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
  82                 else {
  83                         vector<string> myArray = setParameters();
  84
  85                         OptionParser parser(option);
  86                         map<string,string> parameters = parser.getParameters();
  87
  88                         ValidParameters validParameter("filter.seqs");
  89                         map<string,string>::iterator it;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95
  96                         //initialize outputTypes
  97                         vector<string> tempOutNames;
  98                         outputTypes["fasta"] = tempOutNames;
  99                         outputTypes["filter"] = tempOutNames;
 100
 101                         //if the user changes the input directory command factory will send this info to us in the output parameter
 102                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 103                         if (inputDir == "not found"){   inputDir = "";          }
 104                         else {
 105                                 string path;
 106                                 it = parameters.find("fasta");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 112                                 }
 113
 114                                 it = parameters.find("hard");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 120                                 }
 121                         }
 122
 123                         //check for required parameters
 124                         fasta = validParameter.validFile(parameters, "fasta", false);
 125                         if (fasta == "not found") {
 126                                 fasta = m->getFastaFile();
 127                                 if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 128                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 129                         }
 130                         else {
 131                                 m->splitAtDash(fasta, fastafileNames);
 132
 133                                 //go through files and make sure they are good, if not, then disregard them
 134                                 for (int i = 0; i < fastafileNames.size(); i++) {
 135                                         if (inputDir != "") {
 136                                                 string path = m->hasPath(fastafileNames[i]);
 137                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 138                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 139                                         }
 140
 141                                         ifstream in;
 142                                         int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 143
 144                                         //if you can't open it, try default location
 145                                         if (ableToOpen == 1) {
 146                                                 if (m->getDefaultPath() != "") { //default path is set
 147                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 148                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 149                                                         ifstream in2;
 150                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 151                                                         in2.close();
 152                                                         fastafileNames[i] = tryPath;
 153                                                 }
 154                                         }
 155
 156                                         //if you can't open it, try default location
 157                                         if (ableToOpen == 1) {
 158                                                 if (m->getOutputDir() != "") { //default path is set
 159                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 160                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 161                                                         ifstream in2;
 162                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 163                                                         in2.close();
 164                                                         fastafileNames[i] = tryPath;
 165                                                 }
 166                                         }
 167
 168                                         in.close();
 169
 170                                         if (ableToOpen == 1) {
 171                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 172                                                 //erase from file list
 173                                                 fastafileNames.erase(fastafileNames.begin()+i);
 174                                                 i--;
 175                                         }else{
 176                                                 string simpleName = m->getSimpleName(fastafileNames[i]);
 177                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 178                                         }
 179                                         in.close();
 180                                 }
 181
 182                                 //make sure there is at least one valid file left
 183                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 184                         }
 185
 186                         if (!abort) {
 187                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 188                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 189                                         outputDir = "";
 190                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 191                                 }
 192                         }
 193                         //check for optional parameter and set defaults
 194                         // ...at some point should added some additional type checking...
 195
 196                         string temp;
 197                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 198                         else if (hard == "not open") { hard = ""; abort = true; }
 199
 200                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 201                         trump = temp[0];
 202
 203                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 204                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 205
 206                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 207                         m->setProcessors(temp);
 208                         convert(temp, processors);
 209
 210                         vertical = validParameter.validFile(parameters, "vertical", false);
 211                         if (vertical == "not found") {
 212                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 213                                 else { vertical = "F";  }
 214                         }
 215
 216                         numSeqs = 0;
 217                 }
 218
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 222                 exit(1);
 223         }
 224 }
 225 /**************************************************************************************/
 226
 227 int FilterSeqsCommand::execute() {
 228         try {
 229
 230                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 231
 232                 ifstream inFASTA;
 233                 m->openInputFile(fastafileNames[0], inFASTA);
 234
 235                 Sequence testSeq(inFASTA);
 236                 alignmentLength = testSeq.getAlignLength();
 237                 inFASTA.close();
 238
 239                 ////////////create filter/////////////////
 240                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 241
 242                 filter = createFilter();
 243
 244                 m->mothurOutEndLine();  m->mothurOutEndLine();
 245
 246                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 247
 248                 #ifdef USE_MPI
 249                         int pid;
 250                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 251
 252                         if (pid == 0) { //only one process should output the filter
 253                 #endif
 254
 255                 ofstream outFilter;
 256
 257                 //prevent giantic file name
 258                 string filterFile;
 259                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 260                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 261
 262                 m->openOutputFile(filterFile, outFilter);
 263                 outFilter << filter << endl;
 264                 outFilter.close();
 265                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 266
 267                 #ifdef USE_MPI
 268                         }
 269                 #endif
 270
 271                 ////////////run filter/////////////////
 272
 273                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 274
