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