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                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 286                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 287
 288                                         //figure out how many sequences you have to do
 289                                         numSeqsPerProcessor = num / processors;
 290                                         int startIndex =  pid * numSeqsPerProcessor;
 291                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 292
 293
 294                                         //do your part
 295                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 296
 297                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 298
 299                                         //wait on chidren
 300                                         for(int i = 1; i < processors; i++) {
 301                                                 char buf[4];
 302                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 303                                         }
 304
 305                                 }else { //you are a child process
 306                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 307                                         numSeqs += num;
 308                                         MPIPos.resize(num+1);
 309                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 310
 311                                         //figure out how many sequences you have to align
 312                                         numSeqsPerProcessor = num / processors;
 313                                         int startIndex =  pid * numSeqsPerProcessor;
 314                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 315
 316
 317                                         //align your part
 318                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 319
 320                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 321
 322                                         char buf[4];
 323                                         strcpy(buf, "done");
 324
 325                                         //tell parent you are done.
 326                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 327                                 }
 328
 329                                 MPI_File_close(&outMPI);
 330                                 MPI_File_close(&inMPI);
 331
 332 #else
 333                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 334                                 if(processors == 1){
 335                                         ifstream inFASTA;
 336                                         openInputFile(fastafileNames[s], inFASTA);
 337                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 338                                         inFASTA.close();
 339
 340                                         lines.push_back(new linePair(0, numFastaSeqs));
 341
 342                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 343                                 }else{
 344                                         setLines(fastafileNames[s]);
 345                                         createProcessesRunFilter(filter, fastafileNames[s]);
 346
 347                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 348
 349                                         //append fasta files
 350                                         for(int i=1;i<processors;i++){
 351                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 352                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 353                                         }
 354                                 }
 355
 356                                 if (m->control_pressed) {  return 1; }
 357                 #else
 358                                 ifstream inFASTA;
 359                                 openInputFile(fastafileNames[s], inFASTA);
 360                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 361                                 inFASTA.close();
 362
 363                                 lines.push_back(new linePair(0, numFastaSeqs));
 364
 365                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 366
 367                                 if (m->control_pressed) {  return 1; }
 368                 #endif
 369 #endif
 370                         outputNames.push_back(filteredFasta);
 371                 }
 372
 373                 return 0;
 374         }
 375         catch(exception& e) {
 376                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 377                 exit(1);
 378         }
 379 }
 380 #ifdef USE_MPI
 381 /**************************************************************************************/
 382 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
 383         try {
 384                 string outputString = "";
 385                 int count = 0;
 386                 MPI_Status status;
 387
 388                 for(int i=0;i<num;i++){
 389
 390                         if (m->control_pressed) { return 0; }
 391
 392                         //read next sequence
 393                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 394                         char* buf4 = new char[length];
 395                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 396
 397                         string tempBuf = buf4;
 398                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 399                         istringstream iss (tempBuf,istringstream::in);
 400                         delete buf4;
 401
 402                         Sequence seq(iss);  gobble(iss);
 403
 404                         if (seq.getName() != "") {
 405                                 string align = seq.getAligned();
 406                                 string filterSeq = "";
 407
 408                                 for(int j=0;j<alignmentLength;j++){
 409                                         if(filter[j] == '1'){
 410                                                 filterSeq += align[j];
 411                                         }
 412                                 }
 413
 414                                 count++;
 415                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 416
 417                                 if(count % 10 == 0){ //output to file
 418                                         //send results to parent
 419                                         int length = outputString.length();
 420                                         char* buf = new char[length];
 421                                         memcpy(buf, outputString.c_str(), length);
 422
 423                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 424                                         outputString = "";
 425                                         delete buf;
 426                                 }
 427
