filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> FilterSeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
  19                 CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
  20                 CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
  21                 CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "FilterSeqsCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string FilterSeqsCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
  40                 helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
  41                 helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
  42                 helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
  43                 helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
  44                 helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
  45                 helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
  46                 helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
  47                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  48                 helpString += "The filter.seqs command should be in the following format: \n";
  49                 helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
  50                 helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "FilterSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 FilterSeqsCommand::FilterSeqsCommand(){
  61         try {
  62                 abort = true; calledHelp = true;
  63                 setParameters();
  64                 vector<string> tempOutNames;
  65                 outputTypes["fasta"] = tempOutNames;
  66                 outputTypes["filter"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  70                 exit(1);
  71         }
  72 }
  73 /**************************************************************************************/
  74 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77                 filterFileName = "";
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter("filter.seqs");
  90                         map<string,string>::iterator it;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["fasta"] = tempOutNames;
 100                         outputTypes["filter"] = tempOutNames;
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106                                 string path;
 107                                 it = parameters.find("fasta");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 113                                 }
 114
 115                                 it = parameters.find("hard");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 121                                 }
 122                         }
 123
 124                         //check for required parameters
 125                         fasta = validParameter.validFile(parameters, "fasta", false);
 126                         if (fasta == "not found") {
 127                                 fasta = m->getFastaFile();
 128                                 if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 129                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 130                         }
 131                         else {
 132                                 m->splitAtDash(fasta, fastafileNames);
 133
 134                                 //go through files and make sure they are good, if not, then disregard them
 135                                 for (int i = 0; i < fastafileNames.size(); i++) {
 136
 137                                         bool ignore = false;
 138                                         if (fastafileNames[i] == "current") {
 139                                                 fastafileNames[i] = m->getFastaFile();
 140                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 141                                                 else {
 142                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 143                                                         //erase from file list
 144                                                         fastafileNames.erase(fastafileNames.begin()+i);
 145                                                         i--;
 146                                                 }
 147                                         }
 148
 149                                         if (!ignore) {
 150                                                 if (inputDir != "") {
 151                                                         string path = m->hasPath(fastafileNames[i]);
 152                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 154                                                 }
 155
 156                                                 ifstream in;
 157                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 158
 159                                                 //if you can't open it, try default location
 160                                                 if (ableToOpen == 1) {
 161                                                         if (m->getDefaultPath() != "") { //default path is set
 162                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 163                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 164                                                                 ifstream in2;
 165                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 166                                                                 in2.close();
 167                                                                 fastafileNames[i] = tryPath;
 168                                                         }
 169                                                 }
 170
 171                                                 //if you can't open it, try default location
 172                                                 if (ableToOpen == 1) {
 173                                                         if (m->getOutputDir() != "") { //default path is set
 174                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 175                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 176                                                                 ifstream in2;
 177                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 178                                                                 in2.close();
 179                                                                 fastafileNames[i] = tryPath;
 180                                                         }
 181                                                 }
 182
 183                                                 in.close();
 184
 185                                                 if (ableToOpen == 1) {
 186                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 187                                                         //erase from file list
 188                                                         fastafileNames.erase(fastafileNames.begin()+i);
 189                                                         i--;
 190                                                 }else{
 191                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 192                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 193                                                 }
 194                                                 in.close();
 195                                         }
 196                                 }
 197
 198                                 //make sure there is at least one valid file left
 199                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 200                         }
 201
 202                         if (!abort) {
 203                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 204                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 205                                         outputDir = "";
 206                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 207                                 }
 208                         }
 209                         //check for optional parameter and set defaults
 210                         // ...at some point should added some additional type checking...
