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                                                         ifstream in2;
 136                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 137                                                         in2.close();
 138                                                         fastafileNames[i] = tryPath;
 139                                                 }
 140                                         }
 141
 142                                         //if you can't open it, try default location
 143                                         if (ableToOpen == 1) {
 144                                                 if (m->getOutputDir() != "") { //default path is set
 145                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 146                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 147                                                         ifstream in2;
 148                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 149                                                         in2.close();
 150                                                         fastafileNames[i] = tryPath;
 151                                                 }
 152                                         }
 153
 154                                         in.close();
 155
 156                                         if (ableToOpen == 1) {
 157                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 158                                                 //erase from file list
 159                                                 fastafileNames.erase(fastafileNames.begin()+i);
 160                                                 i--;
 161                                         }else{
 162                                                 string simpleName = m->getSimpleName(fastafileNames[i]);
 163                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 164                                         }
 165                                         in.close();
 166                                 }
 167
 168                                 //make sure there is at least one valid file left
 169                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 170                         }
 171
 172                         if (!abort) {
 173                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 174                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 175                                         outputDir = "";
 176                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 177                                 }
 178                         }
 179                         //check for optional parameter and set defaults
 180                         // ...at some point should added some additional type checking...
 181
 182                         string temp;
 183                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 184                         else if (hard == "not open") { hard = ""; abort = true; }
 185
 186                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 187                         trump = temp[0];
 188
 189                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 190                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 191
 192                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 193                         convert(temp, processors);
 194
 195                         vertical = validParameter.validFile(parameters, "vertical", false);
 196                         if (vertical == "not found") {
 197                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 198                                 else { vertical = "F";  }
 199                         }
 200
 201                         numSeqs = 0;
 202                 }
 203
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 207                 exit(1);
 208         }
 209 }
 210
 211 //**********************************************************************************************************************
 212
 213 void FilterSeqsCommand::help(){
 214         try {
 215
 216                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 217                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n");
 218                 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");
 219                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 220                 m->mothurOut("The trump parameter .... The default is ...\n");
 221                 m->mothurOut("The soft parameter .... The default is ....\n");
 222                 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
 223                 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
 224                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 225                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 226                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 227                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 228                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "FilterSeqsCommand", "help");
 233                 exit(1);
 234         }
 235 }
 236
 237 /**************************************************************************************/
 238
 239 int FilterSeqsCommand::execute() {
 240         try {
 241
 242                 if (abort == true) { return 0; }
 243
 244                 ifstream inFASTA;
 245                 m->openInputFile(fastafileNames[0], inFASTA);
 246
 247                 Sequence testSeq(inFASTA);
 248                 alignmentLength = testSeq.getAlignLength();
 249                 inFASTA.close();
 250
 251                 ////////////create filter/////////////////
 252                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 253
 254                 filter = createFilter();
 255
 256                 m->mothurOutEndLine();  m->mothurOutEndLine();
 257
 258                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 259
 260                 #ifdef USE_MPI
 261                         int pid;
 262                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 263
 264                         if (pid == 0) { //only one process should output the filter
 265                 #endif
 266
 267                 ofstream outFilter;
 268
 269                 //prevent giantic file name
 270                 string filterFile;
 271                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 272                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 273
 274                 m->openOutputFile(filterFile, outFilter);
 275                 outFilter << filter << endl;
 276                 outFilter.close();
 277                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 278
 279                 #ifdef USE_MPI
 280                         }
 281                 #endif
 282
 283                 ////////////run filter/////////////////
 284
 285                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 286
 287                 filterSequences();
 288
 289                 m->mothurOutEndLine();  m->mothurOutEndLine();
 290
 291                 int filteredLength = 0;
 292                 for(int i=0;i<alignmentLength;i++){
 293                         if(filter[i] == '1'){   filteredLength++;       }
 294                 }
 295
 296                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 297
 298
 299                 m->mothurOutEndLine();
 300                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 301                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 302                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 303                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 304
 305
 306                 m->mothurOutEndLine();
