 127         }
 128 }
 129
 130 //**********************************************************************************************************************
 131
 132 void FilterSeqsCommand::help(){
 133         try {
 134
 135                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 136                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 137                 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");
 138                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 139                 m->mothurOut("The trump parameter .... The default is ...\n");
 140                 m->mothurOut("The soft parameter .... The default is ....\n");
 141                 m->mothurOut("The hard parameter .... The default is ....\n");
 142                 m->mothurOut("The vertical parameter .... The default is T.\n");
 143                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 144                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
 145                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
 146                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 147
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "FilterSeqsCommand", "help");
 151                 exit(1);
 152         }
 153 }
 154
 155 /**************************************************************************************/
 156
 157 int FilterSeqsCommand::execute() {
 158         try {
 159
 160                 if (abort == true) { return 0; }
 161
 162                 ifstream inFASTA;
 163                 openInputFile(fastafileNames[0], inFASTA);
 164
 165                 Sequence testSeq(inFASTA);
 166                 alignmentLength = testSeq.getAlignLength();
 167                 inFASTA.close();
 168
 169                 ////////////create filter/////////////////
 170                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 171
 172                 filter = createFilter();
 173
 174                 m->mothurOutEndLine();  m->mothurOutEndLine();
 175
 176                 if (m->control_pressed) { return 0; }
 177
 178                 #ifdef USE_MPI
 179                         int pid;
 180                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 181
 182                         if (pid == 0) { //only one process should output the filter
 183                 #endif
 184
 185                 ofstream outFilter;
 186
 187                 string filterFile = outputDir + filterFileName + ".filter";
 188                 openOutputFile(filterFile, outFilter);
 189                 outFilter << filter << endl;
 190                 outFilter.close();
 191                 outputNames.push_back(filterFile);
 192
 193                 #ifdef USE_MPI
 194                         }
 195                 #endif
 196
 197                 ////////////run filter/////////////////
 198
 199                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 200
 201                 filterSequences();
 202
 203                 m->mothurOutEndLine();  m->mothurOutEndLine();
 204
 205                 int filteredLength = 0;
 206                 for(int i=0;i<alignmentLength;i++){
 207                         if(filter[i] == '1'){   filteredLength++;       }
 208                 }
 209
 210                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 211
 212
 213                 m->mothurOutEndLine();
 214                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 215                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 216                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 217                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 218
 219
 220                 m->mothurOutEndLine();
 221                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 222                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 223                 m->mothurOutEndLine();
 224
 225                 return 0;
 226
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "FilterSeqsCommand", "execute");
 230                 exit(1);
 231         }
 232 }
 233 /**************************************************************************************/
 234 int FilterSeqsCommand::filterSequences() {
 235         try {
 236
 237                 numSeqs = 0;
 238
 239                 for (int s = 0; s < fastafileNames.size(); s++) {
 240
 241                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 242
 243                                 string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
 244 #ifdef USE_MPI
 245                                 int pid, start, end, numSeqsPerProcessor, num;
 246                                 int tag = 2001;
 247                                 vector<long>MPIPos;
 248
 249                                 MPI_Status status;
 250                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 251                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 252
 253                                 MPI_File outMPI;
 254                                 MPI_File tempMPI;
 255                                 MPI_File inMPI;
 256                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 257                                 int inMode=MPI_MODE_RDONLY;
 258
 259                                 //char* outFilename = new char[filteredFasta.length()];
 260                                 //memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
 261
 262                                 char outFilename[1024];
 263                                 strcpy(outFilename, filteredFasta.c_str());
 264
 265                                 //char* inFileName = new char[fastafileNames[s].length()];
 266                                 //memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
 267
 268                                 char inFileName[1024];
 269                                 strcpy(inFileName, fastafileNames[s].c_str());
 270
 271                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 272                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 273
 274                                 //delete inFileName;
 275                                 //delete outFilename;
 276
 277                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 278
 279                                 if (pid == 0) { //you are the root process
 280
 281                                         MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 282                                         numSeqs += num;
 283
 284                                         //send file positions to all processes
 285                                         for(int i = 1; i < processors; i++) {
 286                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 287                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 288                                         }
 289
 290                                         //figure out how many sequences you have to do
 291                                         numSeqsPerProcessor = num / processors;
 292                                         int startIndex =  pid * numSeqsPerProcessor;
 293                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 294
 295
 296                                         //do your part
 297                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 298
 299                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 300
 301                                         //wait on chidren
 302                                         for(int i = 1; i < processors; i++) {
 303                                                 char buf[4];
 304                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 305                                         }
 306
 307                                 }else { //you are a child process
 308                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 309                                         MPIPos.resize(num+1);
 310                                         numSeqs += num;
 311                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 312
 313                                         //figure out how many sequences you have to align
 314                                         numSeqsPerProcessor = num / processors;
 315                                         int startIndex =  pid * numSeqsPerProcessor;
 316                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 317
 318
 319                                         //align your part
 320                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 321
 322                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 323
 324                                         char buf[4];
 325                                         strcpy(buf, "done");
 326
 327                                         //tell parent you are done.
