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 vector<string> FilterSeqsCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "FilterSeqsCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 FilterSeqsCommand::FilterSeqsCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["fasta"] = tempOutNames;
  31                 outputTypes["filter"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> FilterSeqsCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> FilterSeqsCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 /**************************************************************************************/
  62 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  63         try {
  64                 abort = false;
  65                 filterFileName = "";
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter("filter.seqs");
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["fasta"] = tempOutNames;
  89                         outputTypes["filter"] = tempOutNames;
  90
  91                         //if the user changes the input directory command factory will send this info to us in the output parameter
  92                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  93                         if (inputDir == "not found"){   inputDir = "";          }
  94                         else {
  95                                 string path;
  96                                 it = parameters.find("fasta");
  97                                 //user has given a template file
  98                                 if(it != parameters.end()){
  99                                         path = m->hasPath(it->second);
 100                                         //if the user has not given a path then, add inputdir. else leave path alone.
 101                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 102                                 }
 103
 104                                 it = parameters.find("hard");
 105                                 //user has given a template file
 106                                 if(it != parameters.end()){
 107                                         path = m->hasPath(it->second);
 108                                         //if the user has not given a path then, add inputdir. else leave path alone.
 109                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 110                                 }
 111                         }
 112
 113                         //check for required parameters
 114                         fasta = validParameter.validFile(parameters, "fasta", false);
 115                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
 116                         else {
 117                                 m->splitAtDash(fasta, fastafileNames);
 118
 119                                 //go through files and make sure they are good, if not, then disregard them
 120                                 for (int i = 0; i < fastafileNames.size(); i++) {
 121                                         if (inputDir != "") {
 122                                                 string path = m->hasPath(fastafileNames[i]);
 123                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 124                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 125                                         }
 126
 127                                         ifstream in;
 128                                         int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 129
 130                                         //if you can't open it, try default location
 131                                         if (ableToOpen == 1) {
 132                                                 if (m->getDefaultPath() != "") { //default path is set
 133                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 134                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 135                                                         ableToOpen = m->openInputFile(tryPath, in, "noerror");
 136                                                         fastafileNames[i] = tryPath;
 137                                                 }
 138                                         }
 139
 140                                         //if you can't open it, try default location
 141                                         if (ableToOpen == 1) {
 142                                                 if (m->getOutputDir() != "") { //default path is set
 143                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 144                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 145                                                         ableToOpen = m->openInputFile(tryPath, in, "noerror");
 146                                                         fastafileNames[i] = tryPath;
 147                                                 }
 148                                         }
 149
 150                                         in.close();
 151
 152                                         if (ableToOpen == 1) {
 153                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 154                                                 //erase from file list
 155                                                 fastafileNames.erase(fastafileNames.begin()+i);
 156                                                 i--;
 157                                         }else{
 158                                                 string simpleName = m->getSimpleName(fastafileNames[i]);
 159                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 160                                         }
 161                                         in.close();
 162                                 }
 163
 164                                 //make sure there is at least one valid file left
 165                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 166                         }
 167
 168                         if (!abort) {
 169                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 170                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 171                                         outputDir = "";
 172                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 173                                 }
 174                         }
 175                         //check for optional parameter and set defaults
 176                         // ...at some point should added some additional type checking...
