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[filteredFasta.length()];
 260                                 strcpy(outFilename, filteredFasta.c_str());
 261
 262                                 char inFileName[fastafileNames[s].length()];
 263                                 strcpy(inFileName, fastafileNames[s].c_str());
 264
 265                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 266                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 267
 268                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 269
 270                                 if (pid == 0) { //you are the root process
 271
 272                                         MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 273                                         numSeqs += num;
 274
 275                                         //send file positions to all processes
 276                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 277                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 278
 279                                         //figure out how many sequences you have to do
 280                                         numSeqsPerProcessor = num / processors;
 281                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 282                                         int startIndex =  pid * numSeqsPerProcessor;
 283
 284                                         //do your part
 285                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 286
 287                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 288
 289                                         //wait on chidren
 290                                         for(int i = 1; i < processors; i++) {
 291                                                 char buf[4];
 292                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 293                                         }
 294
 295                                 }else { //you are a child process
 296                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 297                                         numSeqs += num;
 298                                         MPIPos.resize(num+1);
 299                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 300
 301                                         //figure out how many sequences you have to align
 302                                         numSeqsPerProcessor = num / processors;
 303                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 304                                         int startIndex =  pid * numSeqsPerProcessor;
 305
 306                                         //align 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                                         char buf[4];
 312                                         strcpy(buf, "done");
 313
 314                                         //tell parent you are done.
 315                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 316                                 }
 317
 318                                 MPI_File_close(&outMPI);
 319                                 MPI_File_close(&inMPI);
 320
 321 #else
 322                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 323                                 if(processors == 1){
 324                                         ifstream inFASTA;
 325                                         openInputFile(fastafileNames[s], inFASTA);
 326                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 327                                         inFASTA.close();
 328
 329                                         lines.push_back(new linePair(0, numFastaSeqs));
 330
 331                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 332                                 }else{
 333                                         setLines(fastafileNames[s]);
 334                                         createProcessesRunFilter(filter, fastafileNames[s]);
 335
 336                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 337
 338                                         //append fasta files
 339                                         for(int i=1;i<processors;i++){
 340                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 341                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 342                                         }
 343                                 }
 344
 345                                 if (m->control_pressed) {  return 1; }
 346                 #else
 347                                 ifstream inFASTA;
 348                                 openInputFile(fastafileNames[s], inFASTA);
 349                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 350                                 inFASTA.close();
 351
 352                                 lines.push_back(new linePair(0, numFastaSeqs));
 353
 354                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 355
 356                                 if (m->control_pressed) {  return 1; }
 357                 #endif
 358 #endif
 359                         outputNames.push_back(filteredFasta);
 360                 }
 361
 362                 return 0;
 363         }
 364         catch(exception& e) {
 365                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 366                 exit(1);
 367         }
 368 }
 369 #ifdef USE_MPI
 370 /**************************************************************************************/
 371 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
 372         try {
 373                 string outputString = "";
 374                 int count = 0;
 375                 MPI_Status status;
 376
 377                 for(int i=0;i<num;i++){
 378
 379                         if (m->control_pressed) { return 0; }
 380
 381                         //read next sequence
 382                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 383                         char buf4[length];
 384                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 385
 386                         string tempBuf = buf4;
 387                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 388                         istringstream iss (tempBuf,istringstream::in);
 389
 390                         Sequence seq(iss);  gobble(iss);
 391
 392                         if (seq.getName() != "") {
 393                                 string align = seq.getAligned();
 394                                 string filterSeq = "";
 395
 396                                 for(int j=0;j<alignmentLength;j++){
 397                                         if(filter[j] == '1'){
 398                                                 filterSeq += align[j];
 399                                         }
 400                                 }
 401
 402                                 count++;