 428                         }
 429
 430                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 431                 }
 432
 433                 if(outputString != ""){ //output to file
 434                         //send results to parent
 435                         int length = outputString.length();
 436                         char* buf = new char[length];
 437                         memcpy(buf, outputString.c_str(), length);
 438
 439                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 440                         outputString = "";
 441                         delete buf;
 442                 }
 443
 444                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 445
 446                 return 0;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 450                 exit(1);
 451         }
 452 }
 453 #endif
 454 /**************************************************************************************/
 455 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 456         try {
 457                 ofstream out;
 458                 openOutputFile(outputFilename, out);
 459
 460                 ifstream in;
 461                 openInputFile(inputFilename, in);
 462
 463                 in.seekg(line->start);
 464
 465                 for(int i=0;i<line->num;i++){
 466
 467                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 468
 469                                 Sequence seq(in);
 470                                 if (seq.getName() != "") {
 471                                         string align = seq.getAligned();
 472                                         string filterSeq = "";
 473
 474                                         for(int j=0;j<alignmentLength;j++){
 475                                                 if(filter[j] == '1'){
 476                                                         filterSeq += align[j];
 477                                                 }
 478                                         }
 479
 480                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 481                                 }
 482                                 gobble(in);
 483                 }
 484                 out.close();
 485                 in.close();
 486
 487                 return 0;
 488         }
 489         catch(exception& e) {
 490                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 491                 exit(1);
 492         }
 493 }
 494 /**************************************************************************************************/
 495
 496 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 497         try {
 498 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 499                 int process = 0;
 500                 int exitCommand = 1;
 501                 processIDS.clear();
 502
 503                 //loop through and create all the processes you want
 504                 while (process != processors) {
 505                         int pid = fork();
 506
 507                         if (pid > 0) {
 508                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 509                                 process++;
 510                         }else if (pid == 0){
 511                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 512                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 513                                 exit(0);
 514                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 515                 }
 516
 517                 //force parent to wait until all the processes are done
 518                 for (int i=0;i<processors;i++) {
 519                         int temp = processIDS[i];
 520                         wait(&temp);
 521                 }
 522
 523                 return exitCommand;
 524 #endif
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 528                 exit(1);
 529         }
 530 }
 531 /**************************************************************************************/
 532 string FilterSeqsCommand::createFilter() {
 533         try {
 534                 string filterString = "";
 535                 Filters F;
 536
 537                 if (soft != 0)                  {  F.setSoft(soft);             }
 538                 if (trump != '*')               {  F.setTrump(trump);   }
 539
 540                 F.setLength(alignmentLength);
 541
 542                 if(soft != 0 || isTrue(vertical)){
 543                         F.initialize();
 544                 }
 545
 546                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 547                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 548
 549                 numSeqs = 0;
 550                 if(trump != '*' || isTrue(vertical) || soft != 0){
 551                         for (int s = 0; s < fastafileNames.size(); s++) {
 552
 553                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 554
 555 #ifdef USE_MPI
 556                                 int pid, numSeqsPerProcessor, num;
 557                                 int tag = 2001;
 558                                 vector<long> MPIPos;
 559
 560                                 MPI_Status status;
 561                                 MPI_File inMPI;
 562                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 563                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 564
 565                                 //char* tempFileName = new char(fastafileNames[s].length());
 566                                 //tempFileName = &(fastafileNames[s][0]);
 567
 568                                 char tempFileName[1024];
 569                                 strcpy(tempFileName, fastafileNames[s].c_str());
 570
 571                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 572
 573                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 574
 575                                 if (pid == 0) { //you are the root process
 576                                                 MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 577                                                 numSeqs += num;
 578
 579                                                 //send file positions to all processes
 580                                                 MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 581                                                 MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 582
 583                                                 //figure out how many sequences you have to do
 584                                                 numSeqsPerProcessor = num / processors;
 585                                                 int startIndex =  pid * numSeqsPerProcessor;
 586                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 587
 588
 589                                                 //do your part
 590                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 591