 328                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 329                                 }
 330
 331                                 MPI_File_close(&outMPI);
 332                                 MPI_File_close(&inMPI);
 333                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 334
 335 #else
 336                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 337                                 if(processors == 1){
 338                                         ifstream inFASTA;
 339                                         int numFastaSeqs;
 340                                         openInputFile(fastafileNames[s], inFASTA);
 341                                         getNumSeqs(inFASTA, numFastaSeqs);
 342                                         inFASTA.close();
 343
 344                                         lines.push_back(new linePair(0, numFastaSeqs));
 345
 346                                         numSeqs += numFastaSeqs;
 347
 348                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 349                                 }else{
 350                                         setLines(fastafileNames[s]);
 351                                         createProcessesRunFilter(filter, fastafileNames[s]);
 352
 353                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 354
 355                                         //append fasta files
 356                                         for(int i=1;i<processors;i++){
 357                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 358                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 359                                         }
 360                                 }
 361
 362                                 if (m->control_pressed) {  return 1; }
 363                 #else
 364                                 ifstream inFASTA;
 365                                 int numFastaSeqs;
 366                                 openInputFile(fastafileNames[s], inFASTA);
 367                                 getNumSeqs(inFASTA, numFastaSeqs);
 368                                 inFASTA.close();
 369
 370                                 lines.push_back(new linePair(0, numFastaSeqs));
 371
 372                                 numSeqs += numFastaSeqs;
 373
 374                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 375
 376                                 if (m->control_pressed) {  return 1; }
 377                 #endif
 378 #endif
 379                         outputNames.push_back(filteredFasta);
 380                 }
 381
 382                 return 0;
 383         }
 384         catch(exception& e) {
 385                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 386                 exit(1);
 387         }
 388 }
 389 #ifdef USE_MPI
 390 /**************************************************************************************/
 391 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
 392         try {
 393                 string outputString = "";
 394                 int count = 0;
 395                 MPI_Status status;
 396
 397                 for(int i=0;i<num;i++){
 398
 399                         if (m->control_pressed) { return 0; }
 400
 401                         //read next sequence
 402                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 403                         char* buf4 = new char[length];
 404                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 405
 406                         string tempBuf = buf4;
 407                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 408                         istringstream iss (tempBuf,istringstream::in);
 409                         delete buf4;
 410
 411                         Sequence seq(iss);  gobble(iss);
 412
 413                         if (seq.getName() != "") {
 414                                 string align = seq.getAligned();
 415                                 string filterSeq = "";
 416
 417                                 for(int j=0;j<alignmentLength;j++){
 418                                         if(filter[j] == '1'){
 419                                                 filterSeq += align[j];
 420                                         }
 421                                 }
 422
 423                                 count++;
 424                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 425
 426                                 if(count % 10 == 0){ //output to file
 427                                         //send results to parent
 428                                         int length = outputString.length();
 429                                         char* buf = new char[length];
 430                                         memcpy(buf, outputString.c_str(), length);
 431
 432                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 433                                         outputString = "";
 434                                         delete buf;
 435                                 }
 436
 437                         }
 438
 439                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 440                 }
 441
 442                 if(outputString != ""){ //output to file
 443                         //send results to parent
 444                         int length = outputString.length();
 445                         char* buf = new char[length];
 446                         memcpy(buf, outputString.c_str(), length);
 447
 448                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 449                         outputString = "";
 450                         delete buf;
 451                 }
 452
 453                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 454
 455                 return 0;
 456         }
 457         catch(exception& e) {
 458                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 459                 exit(1);
 460         }
 461 }
 462 #endif
 463 /**************************************************************************************/
 464 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 465         try {
 466                 ofstream out;
 467                 openOutputFile(outputFilename, out);
 468
 469                 ifstream in;
 470                 openInputFile(inputFilename, in);
 471
 472                 in.seekg(line->start);
 473