 177
 178                         string temp;
 179                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 180                         else if (hard == "not open") { hard = ""; abort = true; }
 181
 182                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 183                         trump = temp[0];
 184
 185                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 186                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 187
 188                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 189                         convert(temp, processors);
 190
 191                         vertical = validParameter.validFile(parameters, "vertical", false);
 192                         if (vertical == "not found") {
 193                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 194                                 else { vertical = "F";  }
 195                         }
 196
 197                         numSeqs = 0;
 198                 }
 199
 200         }
 201         catch(exception& e) {
 202                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 203                 exit(1);
 204         }
 205 }
 206
 207 //**********************************************************************************************************************
 208
 209 void FilterSeqsCommand::help(){
 210         try {
 211
 212                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 213                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n");
 214                 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");
 215                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 216                 m->mothurOut("The trump parameter .... The default is ...\n");
 217                 m->mothurOut("The soft parameter .... The default is ....\n");
 218                 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
 219                 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
 220                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 221                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 222                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 223                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 224                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 225
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "FilterSeqsCommand", "help");
 229                 exit(1);
 230         }
 231 }
 232
 233 /**************************************************************************************/
 234
 235 int FilterSeqsCommand::execute() {
 236         try {
 237
 238                 if (abort == true) { return 0; }
 239
 240                 ifstream inFASTA;
 241                 m->openInputFile(fastafileNames[0], inFASTA);
 242
 243                 Sequence testSeq(inFASTA);
 244                 alignmentLength = testSeq.getAlignLength();
 245                 inFASTA.close();
 246
 247                 ////////////create filter/////////////////
 248                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 249
 250                 filter = createFilter();
 251
 252                 m->mothurOutEndLine();  m->mothurOutEndLine();
 253
 254                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 255
 256                 #ifdef USE_MPI
 257                         int pid;
 258                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 259
 260                         if (pid == 0) { //only one process should output the filter
 261                 #endif
 262
 263                 ofstream outFilter;
 264
 265                 //prevent giantic file name
 266                 string filterFile;
 267                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 268                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 269
 270                 m->openOutputFile(filterFile, outFilter);
 271                 outFilter << filter << endl;
 272                 outFilter.close();
 273                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 274
 275                 #ifdef USE_MPI
 276                         }
 277                 #endif
 278
 279                 ////////////run filter/////////////////
 280
 281                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 282
 283                 filterSequences();
 284
 285                 m->mothurOutEndLine();  m->mothurOutEndLine();
 286
 287                 int filteredLength = 0;
 288                 for(int i=0;i<alignmentLength;i++){
 289                         if(filter[i] == '1'){   filteredLength++;       }
 290                 }
 291
 292                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 293
 294
 295                 m->mothurOutEndLine();
 296                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 297                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 298                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 299                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 300
 301
 302                 m->mothurOutEndLine();
 303                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 304                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 305                 m->mothurOutEndLine();
 306
 307                 return 0;
 308
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "FilterSeqsCommand", "execute");
 312                 exit(1);
 313         }
 314 }
 315 /**************************************************************************************/
 316 int FilterSeqsCommand::filterSequences() {
 317         try {
 318
 319                 numSeqs = 0;
 320
 321                 for (int s = 0; s < fastafileNames.size(); s++) {
 322
 323                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 324
 325                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 326 #ifdef USE_MPI
 327                                 int pid, start, end, numSeqsPerProcessor, num;
 328                                 int tag = 2001;
 329                                 vector<unsigned long int>MPIPos;
 330
 331                                 MPI_Status status;
 332                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 333                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 334
 335                                 MPI_File outMPI;
 336                                 MPI_File tempMPI;
 337                                 MPI_File inMPI;
 338                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 339                                 int inMode=MPI_MODE_RDONLY;
 340
 341                                 char outFilename[1024];
 342                                 strcpy(outFilename, filteredFasta.c_str());
 343
 344                                 char inFileName[1024];
 345                                 strcpy(inFileName, fastafileNames[s].c_str());
 346
 347                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 348                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 349
 350                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 351
 352                                 if (pid == 0) { //you are the root process
 353
 354                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 355                                         numSeqs += num;
 356
 357                                         //send file positions to all processes
 358                                         for(int i = 1; i < processors; i++) {
 359                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 360                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 361                                         }
 362
 363                                         //figure out how many sequences you have to do
 364                                         numSeqsPerProcessor = num / processors;
 365                                         int startIndex =  pid * numSeqsPerProcessor;
 366                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 367
 368
 369                                         //do your part
 370                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 371
 372                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 373
 374                                         //wait on chidren
 375                                         for(int i = 1; i < processors; i++) {
 376                                                 char buf[5];
 377                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 378                                         }
 379
 380                                 }else { //you are a child process
 381                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 382                                         MPIPos.resize(num+1);
 383                                         numSeqs += num;
 384                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 385
 386                                         //figure out how many sequences you have to align
 387                                         numSeqsPerProcessor = num / processors;
 388                                         int startIndex =  pid * numSeqsPerProcessor;
 389                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 390
 391
 392                                         //align your part
 393                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 394
 395                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 396
 397                                         char buf[5];
 398                                         strcpy(buf, "done");
 399
 400                                         //tell parent you are done.