 275                 filterSequences();
 276
 277                 m->mothurOutEndLine();  m->mothurOutEndLine();
 278
 279                 int filteredLength = 0;
 280                 for(int i=0;i<alignmentLength;i++){
 281                         if(filter[i] == '1'){   filteredLength++;       }
 282                 }
 283
 284                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 285
 286
 287                 m->mothurOutEndLine();
 288                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 289                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 290                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 291                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 292
 293                 //set fasta file as new current fastafile
 294                 string current = "";
 295                 itTypes = outputTypes.find("fasta");
 296                 if (itTypes != outputTypes.end()) {
 297                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 298                 }
 299
 300                 m->mothurOutEndLine();
 301                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 302                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 303                 m->mothurOutEndLine();
 304
 305                 return 0;
 306
 307         }
 308         catch(exception& e) {
 309                 m->errorOut(e, "FilterSeqsCommand", "execute");
 310                 exit(1);
 311         }
 312 }
 313 /**************************************************************************************/
 314 int FilterSeqsCommand::filterSequences() {
 315         try {
 316
 317                 numSeqs = 0;
 318
 319                 for (int s = 0; s < fastafileNames.size(); s++) {
 320
 321                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 322
 323                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 324 #ifdef USE_MPI
 325                                 int pid, numSeqsPerProcessor, num;
 326                                 int tag = 2001;
 327                                 vector<unsigned long int>MPIPos;
 328
 329                                 MPI_Status status;
 330                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 331                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 332
 333                                 MPI_File outMPI;
 334                                 MPI_File inMPI;
 335                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 336                                 int inMode=MPI_MODE_RDONLY;
 337
 338                                 char outFilename[1024];
 339                                 strcpy(outFilename, filteredFasta.c_str());
 340
 341                                 char inFileName[1024];
 342                                 strcpy(inFileName, fastafileNames[s].c_str());
 343
 344                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 345                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 346
 347                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 348
 349                                 if (pid == 0) { //you are the root process
 350
 351                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 352                                         numSeqs += num;
 353
 354                                         //send file positions to all processes
 355                                         for(int i = 1; i < processors; i++) {
 356                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 357                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 358                                         }
 359
 360                                         //figure out how many sequences you have to do
 361                                         numSeqsPerProcessor = num / processors;
 362                                         int startIndex =  pid * numSeqsPerProcessor;
 363                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 364
 365
 366                                         //do your part
 367                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 368
 369                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 370
 371                                         //wait on chidren
 372                                         for(int i = 1; i < processors; i++) {
 373                                                 char buf[5];
 374                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 375                                         }
 376
 377                                 }else { //you are a child process
 378                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 379                                         MPIPos.resize(num+1);
 380                                         numSeqs += num;
 381                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 382
 383                                         //figure out how many sequences you have to align
 384                                         numSeqsPerProcessor = num / processors;
 385                                         int startIndex =  pid * numSeqsPerProcessor;
 386                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 387
 388
 389                                         //align your part
 390                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 391
 392                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 393
 394                                         char buf[5];
 395                                         strcpy(buf, "done");
 396
 397                                         //tell parent you are done.
 398                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 399                                 }
 400
 401                                 MPI_File_close(&outMPI);
 402                                 MPI_File_close(&inMPI);
 403                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 404
 405 #else
 406                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 407
 408                         for (int i = 0; i < (positions.size()-1); i++) {
 409                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 410                         }
 411                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 412                                 if(processors == 1){
 413                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 414                                         numSeqs += numFastaSeqs;
 415                                 }else{
 416                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 417                                         numSeqs += numFastaSeqs;
 418
 419                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 420
 421                                         //append fasta files
 422                                         for(int i=1;i<processors;i++){
 423                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 424                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 425                                         }
 426                                 }
 427
 428                                 if (m->control_pressed) {  return 1; }
 429                 #else
 430                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 431                                 numSeqs += numFastaSeqs;
 432
 433                                 if (m->control_pressed) {  return 1; }
 434                 #endif
 435 #endif
 436                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 437                 }
 438
 439                 return 0;
 440         }
 441         catch(exception& e) {
 442                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 443                 exit(1);
 444         }
 445 }
 446 #ifdef USE_MPI
 447 /**************************************************************************************/
 448 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 449         try {
 450                 string outputString = "";
 451                 int count = 0;
 452                 MPI_Status status;
 453
 454                 for(int i=0;i<num;i++){
 455
 456                         if (m->control_pressed) { return 0; }
 457
 458                         //read next sequence
 459                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 460                         char* buf4 = new char[length];
 461                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 462
 463                         string tempBuf = buf4;
 464                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 465                         istringstream iss (tempBuf,istringstream::in);
 466                         delete buf4;
 467
 468                         Sequence seq(iss);  m->gobble(iss);
 469
 470                         if (seq.getName() != "") {
 471                                 string align = seq.getAligned();
 472                                 string filterSeq = "";