 307                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 308                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 309                 m->mothurOutEndLine();
 310
 311                 return 0;
 312
 313         }
 314         catch(exception& e) {
 315                 m->errorOut(e, "FilterSeqsCommand", "execute");
 316                 exit(1);
 317         }
 318 }
 319 /**************************************************************************************/
 320 int FilterSeqsCommand::filterSequences() {
 321         try {
 322
 323                 numSeqs = 0;
 324
 325                 for (int s = 0; s < fastafileNames.size(); s++) {
 326
 327                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 328
 329                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 330 #ifdef USE_MPI
 331                                 int pid, start, end, numSeqsPerProcessor, num;
 332                                 int tag = 2001;
 333                                 vector<unsigned long int>MPIPos;
 334
 335                                 MPI_Status status;
 336                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 337                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 338
 339                                 MPI_File outMPI;
 340                                 MPI_File tempMPI;
 341                                 MPI_File inMPI;
 342                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 343                                 int inMode=MPI_MODE_RDONLY;
 344
 345                                 char outFilename[1024];
 346                                 strcpy(outFilename, filteredFasta.c_str());
 347
 348                                 char inFileName[1024];
 349                                 strcpy(inFileName, fastafileNames[s].c_str());
 350
 351                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 352                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 353
 354                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 355
 356                                 if (pid == 0) { //you are the root process
 357
 358                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 359                                         numSeqs += num;
 360
 361                                         //send file positions to all processes
 362                                         for(int i = 1; i < processors; i++) {
 363                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 364                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 365                                         }
 366
 367                                         //figure out how many sequences you have to do
 368                                         numSeqsPerProcessor = num / processors;
 369                                         int startIndex =  pid * numSeqsPerProcessor;
 370                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 371
 372
 373                                         //do your part
 374                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 375
 376                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 377
 378                                         //wait on chidren
 379                                         for(int i = 1; i < processors; i++) {
 380                                                 char buf[5];
 381                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 382                                         }
 383
 384                                 }else { //you are a child process
 385                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 386                                         MPIPos.resize(num+1);
 387                                         numSeqs += num;
 388                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 389
 390                                         //figure out how many sequences you have to align
 391                                         numSeqsPerProcessor = num / processors;
 392                                         int startIndex =  pid * numSeqsPerProcessor;
 393                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 394
 395
 396                                         //align your part
 397                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 398
 399                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 400
 401                                         char buf[5];
 402                                         strcpy(buf, "done");
 403
 404                                         //tell parent you are done.
 405                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 406                                 }
 407
 408                                 MPI_File_close(&outMPI);
 409                                 MPI_File_close(&inMPI);
 410                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 411
 412 #else
 413                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 414
 415                         for (int i = 0; i < (positions.size()-1); i++) {
 416                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 417                         }
 418                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 419                                 if(processors == 1){
 420                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 421                                         numSeqs += numFastaSeqs;
 422                                 }else{
 423                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 424                                         numSeqs += numFastaSeqs;
 425
 426                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 427
 428                                         //append fasta files
 429                                         for(int i=1;i<processors;i++){
 430                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 431                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 432                                         }
 433                                 }
 434
 435                                 if (m->control_pressed) {  return 1; }
 436                 #else
 437                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 438                                 numSeqs += numFastaSeqs;
 439
 440                                 if (m->control_pressed) {  return 1; }
 441                 #endif
 442 #endif
 443                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 444                 }
 445
 446                 return 0;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 450                 exit(1);
 451         }
 452 }
 453 #ifdef USE_MPI
 454 /**************************************************************************************/
 455 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 456         try {
 457                 string outputString = "";
 458                 int count = 0;
 459                 MPI_Status status;
 460
 461                 for(int i=0;i<num;i++){
 462
 463                         if (m->control_pressed) { return 0; }
 464
 465                         //read next sequence
 466                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 467                         char* buf4 = new char[length];
 468                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 469
 470                         string tempBuf = buf4;
 471                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 472                         istringstream iss (tempBuf,istringstream::in);
 473                         delete buf4;
 474
 475                         Sequence seq(iss);  m->gobble(iss);
 476
 477                         if (seq.getName() != "") {
 478                                 string align = seq.getAligned();
 479                                 string filterSeq = "";
 480
 481                                 for(int j=0;j<alignmentLength;j++){