 211
 212                         string temp;
 213                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 214                         else if (hard == "not open") { hard = ""; abort = true; }
 215
 216                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 217                         trump = temp[0];
 218
 219                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 220                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 221
 222                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 223                         m->setProcessors(temp);
 224                         convert(temp, processors);
 225
 226                         vertical = validParameter.validFile(parameters, "vertical", false);
 227                         if (vertical == "not found") {
 228                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 229                                 else { vertical = "F";  }
 230                         }
 231
 232                         numSeqs = 0;
 233                 }
 234
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 238                 exit(1);
 239         }
 240 }
 241 /**************************************************************************************/
 242
 243 int FilterSeqsCommand::execute() {
 244         try {
 245
 246                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 247
 248                 ifstream inFASTA;
 249                 m->openInputFile(fastafileNames[0], inFASTA);
 250
 251                 Sequence testSeq(inFASTA);
 252                 alignmentLength = testSeq.getAlignLength();
 253                 inFASTA.close();
 254
 255                 ////////////create filter/////////////////
 256                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 257
 258                 filter = createFilter();
 259
 260                 m->mothurOutEndLine();  m->mothurOutEndLine();
 261
 262                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 263
 264                 #ifdef USE_MPI
 265                         int pid;
 266                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 267
 268                         if (pid == 0) { //only one process should output the filter
 269                 #endif
 270
 271                 ofstream outFilter;
 272
 273                 //prevent giantic file name
 274                 string filterFile;
 275                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 276                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 277
 278                 m->openOutputFile(filterFile, outFilter);
 279                 outFilter << filter << endl;
 280                 outFilter.close();
 281                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 282
 283                 #ifdef USE_MPI
 284                         }
 285                 #endif
 286
 287                 ////////////run filter/////////////////
 288
 289                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 290
 291                 filterSequences();
 292
 293                 m->mothurOutEndLine();  m->mothurOutEndLine();
 294
 295                 int filteredLength = 0;
 296                 for(int i=0;i<alignmentLength;i++){
 297                         if(filter[i] == '1'){   filteredLength++;       }
 298                 }
 299
 300                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 301
 302
 303                 m->mothurOutEndLine();
 304                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 305                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 306                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 307                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 308
 309                 //set fasta file as new current fastafile
 310                 string current = "";
 311                 itTypes = outputTypes.find("fasta");
 312                 if (itTypes != outputTypes.end()) {
 313                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 314                 }
 315
 316                 m->mothurOutEndLine();
 317                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 318                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 319                 m->mothurOutEndLine();
 320
 321                 return 0;
 322
 323         }
 324         catch(exception& e) {
 325                 m->errorOut(e, "FilterSeqsCommand", "execute");
 326                 exit(1);
 327         }
 328 }
 329 /**************************************************************************************/
 330 int FilterSeqsCommand::filterSequences() {
 331         try {
 332
 333                 numSeqs = 0;
 334
 335                 for (int s = 0; s < fastafileNames.size(); s++) {
 336
 337                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 338
 339                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 340 #ifdef USE_MPI
 341                                 int pid, numSeqsPerProcessor, num;
 342                                 int tag = 2001;
 343                                 vector<unsigned long int>MPIPos;
 344
 345                                 MPI_Status status;
 346                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 347                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 348
 349                                 MPI_File outMPI;
 350                                 MPI_File inMPI;
 351                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 352                                 int inMode=MPI_MODE_RDONLY;
 353
 354                                 char outFilename[1024];
 355                                 strcpy(outFilename, filteredFasta.c_str());
 356
 357                                 char inFileName[1024];
 358                                 strcpy(inFileName, fastafileNames[s].c_str());
 359
 360                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 361                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 362
 363                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 364
 365                                 if (pid == 0) { //you are the root process
 366
 367                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 368                                         numSeqs += num;
 369
 370                                         //send file positions to all processes
 371                                         for(int i = 1; i < processors; i++) {
 372                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 373                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 374                                         }
 375
 376                                         //figure out how many sequences you have to do
 377                                         numSeqsPerProcessor = num / processors;
 378                                         int startIndex =  pid * numSeqsPerProcessor;
 379                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 380
 381
 382                                         //do your part
 383                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 384
 385                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 386
 387                                         //wait on chidren
 388                                         for(int i = 1; i < processors; i++) {
 389                                                 char buf[5];
 390                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 391                                         }
 392
 393                                 }else { //you are a child process
 394                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 395                                         MPIPos.resize(num+1);
 396                                         numSeqs += num;
 397                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 398
 399                                         //figure out how many sequences you have to align
 400                                         numSeqsPerProcessor = num / processors;
 401                                         int startIndex =  pid * numSeqsPerProcessor;
 402                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 403
 404
 405                                         //align your part
 406                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 407
 408                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 409
 410                                         char buf[5];
 411                                         strcpy(buf, "done");
 412
 413                                         //tell parent you are done.
