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                                         ifstream in;
  76                                         int ableToOpen = openInputFile(fastafileNames[i], in, "noerror");
  77
  78                                         //if you can't open it, try default location
  79                                         if (ableToOpen == 1) {
  80                                                 if (m->getDefaultPath() != "") { //default path is set
  81                                                         string tryPath = m->getDefaultPath() + getSimpleName(fastafileNames[i]);
  82                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  83                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  84                                                         fastafileNames[i] = tryPath;
  85                                                 }
  86                                         }
  87                                         in.close();
  88
  89                                         if (ableToOpen == 1) {
  90                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
  91                                                 //erase from file list
  92                                                 fastafileNames.erase(fastafileNames.begin()+i);
  93                                                 i--;
  94                                         }else{
  95                                                 string simpleName = getSimpleName(fastafileNames[i]);
  96                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  97                                         }
  98                                         in.close();
  99                                 }
 100
 101                                 //make sure there is at least one valid file left
 102                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 103                         }
 104
 105                         if (!abort) {
 106                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 107                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 108                                         outputDir = "";
 109                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 110                                 }
 111                         }
 112                         //check for optional parameter and set defaults
 113                         // ...at some point should added some additional type checking...
 114
 115                         string temp;
 116                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 117                         else if (hard == "not open") { hard = ""; abort = true; }
 118
 119                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 120                         trump = temp[0];
 121
 122                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 123                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 124
 125                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 126                         convert(temp, processors);
 127
 128                         vertical = validParameter.validFile(parameters, "vertical", false);
 129                         if (vertical == "not found") {
 130                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 131                                 else { vertical = "F";  }
 132                         }
 133
 134                         numSeqs = 0;
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145
 146 void FilterSeqsCommand::help(){
 147         try {
 148
 149                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 150                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 151                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 152                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 153                 m->mothurOut("The trump parameter .... The default is ...\n");
 154                 m->mothurOut("The soft parameter .... The default is ....\n");
 155                 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
 156                 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
 157                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 158                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 159                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 160                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 161
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "FilterSeqsCommand", "help");
 165                 exit(1);
 166         }
 167 }
 168
 169 /**************************************************************************************/
 170
 171 int FilterSeqsCommand::execute() {
 172         try {
 173
 174                 if (abort == true) { return 0; }
 175
 176                 ifstream inFASTA;
 177                 openInputFile(fastafileNames[0], inFASTA);
 178
 179                 Sequence testSeq(inFASTA);
 180                 alignmentLength = testSeq.getAlignLength();
 181                 inFASTA.close();
 182
 183                 ////////////create filter/////////////////
 184                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 185
 186                 filter = createFilter();
 187
 188                 m->mothurOutEndLine();  m->mothurOutEndLine();
 189
 190                 if (m->control_pressed) { return 0; }
 191
 192                 #ifdef USE_MPI
 193                         int pid;
 194                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 195
 196                         if (pid == 0) { //only one process should output the filter
 197                 #endif
 198
 199                 ofstream outFilter;
 200
 201                 string filterFile = outputDir + filterFileName + ".filter";
 202                 openOutputFile(filterFile, outFilter);
 203                 outFilter << filter << endl;
 204                 outFilter.close();
 205                 outputNames.push_back(filterFile);
 206
 207                 #ifdef USE_MPI
 208                         }
 209                 #endif
 210
 211                 ////////////run filter/////////////////
 212
 213                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 214
 215                 filterSequences();
 216
 217                 m->mothurOutEndLine();  m->mothurOutEndLine();
 218
 219                 int filteredLength = 0;
 220                 for(int i=0;i<alignmentLength;i++){
 221                         if(filter[i] == '1'){   filteredLength++;       }
 222                 }
 223
 224                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 225
 226
 227                 m->mothurOutEndLine();
 228                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 229                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 230                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 231                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 232
 233
 234                 m->mothurOutEndLine();
 235                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 236                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 237                 m->mothurOutEndLine();
 238
 239                 return 0;
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "FilterSeqsCommand", "execute");
 244                 exit(1);