 474                 for(int i=0;i<line->num;i++){
 475
 476                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 477
 478                                 Sequence seq(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                                 }
 491                                 gobble(in);
 492                 }
 493                 out.close();
 494                 in.close();
 495
 496                 return 0;
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 500                 exit(1);
 501         }
 502 }
 503 /**************************************************************************************************/
 504
 505 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 506         try {
 507 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 508                 int process = 0;
 509                 int exitCommand = 1;
 510                 processIDS.clear();
 511
 512                 //loop through and create all the processes you want
 513                 while (process != processors) {
 514                         int pid = fork();
 515
 516                         if (pid > 0) {
 517                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 518                                 process++;
 519                         }else if (pid == 0){
 520                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 521                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 522                                 exit(0);
 523                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 524                 }
 525
 526                 //force parent to wait until all the processes are done
 527                 for (int i=0;i<processors;i++) {
 528                         int temp = processIDS[i];
 529                         wait(&temp);
 530                 }
 531
 532                 return exitCommand;
 533 #endif
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 537                 exit(1);
 538         }
 539 }
 540 /**************************************************************************************/
 541 string FilterSeqsCommand::createFilter() {
 542         try {
 543                 string filterString = "";
 544                 Filters F;
 545
 546                 if (soft != 0)                  {  F.setSoft(soft);             }
 547                 if (trump != '*')               {  F.setTrump(trump);   }
 548
 549                 F.setLength(alignmentLength);
 550
 551                 if(trump != '*' || isTrue(vertical) || soft != 0){
 552                         F.initialize();
 553                 }
 554
 555                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 556                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 557
 558                 numSeqs = 0;
 559                 if(trump != '*' || isTrue(vertical) || soft != 0){
 560                         for (int s = 0; s < fastafileNames.size(); s++) {
 561
 562                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 563
 564 #ifdef USE_MPI
 565                                 int pid, numSeqsPerProcessor, num;
 566                                 int tag = 2001;
 567                                 vector<long> MPIPos;
 568
 569                                 MPI_Status status;
 570                                 MPI_File inMPI;
 571                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 572                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 573
 574                                 //char* tempFileName = new char(fastafileNames[s].length());
 575                                 //tempFileName = &(fastafileNames[s][0]);
 576
 577                                 char tempFileName[1024];
 578                                 strcpy(tempFileName, fastafileNames[s].c_str());
 579
 580                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 581
 582                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 583
 584                                 if (pid == 0) { //you are the root process
 585                                                 MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 586                                                 numSeqs += num;
 587
 588                                                 //send file positions to all processes
 589                                                 for(int i = 1; i < processors; i++) {
 590                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 591                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 592                                                 }
 593
 594                                                 //figure out how many sequences you have to do
 595                                                 numSeqsPerProcessor = num / processors;
 596                                                 int startIndex =  pid * numSeqsPerProcessor;
 597                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 598
 599
 600                                                 //do your part
 601                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 602
 603                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 604
 605                                 }else { //i am the child process
 606                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 607                                         MPIPos.resize(num+1);
 608                                         numSeqs += num;
 609                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 610
 611                                         //figure out how many sequences you have to align
 612                                         numSeqsPerProcessor = num / processors;
 613                                         int startIndex =  pid * numSeqsPerProcessor;
 614                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 615
 616
 617                                         //do your part
 618                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 619
 620                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 621                                 }
 622
 623                                 MPI_File_close(&inMPI);
 624                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 625
 626 #else
 627                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 628                                 if(processors == 1){