 401                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 402                                 }
 403
 404                                 MPI_File_close(&outMPI);
 405                                 MPI_File_close(&inMPI);
 406                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 407
 408 #else
 409                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 410
 411                         for (int i = 0; i < (positions.size()-1); i++) {
 412                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 413                         }
 414                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 415                                 if(processors == 1){
 416                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 417                                         numSeqs += numFastaSeqs;
 418                                 }else{
 419                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 420                                         numSeqs += numFastaSeqs;
 421
 422                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 423
 424                                         //append fasta files
 425                                         for(int i=1;i<processors;i++){
 426                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 427                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 428                                         }
 429                                 }
 430
 431                                 if (m->control_pressed) {  return 1; }
 432                 #else
 433                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 434                                 numSeqs += numFastaSeqs;
 435
 436                                 if (m->control_pressed) {  return 1; }
 437                 #endif
 438 #endif
 439                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 440                 }
 441
 442                 return 0;
 443         }
 444         catch(exception& e) {
 445                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 446                 exit(1);
 447         }
 448 }
 449 #ifdef USE_MPI
 450 /**************************************************************************************/
 451 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 452         try {
 453                 string outputString = "";
 454                 int count = 0;
 455                 MPI_Status status;
 456
 457                 for(int i=0;i<num;i++){
 458
 459                         if (m->control_pressed) { return 0; }
 460
 461                         //read next sequence
 462                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 463                         char* buf4 = new char[length];
 464                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 465
 466                         string tempBuf = buf4;
 467                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 468                         istringstream iss (tempBuf,istringstream::in);
 469                         delete buf4;
 470
 471                         Sequence seq(iss);  m->gobble(iss);
 472
 473                         if (seq.getName() != "") {
 474                                 string align = seq.getAligned();
 475                                 string filterSeq = "";
 476
 477                                 for(int j=0;j<alignmentLength;j++){
 478                                         if(filter[j] == '1'){
 479                                                 filterSeq += align[j];
 480                                         }
 481                                 }
 482
 483                                 count++;
 484                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 485
 486                                 if(count % 10 == 0){ //output to file
 487                                         //send results to parent
 488                                         int length = outputString.length();
 489                                         char* buf = new char[length];
 490                                         memcpy(buf, outputString.c_str(), length);
 491
 492                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 493                                         outputString = "";
 494                                         delete buf;
 495                                 }
 496
 497                         }
 498
 499                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 500                 }
 501
 502                 if(outputString != ""){ //output to file
 503                         //send results to parent
 504                         int length = outputString.length();
 505                         char* buf = new char[length];
 506                         memcpy(buf, outputString.c_str(), length);
 507
 508                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 509                         outputString = "";
 510                         delete buf;
 511                 }
 512
 513                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 514
 515                 return 0;
 516         }
 517         catch(exception& e) {
 518                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 519                 exit(1);
 520         }
 521 }
 522 #endif
 523 /**************************************************************************************/
 524 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 525         try {
 526                 ofstream out;
 527                 m->openOutputFile(outputFilename, out);
 528
 529                 ifstream in;
 530                 m->openInputFile(inputFilename, in);
 531
 532                 in.seekg(filePos->start);
 533
 534                 bool done = false;
 535                 int count = 0;
 536
 537                 while (!done) {
 538
 539                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 540
 541                                 Sequence seq(in); m->gobble(in);
 542                                 if (seq.getName() != "") {
 543                                         string align = seq.getAligned();
 544                                         string filterSeq = "";
 545
 546                                         for(int j=0;j<alignmentLength;j++){
 547                                                 if(filter[j] == '1'){
 548                                                         filterSeq += align[j];
 549                                                 }
 550                                         }
 551
 552                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 553                                 count++;
 554                         }
 555
 556                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 557                                 unsigned long int pos = in.tellg();
 558                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 559                         #else
 560                                 if (in.eof()) { break; }
 561                         #endif
 562
 563                         //report progress
 564                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 565                 }
 566                 //report progress
 567                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 568
 569
 570                 out.close();
 571                 in.close();
 572
 573                 return count;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 577                 exit(1);
 578         }
 579 }
 580 /**************************************************************************************************/
 581
 582 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 583         try {
 584 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 585                 int process = 0;
 586                 int num = 0;
 587                 processIDS.clear();
 588
 589                 //loop through and create all the processes you want
 590                 while (process != processors) {
 591                         int pid = fork();
 592
 593                         if (pid > 0) {
 594                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 595                                 process++;
 596                         }else if (pid == 0){
 597                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 598                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 599
 600                                 //pass numSeqs to parent
 601                                 ofstream out;
 602                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 603                                 m->openOutputFile(tempFile, out);
 604                                 out << num << endl;
 605                                 out.close();
 606
 607                                 exit(0);
 608                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 609                 }
 610
 611                 //force parent to wait until all the processes are done