 482                                         if(filter[j] == '1'){
 483                                                 filterSeq += align[j];
 484                                         }
 485                                 }
 486
 487                                 count++;
 488                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 489
 490                                 if(count % 10 == 0){ //output to file
 491                                         //send results to parent
 492                                         int length = outputString.length();
 493                                         char* buf = new char[length];
 494                                         memcpy(buf, outputString.c_str(), length);
 495
 496                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 497                                         outputString = "";
 498                                         delete buf;
 499                                 }
 500
 501                         }
 502
 503                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 504                 }
 505
 506                 if(outputString != ""){ //output to file
 507                         //send results to parent
 508                         int length = outputString.length();
 509                         char* buf = new char[length];
 510                         memcpy(buf, outputString.c_str(), length);
 511
 512                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 513                         outputString = "";
 514                         delete buf;
 515                 }
 516
 517                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 518
 519                 return 0;
 520         }
 521         catch(exception& e) {
 522                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 523                 exit(1);
 524         }
 525 }
 526 #endif
 527 /**************************************************************************************/
 528 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 529         try {
 530                 ofstream out;
 531                 m->openOutputFile(outputFilename, out);
 532
 533                 ifstream in;
 534                 m->openInputFile(inputFilename, in);
 535
 536                 in.seekg(filePos->start);
 537
 538                 bool done = false;
 539                 int count = 0;
 540
 541                 while (!done) {
 542
 543                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 544
 545                                 Sequence seq(in); m->gobble(in);
 546                                 if (seq.getName() != "") {
 547                                         string align = seq.getAligned();
 548                                         string filterSeq = "";
 549
 550                                         for(int j=0;j<alignmentLength;j++){
 551                                                 if(filter[j] == '1'){
 552                                                         filterSeq += align[j];
 553                                                 }
 554                                         }
 555
 556                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 557                                 count++;
 558                         }
 559
 560                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 561                                 unsigned long int pos = in.tellg();
 562                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 563                         #else
 564                                 if (in.eof()) { break; }
 565                         #endif
 566
 567                         //report progress
 568                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 569                 }
 570                 //report progress
 571                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 572
 573
 574                 out.close();
 575                 in.close();
 576
 577                 return count;
 578         }
 579         catch(exception& e) {
 580                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 581                 exit(1);
 582         }
 583 }
 584 /**************************************************************************************************/
 585
 586 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 587         try {
 588 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 589                 int process = 0;
 590                 int num = 0;
 591                 processIDS.clear();
 592
 593                 //loop through and create all the processes you want
 594                 while (process != processors) {
 595                         int pid = fork();
 596
 597                         if (pid > 0) {
 598                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 599                                 process++;
 600                         }else if (pid == 0){
 601                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 602                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 603
 604                                 //pass numSeqs to parent
 605                                 ofstream out;
 606                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 607                                 m->openOutputFile(tempFile, out);
 608                                 out << num << endl;
 609                                 out.close();
 610
 611                                 exit(0);
 612                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 613                 }
 614
 615                 //force parent to wait until all the processes are done
 616                 for (int i=0;i<processors;i++) {
 617                         int temp = processIDS[i];
 618                         wait(&temp);
 619                 }
 620
 621                 for (int i = 0; i < processIDS.size(); i++) {
 622                         ifstream in;
 623                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 624                         m->openInputFile(tempFile, in);
 625                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 626                         in.close(); remove(tempFile.c_str());
 627                 }
 628
 629
 630                 return num;
 631 #endif
 632         }
 633         catch(exception& e) {
 634                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 635                 exit(1);
 636         }
 637 }
 638 /**************************************************************************************/
 639 string FilterSeqsCommand::createFilter() {
 640         try {
 641                 string filterString = "";
 642                 Filters F;
 643
 644                 if (soft != 0)                  {  F.setSoft(soft);             }
 645                 if (trump != '*')               {  F.setTrump(trump);   }
 646
 647                 F.setLength(alignmentLength);
 648
 649                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 650                         F.initialize();
 651                 }
 652
 653                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 654                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 655
 656                 numSeqs = 0;
 657                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 658                         for (int s = 0; s < fastafileNames.size(); s++) {
 659
 660                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 661
 662 #ifdef USE_MPI
 663                                 int pid, numSeqsPerProcessor, num;
 664                                 int tag = 2001;
 665                                 vector<unsigned long int> MPIPos;
 666
 667                                 MPI_Status status;
 668                                 MPI_File inMPI;