 245         }
 246 }
 247 /**************************************************************************************/
 248 int FilterSeqsCommand::filterSequences() {
 249         try {
 250
 251                 numSeqs = 0;
 252
 253                 for (int s = 0; s < fastafileNames.size(); s++) {
 254
 255                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 256
 257                                 string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
 258 #ifdef USE_MPI
 259                                 int pid, start, end, numSeqsPerProcessor, num;
 260                                 int tag = 2001;
 261                                 vector<long>MPIPos;
 262
 263                                 MPI_Status status;
 264                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 265                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 266
 267                                 MPI_File outMPI;
 268                                 MPI_File tempMPI;
 269                                 MPI_File inMPI;
 270                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 271                                 int inMode=MPI_MODE_RDONLY;
 272
 273                                 char outFilename[1024];
 274                                 strcpy(outFilename, filteredFasta.c_str());
 275
 276                                 char inFileName[1024];
 277                                 strcpy(inFileName, fastafileNames[s].c_str());
 278
 279                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 280                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 281
 282                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 283
 284                                 if (pid == 0) { //you are the root process
 285
 286                                         MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 287                                         numSeqs += num;
 288
 289                                         //send file positions to all processes
 290                                         for(int i = 1; i < processors; i++) {
 291                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 292                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 293                                         }
 294
 295                                         //figure out how many sequences you have to do
 296                                         numSeqsPerProcessor = num / processors;
 297                                         int startIndex =  pid * numSeqsPerProcessor;
 298                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 299
 300
 301                                         //do your part
 302                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 303
 304                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 305
 306                                         //wait on chidren
 307                                         for(int i = 1; i < processors; i++) {
 308                                                 char buf[4];
 309                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 310                                         }
 311
 312                                 }else { //you are a child process
 313                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 314                                         MPIPos.resize(num+1);
 315                                         numSeqs += num;
 316                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 317
 318                                         //figure out how many sequences you have to align
 319                                         numSeqsPerProcessor = num / processors;
 320                                         int startIndex =  pid * numSeqsPerProcessor;
 321                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 322
 323
 324                                         //align your part
 325                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 326
 327                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 328
 329                                         char buf[4];
 330                                         strcpy(buf, "done");
 331
 332                                         //tell parent you are done.
 333                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 334                                 }
 335
 336                                 MPI_File_close(&outMPI);
 337                                 MPI_File_close(&inMPI);
 338                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 339
 340 #else
 341                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 342                                 if(processors == 1){
 343                                         ifstream inFASTA;
 344                                         int numFastaSeqs;
 345                                         openInputFile(fastafileNames[s], inFASTA);
 346                                         getNumSeqs(inFASTA, numFastaSeqs);
 347                                         inFASTA.close();
 348
 349                                         lines.push_back(new linePair(0, numFastaSeqs));
 350
 351                                         numSeqs += numFastaSeqs;
 352
 353                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 354                                 }else{
 355                                         setLines(fastafileNames[s]);
 356                                         createProcessesRunFilter(filter, fastafileNames[s]);
 357
 358                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 359
 360                                         //append fasta files
 361                                         for(int i=1;i<processors;i++){
 362                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 363                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 364                                         }
 365                                 }
 366
 367                                 if (m->control_pressed) {  return 1; }
 368                 #else
 369                                 ifstream inFASTA;
 370                                 int numFastaSeqs;
 371                                 openInputFile(fastafileNames[s], inFASTA);
 372                                 getNumSeqs(inFASTA, numFastaSeqs);
 373                                 inFASTA.close();
 374
 375                                 lines.push_back(new linePair(0, numFastaSeqs));
 376
 377                                 numSeqs += numFastaSeqs;
 378
 379                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 380
 381                                 if (m->control_pressed) {  return 1; }
 382                 #endif
 383 #endif
 384                         outputNames.push_back(filteredFasta);
 385                 }
 386
 387                 return 0;
 388         }
 389         catch(exception& e) {
 390                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 391                 exit(1);
 392         }
 393 }
 394 #ifdef USE_MPI
 395 /**************************************************************************************/
 396 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
 397         try {
 398                 string outputString = "";
 399                 int count = 0;
 400                 MPI_Status status;