 414                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 415                                 }
 416
 417                                 MPI_File_close(&outMPI);
 418                                 MPI_File_close(&inMPI);
 419                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 420
 421 #else
 422                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 423
 424                         for (int i = 0; i < (positions.size()-1); i++) {
 425                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 426                         }
 427                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 428                                 if(processors == 1){
 429                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 430                                         numSeqs += numFastaSeqs;
 431                                 }else{
 432                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 433                                         numSeqs += numFastaSeqs;
 434
 435                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 436
 437                                         //append fasta files
 438                                         for(int i=1;i<processors;i++){
 439                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 440                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 441                                         }
 442                                 }
 443
 444                                 if (m->control_pressed) {  return 1; }
 445                 #else
 446                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 447                                 numSeqs += numFastaSeqs;
 448
 449                                 if (m->control_pressed) {  return 1; }
 450                 #endif
 451 #endif
 452                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 453                 }
 454
 455                 return 0;
 456         }
 457         catch(exception& e) {
 458                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 459                 exit(1);
 460         }
 461 }
 462 #ifdef USE_MPI
 463 /**************************************************************************************/
 464 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 465         try {
 466                 string outputString = "";
 467                 int count = 0;
 468                 MPI_Status status;
 469
 470                 for(int i=0;i<num;i++){
 471
 472                         if (m->control_pressed) { return 0; }
 473
 474                         //read next sequence
 475                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 476                         char* buf4 = new char[length];
 477                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 478
 479                         string tempBuf = buf4;
 480                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 481                         istringstream iss (tempBuf,istringstream::in);
 482                         delete buf4;
 483
 484                         Sequence seq(iss);  m->gobble(iss);
 485
 486                         if (seq.getName() != "") {
 487                                 string align = seq.getAligned();
 488                                 string filterSeq = "";
 489
 490                                 for(int j=0;j<alignmentLength;j++){
 491                                         if(filter[j] == '1'){
 492                                                 filterSeq += align[j];
 493                                         }
 494                                 }
 495
 496                                 count++;
 497                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 498
 499                                 if(count % 10 == 0){ //output to file
 500                                         //send results to parent
 501                                         int length = outputString.length();
 502                                         char* buf = new char[length];
 503                                         memcpy(buf, outputString.c_str(), length);
 504
 505                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 506                                         outputString = "";
 507                                         delete buf;
 508                                 }
 509
 510                         }
 511
 512                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 513                 }
 514
 515                 if(outputString != ""){ //output to file
 516                         //send results to parent
 517                         int length = outputString.length();
 518                         char* buf = new char[length];
 519                         memcpy(buf, outputString.c_str(), length);
 520
 521                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 522                         outputString = "";
 523                         delete buf;
 524                 }
 525
 526                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 527
 528                 return 0;
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 532                 exit(1);
 533         }
 534 }
 535 #endif
 536 /**************************************************************************************/
 537 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 538         try {
 539                 ofstream out;
 540                 m->openOutputFile(outputFilename, out);
 541
 542                 ifstream in;
 543                 m->openInputFile(inputFilename, in);
 544
 545                 in.seekg(filePos->start);
 546
 547                 bool done = false;
 548                 int count = 0;
 549
 550                 while (!done) {
 551
 552                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 553
 554                                 Sequence seq(in); m->gobble(in);
 555                                 if (seq.getName() != "") {
 556                                         string align = seq.getAligned();
 557                                         string filterSeq = "";
 558
 559                                         for(int j=0;j<alignmentLength;j++){
 560                                                 if(filter[j] == '1'){
 561                                                         filterSeq += align[j];
 562                                                 }
 563                                         }
 564
 565                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 566                                 count++;
 567                         }
 568
 569                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 570                                 unsigned long int pos = in.tellg();
 571                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 572                         #else
 573                                 if (in.eof()) { break; }
 574                         #endif
 575
 576                         //report progress
 577                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 578                 }
 579                 //report progress
 580                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 581
 582
 583                 out.close();
 584                 in.close();
 585
 586                 return count;
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 590                 exit(1);
 591         }
 592 }
 593 /**************************************************************************************************/
 594
 595 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 596         try {
 597 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 598                 int process = 0;
 599                 int num = 0;
 600                 processIDS.clear();
 601
 602                 //loop through and create all the processes you want
 603                 while (process != processors) {
 604                         int pid = fork();
 605
 606                         if (pid > 0) {
 607                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 608                                 process++;
 609                         }else if (pid == 0){
 610                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 611                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 612
 613                                 //pass numSeqs to parent
 614                                 ofstream out;
 615                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 616                                 m->openOutputFile(tempFile, out);
 617                                 out << num << endl;
 618                                 out.close();
 619
 620                                 exit(0);
 621                         }else {
 622                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 623                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 624                                 exit(0);