 403                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 404
 405                                 if(count % 10 == 0){ //output to file
 406                                         //send results to parent
 407                                         int length = outputString.length();
 408                                         char buf[length];
 409                                         strcpy(buf, outputString.c_str());
 410
 411                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 412                                         outputString = "";
 413                                 }
 414
 415                         }
 416
 417                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 418                 }
 419
 420                 if(outputString != ""){ //output to file
 421                         //send results to parent
 422                         int length = outputString.length();
 423                         char buf[length];
 424                         strcpy(buf, outputString.c_str());
 425
 426                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 427                         outputString = "";
 428                 }
 429
 430                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 431
 432                 return 0;
 433         }
 434         catch(exception& e) {
 435                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 436                 exit(1);
 437         }
 438 }
 439 #endif
 440 /**************************************************************************************/
 441 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 442         try {
 443                 ofstream out;
 444                 openOutputFile(outputFilename, out);
 445
 446                 ifstream in;
 447                 openInputFile(inputFilename, in);
 448
 449                 in.seekg(line->start);
 450
 451                 for(int i=0;i<line->num;i++){
 452
 453                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 454
 455                                 Sequence seq(in);
 456                                 if (seq.getName() != "") {
 457                                         string align = seq.getAligned();
 458                                         string filterSeq = "";
 459
 460                                         for(int j=0;j<alignmentLength;j++){
 461                                                 if(filter[j] == '1'){
 462                                                         filterSeq += align[j];
 463                                                 }
 464                                         }
 465
 466                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 467                                 }
 468                                 gobble(in);
 469                 }
 470                 out.close();
 471                 in.close();
 472
 473                 return 0;
 474         }
 475         catch(exception& e) {
 476                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 477                 exit(1);
 478         }
 479 }
 480 /**************************************************************************************************/
 481
 482 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 483         try {
 484 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 485                 int process = 0;
 486                 int exitCommand = 1;
 487                 processIDS.clear();
 488
 489                 //loop through and create all the processes you want
 490                 while (process != processors) {
 491                         int pid = fork();
 492
 493                         if (pid > 0) {
 494                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 495                                 process++;
 496                         }else if (pid == 0){
 497                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 498                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 499                                 exit(0);
 500                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 501                 }
 502
 503                 //force parent to wait until all the processes are done
 504                 for (int i=0;i<processors;i++) {
 505                         int temp = processIDS[i];
 506                         wait(&temp);
 507                 }
 508
 509                 return exitCommand;
 510 #endif
 511         }
 512         catch(exception& e) {
 513                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 514                 exit(1);
 515         }
 516 }
 517 /**************************************************************************************/
 518 string FilterSeqsCommand::createFilter() {
 519         try {
 520                 string filterString = "";
 521                 Filters F;
 522
 523                 if (soft != 0)                  {  F.setSoft(soft);             }
 524                 if (trump != '*')               {  F.setTrump(trump);   }
 525
 526                 F.setLength(alignmentLength);
 527
 528                 if(soft != 0 || isTrue(vertical)){
 529                         F.initialize();
 530                 }
 531
 532                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 533                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 534
 535                 numSeqs = 0;
 536                 if(trump != '*' || isTrue(vertical) || soft != 0){
 537                         for (int s = 0; s < fastafileNames.size(); s++) {
 538
 539                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 540
 541 #ifdef USE_MPI
 542                                 int pid, numSeqsPerProcessor, num;
 543                                 int tag = 2001;
 544                                 vector<long> MPIPos;
 545
 546                                 MPI_Status status;
 547                                 MPI_File inMPI;
 548                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 549                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 550
 551                                 char* tempFileName = new char(fastafileNames[s].length());
 552                                 tempFileName = &(fastafileNames[s][0]);
 553
 554                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 555
 556                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 557
 558                                 if (pid == 0) { //you are the root process
 559                                                 MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 560                                                 numSeqs += num;
 561
 562                                                 //send file positions to all processes
 563                                                 MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 564                                                 MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 565