 612                 for (int i=0;i<processors;i++) {
 613                         int temp = processIDS[i];
 614                         wait(&temp);
 615                 }
 616
 617                 for (int i = 0; i < processIDS.size(); i++) {
 618                         ifstream in;
 619                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 620                         m->openInputFile(tempFile, in);
 621                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 622                         in.close(); remove(tempFile.c_str());
 623                 }
 624
 625
 626                 return num;
 627 #endif
 628         }
 629         catch(exception& e) {
 630                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 631                 exit(1);
 632         }
 633 }
 634 /**************************************************************************************/
 635 string FilterSeqsCommand::createFilter() {
 636         try {
 637                 string filterString = "";
 638                 Filters F;
 639
 640                 if (soft != 0)                  {  F.setSoft(soft);             }
 641                 if (trump != '*')               {  F.setTrump(trump);   }
 642
 643                 F.setLength(alignmentLength);
 644
 645                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 646                         F.initialize();
 647                 }
 648
 649                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 650                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 651
 652                 numSeqs = 0;
 653                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 654                         for (int s = 0; s < fastafileNames.size(); s++) {
 655
 656                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 657
 658 #ifdef USE_MPI
 659                                 int pid, numSeqsPerProcessor, num;
 660                                 int tag = 2001;
 661                                 vector<unsigned long int> MPIPos;
 662
 663                                 MPI_Status status;
 664                                 MPI_File inMPI;
 665                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 666                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 667
 668                                 //char* tempFileName = new char(fastafileNames[s].length());
 669                                 //tempFileName = &(fastafileNames[s][0]);
 670
 671                                 char tempFileName[1024];
 672                                 strcpy(tempFileName, fastafileNames[s].c_str());
 673
 674                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 675
 676                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 677
 678                                 if (pid == 0) { //you are the root process
 679                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 680                                                 numSeqs += num;
 681
 682                                                 //send file positions to all processes
 683                                                 for(int i = 1; i < processors; i++) {
 684                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 685                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 686                                                 }
 687
 688                                                 //figure out how many sequences you have to do
 689                                                 numSeqsPerProcessor = num / processors;
 690                                                 int startIndex =  pid * numSeqsPerProcessor;
 691                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 692
 693
 694                                                 //do your part
 695                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 696
 697                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 698
 699                                 }else { //i am the child process
 700                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 701                                         MPIPos.resize(num+1);
 702                                         numSeqs += num;
 703                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 704
 705                                         //figure out how many sequences you have to align
 706                                         numSeqsPerProcessor = num / processors;
 707                                         int startIndex =  pid * numSeqsPerProcessor;
 708                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 709
 710
 711                                         //do your part
 712                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 713
 714                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 715                                 }
 716
 717                                 MPI_File_close(&inMPI);
 718                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 719
 720 #else
 721                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 722
 723                 for (int i = 0; i < (positions.size()-1); i++) {
 724                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 725                 }
 726                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 727                                 if(processors == 1){
 728                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 729                                         numSeqs += numFastaSeqs;
 730                                 }else{
 731                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 732                                         numSeqs += numFastaSeqs;
 733                                 }
 734
 735                                 if (m->control_pressed) {  return filterString; }
 736                 #else
 737                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 738                                 numSeqs += numFastaSeqs;
 739                                 if (m->control_pressed) {  return filterString; }
 740                 #endif
 741 #endif
 742
 743                         }
 744                 }
 745
 746
 747 #ifdef USE_MPI
 748                 int pid;
 749                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 750                 MPI_Status status;
 751
 752                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 753
 754                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 755
 756                         if (pid == 0) { //only one process should output the filter
 757
 758                                 vector<int> temp; temp.resize(alignmentLength+1);
 759
 760                                 //get the frequencies from the child processes
 761                                 for(int i = 1; i < processors; i++) {
 762
 763                                         for (int j = 0; j < 5; j++) {
 764
 765                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 766                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 767
 768                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 769                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 770                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 771                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 772                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 773                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 774                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 775                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 776                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 777                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 778                                                 }
 779                                         }
 780                                 }
 781                         }else{
 782
 783                                 //send my fequency counts
 784                                 F.a.push_back(Atag);
 785                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 786                                 F.t.push_back(Ttag);
 787                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 788                                 F.c.push_back(Ctag);
 789                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 790                                 F.g.push_back(Gtag);
 791                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 792                                 F.gap.push_back(Gaptag);
 793                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 794                         }
 795
 796                 }
 797
 798                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 799
 800                 if (pid == 0) { //only one process should output the filter
 801 #endif
 802
 803                 F.setNumSeqs(numSeqs);