 625                         }
 626                 }
 627
 628                 //force parent to wait until all the processes are done
 629                 for (int i=0;i<processors;i++) {
 630                         int temp = processIDS[i];
 631                         wait(&temp);
 632                 }
 633
 634                 for (int i = 0; i < processIDS.size(); i++) {
 635                         ifstream in;
 636                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 637                         m->openInputFile(tempFile, in);
 638                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 639                         in.close(); remove(tempFile.c_str());
 640                 }
 641
 642
 643                 return num;
 644 #endif
 645         }
 646         catch(exception& e) {
 647                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 648                 exit(1);
 649         }
 650 }
 651 /**************************************************************************************/
 652 string FilterSeqsCommand::createFilter() {
 653         try {
 654                 string filterString = "";
 655                 Filters F;
 656
 657                 if (soft != 0)                  {  F.setSoft(soft);             }
 658                 if (trump != '*')               {  F.setTrump(trump);   }
 659
 660                 F.setLength(alignmentLength);
 661
 662                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 663                         F.initialize();
 664                 }
 665
 666                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 667                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 668
 669                 numSeqs = 0;
 670                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 671                         for (int s = 0; s < fastafileNames.size(); s++) {
 672
 673                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 674
 675 #ifdef USE_MPI
 676                                 int pid, numSeqsPerProcessor, num;
 677                                 int tag = 2001;
 678                                 vector<unsigned long int> MPIPos;
 679
 680                                 MPI_Status status;
 681                                 MPI_File inMPI;
 682                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 683                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 684
 685                                 //char* tempFileName = new char(fastafileNames[s].length());
 686                                 //tempFileName = &(fastafileNames[s][0]);
 687
 688                                 char tempFileName[1024];
 689                                 strcpy(tempFileName, fastafileNames[s].c_str());
 690
 691                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 692
 693                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 694
 695                                 if (pid == 0) { //you are the root process
 696                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 697                                                 numSeqs += num;
 698
 699                                                 //send file positions to all processes
 700                                                 for(int i = 1; i < processors; i++) {
 701                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 702                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 703                                                 }
 704
 705                                                 //figure out how many sequences you have to do
 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                                 }else { //i am the child process
 717                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 718                                         MPIPos.resize(num+1);
 719                                         numSeqs += num;
 720                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 721
 722                                         //figure out how many sequences you have to align
 723                                         numSeqsPerProcessor = num / processors;
 724                                         int startIndex =  pid * numSeqsPerProcessor;
 725                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 726
 727
 728                                         //do your part
 729                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 730
 731                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 732                                 }
 733
 734                                 MPI_File_close(&inMPI);
 735                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 736
 737 #else
 738                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 739
 740                 for (int i = 0; i < (positions.size()-1); i++) {
 741                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 742                 }
 743                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 744                                 if(processors == 1){
 745                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 746                                         numSeqs += numFastaSeqs;
 747                                 }else{
 748                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 749                                         numSeqs += numFastaSeqs;
 750                                 }
 751
 752                                 if (m->control_pressed) {  return filterString; }
 753                 #else
 754                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 755                                 numSeqs += numFastaSeqs;
 756                                 if (m->control_pressed) {  return filterString; }
 757                 #endif
 758 #endif
 759
 760                         }
 761                 }
 762
 763
 764 #ifdef USE_MPI
 765                 int pid;
 766                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 767                 MPI_Status status;
 768
 769                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 770
 771                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 772
 773                         if (pid == 0) { //only one process should output the filter
 774
 775                                 vector<int> temp; temp.resize(alignmentLength+1);
 776
 777                                 //get the frequencies from the child processes
 778                                 for(int i = 1; i < processors; i++) {
 779
 780                                         for (int j = 0; j < 5; j++) {
 781
 782                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 783                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 784
 785                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 786                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 787                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 788                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 789                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 790                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 791                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 792                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 793                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 794                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 795                                                 }
 796                                         }
 797                                 }
 798                         }else{
 799
 800                                 //send my fequency counts
 801                                 F.a.push_back(Atag);
 802                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 803                                 F.t.push_back(Ttag);
 804                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 805                                 F.c.push_back(Ctag);
 806                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 807                                 F.g.push_back(Gtag);
 808                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 809                                 F.gap.push_back(Gaptag);
 810                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 811                         }
 812
 813                 }
 814
 815                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 816
 817                 if (pid == 0) { //only one process should output the filter
 818 #endif
 819
 820                 F.setNumSeqs(numSeqs);
 821                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 822                 if(soft != 0)                           {       F.doSoft();             }
 823                 filterString = F.getFilter();
 824