 592                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 593
 594                                 }else { //i am the child process
 595
 596                                         MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 597                                         MPIPos.resize(num+1);
 598                                         numSeqs += num;
 599                                         MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 600
 601                                         //figure out how many sequences you have to align
 602                                         numSeqsPerProcessor = num / processors;
 603                                         int startIndex =  pid * numSeqsPerProcessor;
 604                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 605
 606
 607                                         //do your part
 608                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 609
 610                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 611                                 }
 612
 613                                 MPI_File_close(&inMPI);
 614
 615 #else
 616                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 617                                 if(processors == 1){
 618                                         ifstream inFASTA;
 619                                         openInputFile(fastafileNames[s], inFASTA);
 620                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 621                                         inFASTA.close();
 622
 623                                         numSeqs += numFastaSeqs;
 624
 625                                         lines.push_back(new linePair(0, numFastaSeqs));
 626
 627                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 628                                 }else{
 629                                         setLines(fastafileNames[s]);
 630                                         createProcessesCreateFilter(F, fastafileNames[s]);
 631                                 }
 632
 633                                 if (m->control_pressed) {  return filterString; }
 634                 #else
 635                                 ifstream inFASTA;
 636                                 openInputFile(fastafileNames[s], inFASTA);
 637                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 638                                 inFASTA.close();
 639
 640                                 numSeqs += numFastaSeqs;
 641
 642                                 lines.push_back(new linePair(0, numFastaSeqs));
 643
 644                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 645                                 if (m->control_pressed) {  return filterString; }
 646                 #endif
 647 #endif
 648
 649                         }
 650                 }
 651
 652
 653 #ifdef USE_MPI
 654                 int pid;
 655                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 656                 MPI_Status status;
 657
 658                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 659
 660                 if(trump != '*' || isTrue(vertical) || soft != 0){
 661
 662                         if (pid == 0) { //only one process should output the filter
 663
 664                                 vector<int> temp; temp.resize(alignmentLength+1);
 665
 666                                 //get the frequencies from the child processes
 667                                 for(int i = 0; i < ((processors-1)*5); i++) {
 668                                         MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 2001, MPI_COMM_WORLD, &status);
 669                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 670
 671                                         if (receiveTag == Atag) { //you are recieveing the A frequencies
 672                                                 for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 673                                         }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 674                                                 for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 675                                         }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 676                                                 for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 677                                         }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 678                                                 for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 679                                         }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 680                                                 for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 681                                         }
 682                                 }
 683                         }else{
 684
 685                                 //send my fequency counts
 686                                 F.a.push_back(Atag);
 687                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 688                                 F.t.push_back(Ttag);
 689                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 690                                 F.c.push_back(Ctag);
 691                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 692                                 F.g.push_back(Gtag);
 693                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 694                                 F.gap.push_back(Gaptag);
 695                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 696                         }
 697
 698                 }
 699
 700                 if (pid == 0) { //only one process should output the filter
 701 #endif
 702                 F.setNumSeqs(numSeqs);
 703
 704                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 705                 if(soft != 0)                           {       F.doSoft();             }
 706
 707                 filterString = F.getFilter();
 708
 709 #ifdef USE_MPI
 710                 //send filter string to kids
 711                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 712         }else{
 713                 //recieve filterString
 714                 char* tempBuf = new char[alignmentLength];
 715                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 716
 717                 filterString = tempBuf;
 718                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 719                 delete tempBuf;
 720         }
 721
 722         MPI_Barrier(MPI_COMM_WORLD);
 723 #endif
 724
 725
 726                 return filterString;
 727         }
 728         catch(exception& e) {
 729                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 730                 exit(1);
 731         }
 732 }