 804                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 805                 if(soft != 0)                           {       F.doSoft();             }
 806                 filterString = F.getFilter();
 807
 808 #ifdef USE_MPI
 809                 //send filter string to kids
 810                 //for(int i = 1; i < processors; i++) {
 811                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 812                 //}
 813                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 814         }else{
 815                 //recieve filterString
 816                 char* tempBuf = new char[alignmentLength];
 817                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 818                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 819
 820                 filterString = tempBuf;
 821                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 822                 delete tempBuf;
 823         }
 824
 825         MPI_Barrier(MPI_COMM_WORLD);
 826 #endif
 827
 828                 return filterString;
 829         }
 830         catch(exception& e) {
 831                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 832                 exit(1);
 833         }
 834 }
 835 /**************************************************************************************/
 836 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 837         try {
 838
 839                 ifstream in;
 840                 m->openInputFile(filename, in);
 841
 842                 in.seekg(filePos->start);
 843
 844                 bool done = false;
 845                 int count = 0;
 846
 847                 while (!done) {
 848
 849                         if (m->control_pressed) { in.close(); return 1; }
 850
 851                         Sequence seq(in); m->gobble(in);
 852                         if (seq.getName() != "") {
 853                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 854
 855                                         if(trump != '*')                        {       F.doTrump(seq);         }
 856                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 857                                         cout.flush();
 858                                         count++;
 859                         }
 860
 861                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 862                                 unsigned long int pos = in.tellg();
 863                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 864                         #else
 865                                 if (in.eof()) { break; }
 866                         #endif
 867
 868                         //report progress
 869                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 870                 }
 871                 //report progress
 872                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 873                 in.close();
 874
 875                 return count;
 876         }
 877         catch(exception& e) {
 878                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 879                 exit(1);
 880         }
 881 }
 882 #ifdef USE_MPI
 883 /**************************************************************************************/
 884 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 885         try {
 886
 887                 MPI_Status status;
 888                 int pid;
 889                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 890
 891                 for(int i=0;i<num;i++){
 892
 893                         if (m->control_pressed) { return 0; }
 894
 895                         //read next sequence
 896                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 897
 898                         char* buf4 = new char[length];
 899                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 900
 901                         string tempBuf = buf4;
 902                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 903                         istringstream iss (tempBuf,istringstream::in);
 904                         delete buf4;
 905
 906                         Sequence seq(iss);
 907
 908                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 909
 910                         if(trump != '*'){       F.doTrump(seq); }
 911                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 912                         cout.flush();
 913
 914                         //report progress
 915                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 916                 }
 917
 918                 //report progress
 919                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 920
 921                 return 0;
 922         }
 923         catch(exception& e) {
 924                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 925                 exit(1);
 926         }
 927 }
 928 #endif
 929 /**************************************************************************************************/
 930
 931 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 932         try {
 933 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 934                 int process = 1;
 935                 int num = 0;
 936                 processIDS.clear();
 937
 938                 //loop through and create all the processes you want
 939                 while (process != processors) {
 940                         int pid = fork();
 941
 942                         if (pid > 0) {
 943                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 944                                 process++;
 945                         }else if (pid == 0){
 946                                 //reset child's filter counts to 0;
 947                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 948                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 949                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 950                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 951                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 952
 953                                 num = driverCreateFilter(F, filename, lines[process]);
 954
 955                                 //write out filter counts to file
 956                                 filename += toString(getpid()) + "filterValues.temp";
 957                                 ofstream out;
 958                                 m->openOutputFile(filename, out);
 959
 960                                 out << num << endl;
 961                                 out << F.getFilter() << endl;
 962                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 963                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 964                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 965                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 966                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 967
 968                                 //cout << F.getFilter() << endl;
 969                                 out.close();
 970
 971                                 exit(0);
 972                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 973                 }
 974
 975                 //parent do your part
 976                 num = driverCreateFilter(F, filename, lines[0]);
 977
 978                 //force parent to wait until all the processes are done
 979                 for (int i=0;i<(processors-1);i++) {
 980                         int temp = processIDS[i];
 981                         wait(&temp);
 982                 }
 983
 984                 //parent reads in and combines Filter info
 985                 for (int i = 0; i < processIDS.size(); i++) {
 986                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 987                         ifstream in;
 988                         m->openInputFile(tempFilename, in);
 989
 990                         int temp, tempNum;
 991                         string tempFilterString;
 992
 993                         in >> tempNum; m->gobble(in); num += tempNum;
 994
 995                         in >> tempFilterString;
 996                         F.mergeFilter(tempFilterString);
 997
 998                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
 999                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1000                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1001                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1002                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1003
1004                         in.close();
1005                         remove(tempFilename.c_str());
1006                 }
1007
1008                 return num;
1009 #endif
1010         }
1011         catch(exception& e) {
1012                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1013                 exit(1);
1014         }
1015 }
1016 /**************************************************************************************/