 401
 402                 for(int i=0;i<num;i++){
 403
 404                         if (m->control_pressed) { return 0; }
 405
 406                         //read next sequence
 407                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 408                         char* buf4 = new char[length];
 409                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 410
 411                         string tempBuf = buf4;
 412                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 413                         istringstream iss (tempBuf,istringstream::in);
 414                         delete buf4;
 415
 416                         Sequence seq(iss);  gobble(iss);
 417
 418                         if (seq.getName() != "") {
 419                                 string align = seq.getAligned();
 420                                 string filterSeq = "";
 421
 422                                 for(int j=0;j<alignmentLength;j++){
 423                                         if(filter[j] == '1'){
 424                                                 filterSeq += align[j];
 425                                         }
 426                                 }
 427
 428                                 count++;
 429                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 430
 431                                 if(count % 10 == 0){ //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                         }
 443
 444                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 445                 }
 446
 447                 if(outputString != ""){ //output to file
 448                         //send results to parent
 449                         int length = outputString.length();
 450                         char* buf = new char[length];
 451                         memcpy(buf, outputString.c_str(), length);
 452
 453                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 454                         outputString = "";
 455                         delete buf;
 456                 }
 457
 458                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 459
 460                 return 0;
 461         }
 462         catch(exception& e) {
 463                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 464                 exit(1);
 465         }
 466 }
 467 #endif
 468 /**************************************************************************************/
 469 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 470         try {
 471                 ofstream out;
 472                 openOutputFile(outputFilename, out);
 473
 474                 ifstream in;
 475                 openInputFile(inputFilename, in);
 476
 477                 in.seekg(line->start);
 478
 479                 for(int i=0;i<line->num;i++){
 480
 481                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 482
 483                                 Sequence seq(in);
 484                                 if (seq.getName() != "") {
 485                                         string align = seq.getAligned();
 486                                         string filterSeq = "";
 487
 488                                         for(int j=0;j<alignmentLength;j++){
 489                                                 if(filter[j] == '1'){
 490                                                         filterSeq += align[j];
 491                                                 }
 492                                         }
 493
 494                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 495                                 }
 496                                 gobble(in);
 497                 }
 498                 out.close();
 499                 in.close();
 500
 501                 return 0;
 502         }
 503         catch(exception& e) {
 504                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 505                 exit(1);
 506         }
 507 }
 508 /**************************************************************************************************/
 509
 510 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 511         try {
 512 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 513                 int process = 0;
 514                 int exitCommand = 1;
 515                 processIDS.clear();
 516
 517                 //loop through and create all the processes you want
 518                 while (process != processors) {
 519                         int pid = fork();
 520
 521                         if (pid > 0) {
 522                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 523                                 process++;
 524                         }else if (pid == 0){
 525                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 526                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 527                                 exit(0);
 528                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 529                 }
 530
 531                 //force parent to wait until all the processes are done
 532                 for (int i=0;i<processors;i++) {
 533                         int temp = processIDS[i];
 534                         wait(&temp);
 535                 }
 536
 537                 return exitCommand;
 538 #endif
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 542                 exit(1);
 543         }
 544 }
 545 /**************************************************************************************/
 546 string FilterSeqsCommand::createFilter() {
 547         try {
 548                 string filterString = "";
 549                 Filters F;
 550
 551                 if (soft != 0)                  {  F.setSoft(soft);             }
 552                 if (trump != '*')               {  F.setTrump(trump);   }
 553
 554                 F.setLength(alignmentLength);
 555
 556                 if(trump != '*' || isTrue(vertical) || soft != 0){
 557                         F.initialize();
 558                 }
 559
 560                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 561                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 562
 563                 numSeqs = 0;
 564                 if(trump != '*' || isTrue(vertical) || soft != 0){
 565                         for (int s = 0; s < fastafileNames.size(); s++) {
 566
 567                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 568
 569 #ifdef USE_MPI
 570                                 int pid, numSeqsPerProcessor, num;
 571                                 int tag = 2001;
 572                                 vector<long> MPIPos;
 573
 574                                 MPI_Status status;
 575                                 MPI_File inMPI;
 576                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 577                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 578
 579                                 //char* tempFileName = new char(fastafileNames[s].length());
 580                                 //tempFileName = &(fastafileNames[s][0]);
 581
 582                                 char tempFileName[1024];
 583                                 strcpy(tempFileName, fastafileNames[s].c_str());
 584
 585                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 586
 587                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 588
 589                                 if (pid == 0) { //you are the root process