 733 /**************************************************************************************/
 734 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 735         try {
 736
 737                 ifstream in;
 738                 openInputFile(filename, in);
 739
 740                 in.seekg(line->start);
 741
 742                 for(int i=0;i<line->num;i++){
 743
 744                         if (m->control_pressed) { in.close(); return 1; }
 745
 746                         Sequence seq(in);
 747                         if (seq.getName() != "") {
 748                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 749
 750                                         if(trump != '*'){       F.doTrump(seq); }
 751                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 752                                         cout.flush();
 753                         }
 754
 755                         //report progress
 756                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 757                 }
 758
 759                 //report progress
 760                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 761
 762                 in.close();
 763
 764                 return 0;
 765         }
 766         catch(exception& e) {
 767                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 768                 exit(1);
 769         }
 770 }
 771 #ifdef USE_MPI
 772 /**************************************************************************************/
 773 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
 774         try {
 775
 776                 MPI_Status status;
 777                 int pid;
 778                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 779
 780                 for(int i=0;i<num;i++){
 781
 782                         if (m->control_pressed) { return 0; }
 783
 784                         //read next sequence
 785                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 786
 787                         char* buf4 = new char[length];
 788                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 789
 790                         string tempBuf = buf4;
 791                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 792                         istringstream iss (tempBuf,istringstream::in);
 793                         delete buf4;
 794
 795                         Sequence seq(iss);
 796
 797                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 798
 799                         if(trump != '*'){       F.doTrump(seq); }
 800                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 801                         cout.flush();
 802
 803                         //report progress
 804                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 805                 }
 806
 807                 //report progress
 808                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 809
 810                 return 0;
 811         }
 812         catch(exception& e) {
 813                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 814                 exit(1);
 815         }
 816 }
 817 #endif
 818 /**************************************************************************************************/
 819
 820 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 821         try {
 822 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 823                 int process = 0;
 824                 int exitCommand = 1;
 825                 processIDS.clear();
 826
 827                 //loop through and create all the processes you want
 828                 while (process != processors) {
 829                         int pid = vfork();
 830
 831                         if (pid > 0) {
 832                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 833                                 process++;
 834                         }else if (pid == 0){
 835                                 driverCreateFilter(F, filename, lines[process]);
 836                                 exit(0);
 837                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 838                 }
 839
 840                 //force parent to wait until all the processes are done
 841                 for (int i=0;i<processors;i++) {
 842                         int temp = processIDS[i];
 843                         wait(&temp);
 844                 }
 845
 846                 return exitCommand;
 847 #endif
 848         }
 849         catch(exception& e) {
 850                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 851                 exit(1);
 852         }
 853 }
 854 /**************************************************************************************************/
 855
 856 int FilterSeqsCommand::setLines(string filename) {
 857         try {
 858
 859                 vector<long int> positions;
 860                 bufferSizes.clear();
 861
 862                 ifstream inFASTA;
 863                 openInputFile(filename, inFASTA);
 864
 865                 string input;
 866                 while(!inFASTA.eof()){
 867                         input = getline(inFASTA);
 868
 869                         if (input.length() != 0) {
 870                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 871                         }
 872                 }
 873                 inFASTA.close();
 874
 875                 int numFastaSeqs = positions.size();
 876
 877                 FILE * pFile;
 878                 long size;
 879
 880                 //get num bytes in file
 881                 pFile = fopen (filename.c_str(),"rb");
 882                 if (pFile==NULL) perror ("Error opening file");
 883                 else{
 884                         fseek (pFile, 0, SEEK_END);
 885                         size=ftell (pFile);
 886                         fclose (pFile);
 887                 }
 888
 889                 numSeqs += numFastaSeqs;
 890
 891                 int numSeqsPerProcessor = numFastaSeqs / processors;
 892
 893                 for (int i = 0; i < processors; i++) {
 894
 895                         long int startPos = positions[ i * numSeqsPerProcessor ];
 896                         if(i == processors - 1){
 897                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 898                                 bufferSizes.push_back(size - startPos);
 899                         }else{
 900                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 901                                 bufferSizes.push_back(myEnd-startPos);
 902                         }
 903                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 904                 }
 905
 906                 return 0;
 907         }
 908         catch(exception& e) {
 909                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 910                 exit(1);
 911         }
 912 }
 913 /**************************************************************************************/