 473
 474                                 for(int j=0;j<alignmentLength;j++){
 475                                         if(filter[j] == '1'){
 476                                                 filterSeq += align[j];
 477                                         }
 478                                 }
 479
 480                                 count++;
 481                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 482
 483                                 if(count % 10 == 0){ //output to file
 484                                         //send results to parent
 485                                         int length = outputString.length();
 486                                         char* buf = new char[length];
 487                                         memcpy(buf, outputString.c_str(), length);
 488
 489                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 490                                         outputString = "";
 491                                         delete buf;
 492                                 }
 493
 494                         }
 495
 496                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 497                 }
 498
 499                 if(outputString != ""){ //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                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 511
 512                 return 0;
 513         }
 514         catch(exception& e) {
 515                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 516                 exit(1);
 517         }
 518 }
 519 #endif
 520 /**************************************************************************************/
 521 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 522         try {
 523                 ofstream out;
 524                 m->openOutputFile(outputFilename, out);
 525
 526                 ifstream in;
 527                 m->openInputFile(inputFilename, in);
 528
 529                 in.seekg(filePos->start);
 530
 531                 bool done = false;
 532                 int count = 0;
 533
 534                 while (!done) {
 535
 536                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 537
 538                                 Sequence seq(in); m->gobble(in);
 539                                 if (seq.getName() != "") {
 540                                         string align = seq.getAligned();
 541                                         string filterSeq = "";
 542
 543                                         for(int j=0;j<alignmentLength;j++){
 544                                                 if(filter[j] == '1'){
 545                                                         filterSeq += align[j];
 546                                                 }
 547                                         }
 548
 549                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 550                                 count++;
 551                         }
 552
 553                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 554                                 unsigned long int pos = in.tellg();
 555                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 556                         #else
 557                                 if (in.eof()) { break; }
 558                         #endif
 559
 560                         //report progress
 561                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 562                 }
 563                 //report progress
 564                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 565
 566
 567                 out.close();
 568                 in.close();
 569
 570                 return count;
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 574                 exit(1);
 575         }
 576 }
 577 /**************************************************************************************************/
 578
 579 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 580         try {
 581 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 582                 int process = 0;
 583                 int num = 0;
 584                 processIDS.clear();
 585
 586                 //loop through and create all the processes you want
 587                 while (process != processors) {
 588                         int pid = fork();
 589
 590                         if (pid > 0) {
 591                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 592                                 process++;
 593                         }else if (pid == 0){
 594                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 595                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 596
 597                                 //pass numSeqs to parent
 598                                 ofstream out;
 599                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 600                                 m->openOutputFile(tempFile, out);
 601                                 out << num << endl;
 602                                 out.close();
 603
 604                                 exit(0);
 605                         }else {
 606                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 607                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 608                                 exit(0);
 609                         }
 610                 }
 611
 612                 //force parent to wait until all the processes are done
 613                 for (int i=0;i<processors;i++) {
 614                         int temp = processIDS[i];
 615                         wait(&temp);
 616                 }
 617
 618                 for (int i = 0; i < processIDS.size(); i++) {
 619                         ifstream in;
 620                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 621                         m->openInputFile(tempFile, in);
 622                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 623                         in.close(); remove(tempFile.c_str());
 624                 }
 625
 626
 627                 return num;
 628 #endif
 629         }
 630         catch(exception& e) {
 631                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 632                 exit(1);
 633         }
 634 }
 635 /**************************************************************************************/
 636 string FilterSeqsCommand::createFilter() {
 637         try {
 638                 string filterString = "";
 639                 Filters F;
 640
 641                 if (soft != 0)                  {  F.setSoft(soft);             }
 642                 if (trump != '*')               {  F.setTrump(trump);   }
 643
 644                 F.setLength(alignmentLength);
 645
 646                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 647                         F.initialize();
 648                 }
 649
 650                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 651                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 652
 653                 numSeqs = 0;
 654                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 655                         for (int s = 0; s < fastafileNames.size(); s++) {
 656
 657                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 658
 659 #ifdef USE_MPI
 660                                 int pid, numSeqsPerProcessor, num;
 661                                 int tag = 2001;
 662                                 vector<unsigned long int> MPIPos;
 663
 664                                 MPI_Status status;
 665                                 MPI_File inMPI;
 666                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 667                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 668
 669                                 //char* tempFileName = new char(fastafileNames[s].length());
 670                                 //tempFileName = &(fastafileNames[s][0]);
 671
 672                                 char tempFileName[1024];
 673                                 strcpy(tempFileName, fastafileNames[s].c_str());
 674
 675                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 676
 677                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 678
 679                                 if (pid == 0) { //you are the root process
 680                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 681                                                 numSeqs += num;
 682
 683                                                 //send file positions to all processes
 684                                                 for(int i = 1; i < processors; i++) {
 685                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 686                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 687                                                 }
 688
 689                                                 //figure out how many sequences you have to do