 669                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 670                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 671
 672                                 //char* tempFileName = new char(fastafileNames[s].length());
 673                                 //tempFileName = &(fastafileNames[s][0]);
 674
 675                                 char tempFileName[1024];
 676                                 strcpy(tempFileName, fastafileNames[s].c_str());
 677
 678                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 679
 680                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 681
 682                                 if (pid == 0) { //you are the root process
 683                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 684                                                 numSeqs += num;
 685
 686                                                 //send file positions to all processes
 687                                                 for(int i = 1; i < processors; i++) {
 688                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 689                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 690                                                 }
 691
 692                                                 //figure out how many sequences you have to do
 693                                                 numSeqsPerProcessor = num / processors;
 694                                                 int startIndex =  pid * numSeqsPerProcessor;
 695                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 696
 697
 698                                                 //do your part
 699                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 700
 701                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 702
 703                                 }else { //i am the child process
 704                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 705                                         MPIPos.resize(num+1);
 706                                         numSeqs += num;
 707                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 708
 709                                         //figure out how many sequences you have to align
 710                                         numSeqsPerProcessor = num / processors;
 711                                         int startIndex =  pid * numSeqsPerProcessor;
 712                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 713
 714
 715                                         //do your part
 716                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 717
 718                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 719                                 }
 720
 721                                 MPI_File_close(&inMPI);
 722                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 723
 724 #else
 725                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 726
 727                 for (int i = 0; i < (positions.size()-1); i++) {
 728                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 729                 }
 730                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 731                                 if(processors == 1){
 732                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 733                                         numSeqs += numFastaSeqs;
 734                                 }else{
 735                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 736                                         numSeqs += numFastaSeqs;
 737                                 }
 738
 739                                 if (m->control_pressed) {  return filterString; }
 740                 #else
 741                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 742                                 numSeqs += numFastaSeqs;
 743                                 if (m->control_pressed) {  return filterString; }
 744                 #endif
 745 #endif
 746
 747                         }
 748                 }
 749
 750
 751 #ifdef USE_MPI
 752                 int pid;
 753                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 754                 MPI_Status status;
 755
 756                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 757
 758                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 759
 760                         if (pid == 0) { //only one process should output the filter
 761
 762                                 vector<int> temp; temp.resize(alignmentLength+1);
 763
 764                                 //get the frequencies from the child processes
 765                                 for(int i = 1; i < processors; i++) {
 766
 767                                         for (int j = 0; j < 5; j++) {
 768
 769                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 770                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 771
 772                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 773                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 774                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 775                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 776                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 777                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 778                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 779                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 780                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 781                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 782                                                 }
 783                                         }
 784                                 }
 785                         }else{
 786
 787                                 //send my fequency counts
 788                                 F.a.push_back(Atag);
 789                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 790                                 F.t.push_back(Ttag);
 791                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 792                                 F.c.push_back(Ctag);
 793                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 794                                 F.g.push_back(Gtag);
 795                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 796                                 F.gap.push_back(Gaptag);
 797                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 798                         }
 799
 800                 }
 801
 802                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 803
 804                 if (pid == 0) { //only one process should output the filter
 805 #endif
 806
 807                 F.setNumSeqs(numSeqs);
 808                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 809                 if(soft != 0)                           {       F.doSoft();             }
 810                 filterString = F.getFilter();
 811
 812 #ifdef USE_MPI
 813                 //send filter string to kids
 814                 //for(int i = 1; i < processors; i++) {
 815                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 816                 //}
 817                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 818         }else{
 819                 //recieve filterString
 820                 char* tempBuf = new char[alignmentLength];
 821                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 822                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 823
 824                 filterString = tempBuf;
 825                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 826                 delete tempBuf;
 827         }
 828
 829         MPI_Barrier(MPI_COMM_WORLD);
 830 #endif
 831
 832                 return filterString;
 833         }