 825 #ifdef USE_MPI
 826                 //send filter string to kids
 827                 //for(int i = 1; i < processors; i++) {
 828                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 829                 //}
 830                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 831         }else{
 832                 //recieve filterString
 833                 char* tempBuf = new char[alignmentLength];
 834                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 835                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 836
 837                 filterString = tempBuf;
 838                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 839                 delete tempBuf;
 840         }
 841
 842         MPI_Barrier(MPI_COMM_WORLD);
 843 #endif
 844
 845                 return filterString;
 846         }
 847         catch(exception& e) {
 848                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 849                 exit(1);
 850         }
 851 }
 852 /**************************************************************************************/
 853 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 854         try {
 855
 856                 ifstream in;
 857                 m->openInputFile(filename, in);
 858
 859                 in.seekg(filePos->start);
 860
 861                 bool done = false;
 862                 int count = 0;
 863
 864                 while (!done) {
 865
 866                         if (m->control_pressed) { in.close(); return 1; }
 867
 868                         Sequence seq(in); m->gobble(in);
 869                         if (seq.getName() != "") {
 870                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 871
 872                                         if(trump != '*')                        {       F.doTrump(seq);         }
 873                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 874                                         cout.flush();
 875                                         count++;
 876                         }
 877
 878                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 879                                 unsigned long int pos = in.tellg();
 880                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 881                         #else
 882                                 if (in.eof()) { break; }
 883                         #endif
 884
 885                         //report progress
 886                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 887                 }
 888                 //report progress
 889                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 890                 in.close();
 891
 892                 return count;
 893         }
 894         catch(exception& e) {
 895                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 896                 exit(1);
 897         }
 898 }
 899 #ifdef USE_MPI
 900 /**************************************************************************************/
 901 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 902         try {
 903
 904                 MPI_Status status;
 905                 int pid;
 906                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 907
 908                 for(int i=0;i<num;i++){
 909
 910                         if (m->control_pressed) { return 0; }
 911
 912                         //read next sequence
 913                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 914
 915                         char* buf4 = new char[length];
 916                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 917
 918                         string tempBuf = buf4;
 919                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 920                         istringstream iss (tempBuf,istringstream::in);
 921                         delete buf4;
 922
 923                         Sequence seq(iss);
 924
 925                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 926
 927                         if(trump != '*'){       F.doTrump(seq); }
 928                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 929                         cout.flush();
 930
 931                         //report progress
 932                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 933                 }
 934
 935                 //report progress
 936                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 937
 938                 return 0;
 939         }
 940         catch(exception& e) {
 941                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 942                 exit(1);
 943         }
 944 }
 945 #endif
 946 /**************************************************************************************************/
 947
 948 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 949         try {
 950 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 951                 int process = 1;
 952                 int num = 0;
 953                 processIDS.clear();
 954
 955                 //loop through and create all the processes you want
 956                 while (process != processors) {
 957                         int pid = fork();
 958
 959                         if (pid > 0) {
 960                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 961                                 process++;
 962                         }else if (pid == 0){
 963                                 //reset child's filter counts to 0;
 964                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 965                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 966                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 967                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 968                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 969
 970                                 num = driverCreateFilter(F, filename, lines[process]);
 971
 972                                 //write out filter counts to file
 973                                 filename += toString(getpid()) + "filterValues.temp";
 974                                 ofstream out;
 975                                 m->openOutputFile(filename, out);
 976
 977                                 out << num << endl;
 978                                 out << F.getFilter() << endl;
 979                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 980                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 981                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 982                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 983                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 984
 985                                 //cout << F.getFilter() << endl;
 986                                 out.close();
 987
 988                                 exit(0);
 989                         }else {
 990                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 991                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 992                                 exit(0);
 993                         }
 994                 }
 995
 996                 //parent do your part
 997                 num = driverCreateFilter(F, filename, lines[0]);
 998
 999                 //force parent to wait until all the processes are done
1000                 for (int i=0;i<(processors-1);i++) {
1001                         int temp = processIDS[i];
1002                         wait(&temp);
1003                 }
1004
1005                 //parent reads in and combines Filter info
1006                 for (int i = 0; i < processIDS.size(); i++) {
1007                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1008                         ifstream in;
1009                         m->openInputFile(tempFilename, in);
1010
1011                         int temp, tempNum;
1012                         string tempFilterString;
1013
1014                         in >> tempNum; m->gobble(in); num += tempNum;
1015
1016                         in >> tempFilterString;
1017                         F.mergeFilter(tempFilterString);
1018
1019                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1020                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1021                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1022                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1023                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1024
1025                         in.close();
1026                         remove(tempFilename.c_str());
1027                 }
1028
1029                 return num;
1030 #endif
1031         }
1032         catch(exception& e) {
1033                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1034                 exit(1);
1035         }
1036 }
1037 /**************************************************************************************/