 590                                                 MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 591                                                 numSeqs += num;
 592
 593                                                 //send file positions to all processes
 594                                                 for(int i = 1; i < processors; i++) {
 595                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 596                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 597                                                 }
 598
 599                                                 //figure out how many sequences you have to do
 600                                                 numSeqsPerProcessor = num / processors;
 601                                                 int startIndex =  pid * numSeqsPerProcessor;
 602                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 603
 604
 605                                                 //do your part
 606                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 607
 608                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 609
 610                                 }else { //i am the child process
 611                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 612                                         MPIPos.resize(num+1);
 613                                         numSeqs += num;
 614                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 615
 616                                         //figure out how many sequences you have to align
 617                                         numSeqsPerProcessor = num / processors;
 618                                         int startIndex =  pid * numSeqsPerProcessor;
 619                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 620
 621
 622                                         //do your part
 623                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 624
 625                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 626                                 }
 627
 628                                 MPI_File_close(&inMPI);
 629                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 630
 631 #else
 632                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 633                                 if(processors == 1){
 634                                         ifstream inFASTA;
 635                                         int numFastaSeqs;
 636                                         openInputFile(fastafileNames[s], inFASTA);
 637                                         getNumSeqs(inFASTA, numFastaSeqs);
 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                                 }else{
 646                                         setLines(fastafileNames[s]);
 647                                         createProcessesCreateFilter(F, fastafileNames[s]);
 648                                 }
 649
 650                                 if (m->control_pressed) {  return filterString; }
 651                 #else
 652                                 ifstream inFASTA;
 653                                 int numFastaSeqs;
 654                                 openInputFile(fastafileNames[s], inFASTA);
 655                                 getNumSeqs(inFASTA, numFastaSeqs);
 656                                 inFASTA.close();
 657
 658                                 numSeqs += numFastaSeqs;
 659
 660                                 lines.push_back(new linePair(0, numFastaSeqs));
 661
 662                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 663                                 if (m->control_pressed) {  return filterString; }
 664                 #endif
 665 #endif
 666
 667                         }
 668                 }
 669
 670
 671 #ifdef USE_MPI
 672                 int pid;
 673                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 674                 MPI_Status status;
 675
 676                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 677
 678                 if(trump != '*' || isTrue(vertical) || soft != 0){
 679
 680                         if (pid == 0) { //only one process should output the filter
 681
 682                                 vector<int> temp; temp.resize(alignmentLength+1);
 683
 684                                 //get the frequencies from the child processes
 685                                 for(int i = 1; i < processors; i++) {
 686
 687                                         for (int j = 0; j < 5; j++) {
 688
 689                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 690                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 691
 692                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 693                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 694                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 695                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 696                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 697                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 698                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 699                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 700                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 701                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 702                                                 }
 703                                         }
 704                                 }
 705                         }else{
 706
 707                                 //send my fequency counts
 708                                 F.a.push_back(Atag);
 709                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 710                                 F.t.push_back(Ttag);
 711                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 712                                 F.c.push_back(Ctag);
 713                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 714                                 F.g.push_back(Gtag);
 715                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 716                                 F.gap.push_back(Gaptag);
 717                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 718                         }
 719
 720                 }
 721
 722                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 723
 724                 if (pid == 0) { //only one process should output the filter
 725 #endif
 726                 F.setNumSeqs(numSeqs);
 727
 728                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 729                 if(soft != 0)                           {       F.doSoft();             }
 730
 731                 filterString = F.getFilter();
 732
 733 #ifdef USE_MPI
 734                 //send filter string to kids
 735                 //for(int i = 1; i < processors; i++) {
 736                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 737                 //}
 738                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 739         }else{
 740                 //recieve filterString
 741                 char* tempBuf = new char[alignmentLength];
 742                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 743                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 744