 629                                         ifstream inFASTA;
 630                                         int numFastaSeqs;
 631                                         openInputFile(fastafileNames[s], inFASTA);
 632                                         getNumSeqs(inFASTA, numFastaSeqs);
 633                                         inFASTA.close();
 634
 635                                         numSeqs += numFastaSeqs;
 636
 637                                         lines.push_back(new linePair(0, numFastaSeqs));
 638
 639                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 640                                 }else{
 641                                         setLines(fastafileNames[s]);
 642                                         createProcessesCreateFilter(F, fastafileNames[s]);
 643                                 }
 644
 645                                 if (m->control_pressed) {  return filterString; }
 646                 #else
 647                                 ifstream inFASTA;
 648                                 int numFastaSeqs;
 649                                 openInputFile(fastafileNames[s], inFASTA);
 650                                 getNumSeqs(inFASTA, numFastaSeqs);
 651                                 inFASTA.close();
 652
 653                                 numSeqs += numFastaSeqs;
 654
 655                                 lines.push_back(new linePair(0, numFastaSeqs));
 656
 657                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 658                                 if (m->control_pressed) {  return filterString; }
 659                 #endif
 660 #endif
 661
 662                         }
 663                 }
 664
 665
 666 #ifdef USE_MPI
 667                 int pid;
 668                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 669                 MPI_Status status;
 670
 671                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 672
 673                 if(trump != '*' || isTrue(vertical) || soft != 0){
 674
 675                         if (pid == 0) { //only one process should output the filter
 676
 677                                 vector<int> temp; temp.resize(alignmentLength+1);
 678
 679                                 //get the frequencies from the child processes
 680                                 for(int i = 1; i < processors; i++) {
 681
 682                                         for (int j = 0; j < 5; j++) {
 683
 684                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 685                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 686
 687                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 688                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 689                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 690                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 691                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 692                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 693                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 694                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 695                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 696                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 697                                                 }
 698                                         }
 699                                 }
 700                         }else{
 701
 702                                 //send my fequency counts
 703                                 F.a.push_back(Atag);
 704                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 705                                 F.t.push_back(Ttag);
 706                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 707                                 F.c.push_back(Ctag);
 708                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 709                                 F.g.push_back(Gtag);
 710                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 711                                 F.gap.push_back(Gaptag);
 712                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 713                         }
 714
 715                 }
 716
 717                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 718
 719                 if (pid == 0) { //only one process should output the filter
 720 #endif
 721                 F.setNumSeqs(numSeqs);
 722
 723                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 724                 if(soft != 0)                           {       F.doSoft();             }
 725
 726                 filterString = F.getFilter();
 727
 728 #ifdef USE_MPI
 729                 //send filter string to kids
 730                 //for(int i = 1; i < processors; i++) {
 731                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 732                 //}
 733                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 734         }else{
 735                 //recieve filterString
 736                 char* tempBuf = new char[alignmentLength];
 737                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 738                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 739
 740                 filterString = tempBuf;
 741                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 742                 delete tempBuf;
 743         }
 744
 745         MPI_Barrier(MPI_COMM_WORLD);
 746 #endif
 747
 748                 return filterString;
 749         }
 750         catch(exception& e) {
 751                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 752                 exit(1);
 753         }
 754 }
 755 /**************************************************************************************/
 756 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 757         try {
 758
 759                 ifstream in;
 760                 openInputFile(filename, in);
 761
 762                 in.seekg(line->start);
 763
 764                 for(int i=0;i<line->num;i++){
 765
 766                         if (m->control_pressed) { in.close(); return 1; }
 767
 768                         Sequence seq(in);
 769                         if (seq.getName() != "") {