 834         catch(exception& e) {
 835                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 836                 exit(1);
 837         }
 838 }
 839 /**************************************************************************************/
 840 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 841         try {
 842
 843                 ifstream in;
 844                 m->openInputFile(filename, in);
 845
 846                 in.seekg(filePos->start);
 847
 848                 bool done = false;
 849                 int count = 0;
 850
 851                 while (!done) {
 852
 853                         if (m->control_pressed) { in.close(); return 1; }
 854
 855                         Sequence seq(in); m->gobble(in);
 856                         if (seq.getName() != "") {
 857                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 858
 859                                         if(trump != '*')                        {       F.doTrump(seq);         }
 860                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 861                                         cout.flush();
 862                                         count++;
 863                         }
 864
 865                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 866                                 unsigned long int pos = in.tellg();
 867                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 868                         #else
 869                                 if (in.eof()) { break; }
 870                         #endif
 871
 872                         //report progress
 873                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 874                 }
 875                 //report progress
 876                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 877                 in.close();
 878
 879                 return count;
 880         }
 881         catch(exception& e) {
 882                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 883                 exit(1);
 884         }
 885 }
 886 #ifdef USE_MPI
 887 /**************************************************************************************/
 888 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 889         try {
 890
 891                 MPI_Status status;
 892                 int pid;
 893                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 894
 895                 for(int i=0;i<num;i++){
 896
 897                         if (m->control_pressed) { return 0; }
 898
 899                         //read next sequence
 900                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 901
 902                         char* buf4 = new char[length];
 903                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 904
 905                         string tempBuf = buf4;
 906                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 907                         istringstream iss (tempBuf,istringstream::in);
 908                         delete buf4;
 909
 910                         Sequence seq(iss);
 911
 912                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 913
 914                         if(trump != '*'){       F.doTrump(seq); }
 915                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 916                         cout.flush();
 917
 918                         //report progress
 919                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 920                 }
 921
 922                 //report progress
 923                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 924
 925                 return 0;
 926         }
 927         catch(exception& e) {
 928                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 929                 exit(1);
 930         }
 931 }
 932 #endif
 933 /**************************************************************************************************/
 934
 935 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 936         try {
 937 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 938                 int process = 1;
 939                 int num = 0;
 940                 processIDS.clear();
 941
 942                 //loop through and create all the processes you want
 943                 while (process != processors) {
 944                         int pid = fork();
 945
 946                         if (pid > 0) {
 947                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 948                                 process++;
 949                         }else if (pid == 0){
 950                                 //reset child's filter counts to 0;
 951                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 952                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 953                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 954                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 955                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 956
 957                                 num = driverCreateFilter(F, filename, lines[process]);
 958
 959                                 //write out filter counts to file
 960                                 filename += toString(getpid()) + "filterValues.temp";
 961                                 ofstream out;
 962                                 m->openOutputFile(filename, out);
 963
 964                                 out << num << endl;
 965                                 out << F.getFilter() << endl;
 966                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 967                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 968                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 969                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 970                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 971
 972                                 //cout << F.getFilter() << endl;
 973                                 out.close();
 974
 975                                 exit(0);
 976                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 977                 }
 978
 979                 //parent do your part
 980                 num = driverCreateFilter(F, filename, lines[0]);
 981
 982                 //force parent to wait until all the processes are done
 983                 for (int i=0;i<(processors-1);i++) {
 984                         int temp = processIDS[i];
 985                         wait(&temp);
 986                 }
 987
 988                 //parent reads in and combines Filter info
 989                 for (int i = 0; i < processIDS.size(); i++) {
 990                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 991                         ifstream in;
 992                         m->openInputFile(tempFilename, in);
 993
 994                         int temp, tempNum;
 995                         string tempFilterString;
 996
 997                         in >> tempNum; m->gobble(in); num += tempNum;
 998
 999                         in >> tempFilterString;
1000                         F.mergeFilter(tempFilterString);
1001
1002                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1003                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1004                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1005                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1006                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1007
1008                         in.close();
1009                         remove(tempFilename.c_str());
1010                 }
1011
1012                 return num;
1013 #endif
1014         }
1015         catch(exception& e) {
1016                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1017                 exit(1);
1018         }
1019 }
1020 /**************************************************************************************/