 566                                                 //figure out how many sequences you have to do
 567                                                 numSeqsPerProcessor = num / processors;
 568                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 569                                                 int startIndex =  pid * numSeqsPerProcessor;
 570
 571                                                 //do your part
 572                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 573
 574                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 575
 576                                 }else { //i am the child process
 577
 578                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 579                                         MPIPos.resize(num+1);
 580                                         numSeqs += num;
 581                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 582
 583                                         //figure out how many sequences you have to align
 584                                         numSeqsPerProcessor = num / processors;
 585                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 586                                         int startIndex =  pid * numSeqsPerProcessor;
 587
 588                                         //do your part
 589                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 590
 591                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 592                                 }
 593
 594                                 MPI_File_close(&inMPI);
 595
 596 #else
 597                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 598                                 if(processors == 1){
 599                                         ifstream inFASTA;
 600                                         openInputFile(fastafileNames[s], inFASTA);
 601                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 602                                         inFASTA.close();
 603
 604                                         numSeqs += numFastaSeqs;
 605
 606                                         lines.push_back(new linePair(0, numFastaSeqs));
 607
 608                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 609                                 }else{
 610                                         setLines(fastafileNames[s]);
 611                                         createProcessesCreateFilter(F, fastafileNames[s]);
 612                                 }
 613
 614                                 if (m->control_pressed) {  return filterString; }
 615                 #else
 616                                 ifstream inFASTA;
 617                                 openInputFile(fastafileNames[s], inFASTA);
 618                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 619                                 inFASTA.close();
 620
 621                                 numSeqs += numFastaSeqs;
 622
 623                                 lines.push_back(new linePair(0, numFastaSeqs));
 624
 625                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 626                                 if (m->control_pressed) {  return filterString; }
 627                 #endif
 628 #endif
 629
 630                         }
 631                 }
 632
 633
 634 #ifdef USE_MPI
 635                 int pid;
 636                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 637                 MPI_Status status;
 638
 639                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 640                 if (pid == 0) { //only one process should output the filter
 641
 642                         vector<int> temp; temp.resize(alignmentLength+1);
 643
 644                         //get the frequencies from the child processes
 645                         for(int i = 0; i < ((processors-1)*5); i++) {
 646                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 2001, MPI_COMM_WORLD, &status);
 647                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 648
 649                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 650                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 651                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 652                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 653                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 654                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 655                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 656                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 657                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 658                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 659                                 }
 660                         }
 661                 }else{
 662
 663                         //send my fequency counts
 664                         F.a.push_back(Atag);
 665                         int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 666                         F.t.push_back(Ttag);
 667                         ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 668                         F.c.push_back(Ctag);
 669                         ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 670                         F.g.push_back(Gtag);
 671                         ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 672                         F.gap.push_back(Gaptag);
 673                         ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 674                 }
 675
 676                 if (pid == 0) { //only one process should output the filter
 677 #endif
 678                 F.setNumSeqs(numSeqs);
 679
 680                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 681                 if(soft != 0)                           {       F.doSoft();             }
 682
 683                 filterString = F.getFilter();
 684
 685 #ifdef USE_MPI
 686                 //send filter string to kids
 687                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 688         }else{
 689                 //recieve filterString
 690                 char tempBuf[alignmentLength];
 691                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 692
 693                 filterString = tempBuf;
 694                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 695         }
 696
 697         MPI_Barrier(MPI_COMM_WORLD);
 698 #endif
 699
 700
 701                 return filterString;
 702         }
 703         catch(exception& e) {
 704                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 705                 exit(1);
 706         }
 707 }