 745                 filterString = tempBuf;
 746                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 747                 delete tempBuf;
 748         }
 749
 750         MPI_Barrier(MPI_COMM_WORLD);
 751 #endif
 752
 753                 return filterString;
 754         }
 755         catch(exception& e) {
 756                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 757                 exit(1);
 758         }
 759 }
 760 /**************************************************************************************/
 761 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 762         try {
 763
 764                 ifstream in;
 765                 openInputFile(filename, in);
 766
 767                 in.seekg(line->start);
 768
 769                 for(int i=0;i<line->num;i++){
 770
 771                         if (m->control_pressed) { in.close(); return 1; }
 772
 773                         Sequence seq(in);
 774                         if (seq.getName() != "") {
 775                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 776
 777                                         if(trump != '*'){       F.doTrump(seq); }
 778                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 779                                         cout.flush();
 780                         }
 781
 782                         //report progress
 783                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 784                 }
 785
 786                 //report progress
 787                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 788
 789                 in.close();
 790
 791                 return 0;
 792         }
 793         catch(exception& e) {
 794                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 795                 exit(1);
 796         }
 797 }
 798 #ifdef USE_MPI
 799 /**************************************************************************************/
 800 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
 801         try {
 802
 803                 MPI_Status status;
 804                 int pid;
 805                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 806
 807                 for(int i=0;i<num;i++){
 808
 809                         if (m->control_pressed) { return 0; }
 810
 811                         //read next sequence
 812                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 813
 814                         char* buf4 = new char[length];
 815                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 816
 817                         string tempBuf = buf4;
 818                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 819                         istringstream iss (tempBuf,istringstream::in);
 820                         delete buf4;
 821
 822                         Sequence seq(iss);
 823
 824                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 825
 826                         if(trump != '*'){       F.doTrump(seq); }
 827                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 828                         cout.flush();
 829
 830                         //report progress
 831                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 832                 }
 833
 834                 //report progress
 835                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 836
 837                 return 0;
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 841                 exit(1);
 842         }
 843 }
 844 #endif
 845 /**************************************************************************************************/
 846
 847 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 848         try {
 849 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 850                 int process = 0;
 851                 int exitCommand = 1;
 852                 processIDS.clear();
 853
 854                 //loop through and create all the processes you want
 855                 while (process != processors) {
 856                         int pid = vfork();
 857
 858                         if (pid > 0) {
 859                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 860                                 process++;
 861                         }else if (pid == 0){
 862                                 driverCreateFilter(F, filename, lines[process]);
 863                                 exit(0);
 864                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 865                 }
 866
 867                 //force parent to wait until all the processes are done
 868                 for (int i=0;i<processors;i++) {
 869                         int temp = processIDS[i];
 870                         wait(&temp);
 871                 }
 872
 873                 return exitCommand;
 874 #endif
 875         }
 876         catch(exception& e) {
 877                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 878                 exit(1);
 879         }
 880 }
 881 /**************************************************************************************************/
 882
 883 int FilterSeqsCommand::setLines(string filename) {
 884         try {
 885
 886                 vector<unsigned long int> positions;
 887                 bufferSizes.clear();
 888
 889                 ifstream inFASTA;
 890                 openInputFile(filename, inFASTA);
 891
 892                 string input;
 893                 while(!inFASTA.eof()){
 894                         input = getline(inFASTA);
 895
 896                         if (input.length() != 0) {
 897                                 if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);    }
 898                         }
 899                 }
 900                 inFASTA.close();
 901
 902                 int numFastaSeqs = positions.size();
 903
 904                 FILE * pFile;
 905                 unsigned long int size;
 906
 907                 //get num bytes in file
 908                 pFile = fopen (filename.c_str(),"rb");
 909                 if (pFile==NULL) perror ("Error opening file");
 910                 else{
 911                         fseek (pFile, 0, SEEK_END);
 912                         size=ftell (pFile);
 913                         fclose (pFile);
 914                 }
 915
 916                 numSeqs += numFastaSeqs;
 917
 918                 int numSeqsPerProcessor = numFastaSeqs / processors;
 919
 920                 for (int i = 0; i < processors; i++) {
 921
 922                         unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 923                         if(i == processors - 1){
 924                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 925                                 bufferSizes.push_back(size - startPos);
 926                         }else{
 927                                 unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 928                                 bufferSizes.push_back(myEnd-startPos);
 929                         }
 930                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 931                 }
 932
 933                 return 0;
 934         }
 935         catch(exception& e) {
 936                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 937                 exit(1);
 938         }
 939 }
 940 /**************************************************************************************/