 770                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 771
 772                                         if(trump != '*'){       F.doTrump(seq); }
 773                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 774                                         cout.flush();
 775                         }
 776
 777                         //report progress
 778                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 779                 }
 780
 781                 //report progress
 782                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 783
 784                 in.close();
 785
 786                 return 0;
 787         }
 788         catch(exception& e) {
 789                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 790                 exit(1);
 791         }
 792 }
 793 #ifdef USE_MPI
 794 /**************************************************************************************/
 795 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
 796         try {
 797
 798                 MPI_Status status;
 799                 int pid;
 800                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 801
 802                 for(int i=0;i<num;i++){
 803
 804                         if (m->control_pressed) { return 0; }
 805
 806                         //read next sequence
 807                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 808
 809                         char* buf4 = new char[length];
 810                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 811
 812                         string tempBuf = buf4;
 813                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 814                         istringstream iss (tempBuf,istringstream::in);
 815                         delete buf4;
 816
 817                         Sequence seq(iss);
 818
 819                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 820
 821                         if(trump != '*'){       F.doTrump(seq); }
 822                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 823                         cout.flush();
 824
 825                         //report progress
 826                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 827                 }
 828
 829                 //report progress
 830                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 831
 832                 return 0;
 833         }
 834         catch(exception& e) {
 835                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 836                 exit(1);
 837         }
 838 }
 839 #endif
 840 /**************************************************************************************************/
 841
 842 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 843         try {
 844 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 845                 int process = 0;
 846                 int exitCommand = 1;
 847                 processIDS.clear();
 848
 849                 //loop through and create all the processes you want
 850                 while (process != processors) {
 851                         int pid = vfork();
 852
 853                         if (pid > 0) {
 854                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 855                                 process++;
 856                         }else if (pid == 0){
 857                                 driverCreateFilter(F, filename, lines[process]);
 858                                 exit(0);
 859                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 860                 }
 861
 862                 //force parent to wait until all the processes are done
 863                 for (int i=0;i<processors;i++) {
 864                         int temp = processIDS[i];
 865                         wait(&temp);
 866                 }
 867
 868                 return exitCommand;
 869 #endif
 870         }
 871         catch(exception& e) {
 872                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 873                 exit(1);
 874         }
 875 }
 876 /**************************************************************************************************/
 877
 878 int FilterSeqsCommand::setLines(string filename) {
 879         try {
 880
 881                 vector<long int> positions;
 882                 bufferSizes.clear();
 883
 884                 ifstream inFASTA;
 885                 openInputFile(filename, inFASTA);
 886
 887                 string input;
 888                 while(!inFASTA.eof()){
 889                         input = getline(inFASTA);
 890
 891                         if (input.length() != 0) {
 892                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 893                         }
 894                 }
 895                 inFASTA.close();
 896
 897                 int numFastaSeqs = positions.size();
 898
 899                 FILE * pFile;
 900                 long size;
 901
 902                 //get num bytes in file
 903                 pFile = fopen (filename.c_str(),"rb");
 904                 if (pFile==NULL) perror ("Error opening file");
 905                 else{
 906                         fseek (pFile, 0, SEEK_END);
 907                         size=ftell (pFile);
 908                         fclose (pFile);
 909                 }
 910
 911                 numSeqs += numFastaSeqs;
 912
 913                 int numSeqsPerProcessor = numFastaSeqs / processors;
 914
 915                 for (int i = 0; i < processors; i++) {
 916
 917                         long int startPos = positions[ i * numSeqsPerProcessor ];
 918                         if(i == processors - 1){
 919                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 920                                 bufferSizes.push_back(size - startPos);
 921                         }else{
 922                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 923                                 bufferSizes.push_back(myEnd-startPos);
 924                         }
 925                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 926                 }
 927
 928                 return 0;
 929         }
 930         catch(exception& e) {
 931                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 932                 exit(1);
 933         }
 934 }
 935 /**************************************************************************************/