 708 /**************************************************************************************/
 709 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 710         try {
 711
 712                 ifstream in;
 713                 openInputFile(filename, in);
 714
 715                 in.seekg(line->start);
 716
 717                 for(int i=0;i<line->num;i++){
 718
 719                         if (m->control_pressed) { in.close(); return 1; }
 720
 721                         Sequence seq(in);
 722                         if (seq.getName() != "") {
 723                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 724
 725                                         if(trump != '*'){       F.doTrump(seq); }
 726                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 727                                         cout.flush();
 728                         }
 729
 730                         //report progress
 731                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 732                 }
 733
 734                 //report progress
 735                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 736
 737                 in.close();
 738
 739                 return 0;
 740         }
 741         catch(exception& e) {
 742                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 743                 exit(1);
 744         }
 745 }
 746 #ifdef USE_MPI
 747 /**************************************************************************************/
 748 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
 749         try {
 750
 751                 MPI_Status status;
 752                 int pid;
 753                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 754
 755                 for(int i=0;i<num;i++){
 756
 757                         if (m->control_pressed) { return 0; }
 758
 759                         //read next sequence
 760                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 761
 762                         char buf4[length];
 763                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 764
 765                         string tempBuf = buf4;
 766                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 767                         istringstream iss (tempBuf,istringstream::in);
 768
 769                         Sequence seq(iss);
 770
 771                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 772
 773                         if(trump != '*'){       F.doTrump(seq); }
 774                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 775                         cout.flush();
 776
 777                         //report progress
 778                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 779                 }
 780
 781                 //report progress
 782                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 783
 784                 return 0;
 785         }
 786         catch(exception& e) {
 787                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 788                 exit(1);
 789         }
 790 }
 791 #endif
 792 /**************************************************************************************************/
 793
 794 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 795         try {
 796 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 797                 int process = 0;
 798                 int exitCommand = 1;
 799                 processIDS.clear();
 800
 801                 //loop through and create all the processes you want
 802                 while (process != processors) {
 803                         int pid = vfork();
 804
 805                         if (pid > 0) {
 806                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 807                                 process++;
 808                         }else if (pid == 0){
 809                                 driverCreateFilter(F, filename, lines[process]);
 810                                 exit(0);
 811                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 812                 }
 813
 814                 //force parent to wait until all the processes are done
 815                 for (int i=0;i<processors;i++) {
 816                         int temp = processIDS[i];
 817                         wait(&temp);
 818                 }
 819
 820                 return exitCommand;
 821 #endif
 822         }
 823         catch(exception& e) {
 824                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 825                 exit(1);
 826         }
 827 }
 828 /**************************************************************************************************/
 829
 830 int FilterSeqsCommand::setLines(string filename) {
 831         try {
 832
 833                 vector<long int> positions;
 834                 bufferSizes.clear();
 835
 836                 ifstream inFASTA;
 837                 openInputFile(filename, inFASTA);
 838
 839                 string input;
 840                 while(!inFASTA.eof()){
 841                         input = getline(inFASTA);
 842
 843                         if (input.length() != 0) {
 844                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 845                         }
 846                 }
 847                 inFASTA.close();
 848
 849                 int numFastaSeqs = positions.size();
 850
 851                 FILE * pFile;
 852                 long size;
 853
 854                 //get num bytes in file
 855                 pFile = fopen (filename.c_str(),"rb");
 856                 if (pFile==NULL) perror ("Error opening file");
 857                 else{
 858                         fseek (pFile, 0, SEEK_END);
 859                         size=ftell (pFile);
 860                         fclose (pFile);
 861                 }
 862
 863                 numSeqs += numFastaSeqs;
 864
 865                 int numSeqsPerProcessor = numFastaSeqs / processors;
 866
 867                 for (int i = 0; i < processors; i++) {
 868
 869                         long int startPos = positions[ i * numSeqsPerProcessor ];
 870                         if(i == processors - 1){
 871                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 872                                 bufferSizes.push_back(size - startPos);
 873                         }else{
 874                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 875                                 bufferSizes.push_back(myEnd-startPos);
 876                         }
 877                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 878                 }
 879
 880                 return 0;
 881         }
 882         catch(exception& e) {
 883                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 884                 exit(1);
 885         }
 886 }
 887 /**************************************************************************************/