 690                                                 numSeqsPerProcessor = num / processors;
 691                                                 int startIndex =  pid * numSeqsPerProcessor;
 692                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 693
 694
 695                                                 //do your part
 696                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 697
 698                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 699
 700                                 }else { //i am the child process
 701                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 702                                         MPIPos.resize(num+1);
 703                                         numSeqs += num;
 704                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 705
 706                                         //figure out how many sequences you have to align
 707                                         numSeqsPerProcessor = num / processors;
 708                                         int startIndex =  pid * numSeqsPerProcessor;
 709                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 710
 711
 712                                         //do your part
 713                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 714
 715                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 716                                 }
 717
 718                                 MPI_File_close(&inMPI);
 719                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 720
 721 #else
 722                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 723
 724                 for (int i = 0; i < (positions.size()-1); i++) {
 725                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 726                 }
 727                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 728                                 if(processors == 1){
 729                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 730                                         numSeqs += numFastaSeqs;
 731                                 }else{
 732                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 733                                         numSeqs += numFastaSeqs;
 734                                 }
 735
 736                                 if (m->control_pressed) {  return filterString; }
 737                 #else
 738                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 739                                 numSeqs += numFastaSeqs;
 740                                 if (m->control_pressed) {  return filterString; }
 741                 #endif
 742 #endif
 743
 744                         }
 745                 }
 746
 747
 748 #ifdef USE_MPI
 749                 int pid;
 750                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 751                 MPI_Status status;
 752
 753                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 754
 755                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 756
 757                         if (pid == 0) { //only one process should output the filter
 758
 759                                 vector<int> temp; temp.resize(alignmentLength+1);
 760
 761                                 //get the frequencies from the child processes
 762                                 for(int i = 1; i < processors; i++) {
 763
 764                                         for (int j = 0; j < 5; j++) {
 765
 766                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 767                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 768
 769                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 770                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 771                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 772                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 773                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 774                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 775                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 776                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 777                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 778                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 779                                                 }
 780                                         }
 781                                 }
 782                         }else{
 783
 784                                 //send my fequency counts
 785                                 F.a.push_back(Atag);
 786                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 787                                 F.t.push_back(Ttag);
 788                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 789                                 F.c.push_back(Ctag);
 790                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 791                                 F.g.push_back(Gtag);
 792                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 793                                 F.gap.push_back(Gaptag);
 794                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 795                         }
 796
 797                 }
 798
 799                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 800
 801                 if (pid == 0) { //only one process should output the filter
 802 #endif
 803
 804                 F.setNumSeqs(numSeqs);
 805                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 806                 if(soft != 0)                           {       F.doSoft();             }
 807                 filterString = F.getFilter();
 808
 809 #ifdef USE_MPI
 810                 //send filter string to kids
 811                 //for(int i = 1; i < processors; i++) {
 812                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 813                 //}
 814                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 815         }else{
 816                 //recieve filterString
 817                 char* tempBuf = new char[alignmentLength];
 818                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 819                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 820
 821                 filterString = tempBuf;
 822                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 823                 delete tempBuf;
 824         }
 825
 826         MPI_Barrier(MPI_COMM_WORLD);
 827 #endif
 828
 829                 return filterString;
 830         }
 831         catch(exception& e) {
 832                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 833                 exit(1);
 834         }
 835 }
 836 /**************************************************************************************/
 837 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 838         try {
 839
 840                 ifstream in;
 841                 m->openInputFile(filename, in);
 842
 843                 in.seekg(filePos->start);
 844
 845                 bool done = false;
 846                 int count = 0;
 847
 848                 while (!done) {
 849
 850                         if (m->control_pressed) { in.close(); return 1; }
 851
 852                         Sequence seq(in); m->gobble(in);
 853                         if (seq.getName() != "") {
 854                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 855
 856                                         if(trump != '*')                        {       F.doTrump(seq);         }
 857                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 858                                         cout.flush();
 859                                         count++;
 860                         }
 861
 862                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 863                                 unsigned long int pos = in.tellg();
 864                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 865                         #else
 866                                 if (in.eof()) { break; }
 867                         #endif
 868
 869                         //report progress
 870                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 871                 }
 872                 //report progress
 873                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 874                 in.close();
 875
 876                 return count;
 877         }
 878         catch(exception& e) {
 879                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 880                 exit(1);
 881         }
 882 }
 883 #ifdef USE_MPI
 884 /**************************************************************************************/
 885 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 886         try {
 887
 888                 MPI_Status status;
 889                 int pid;
 890                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 891
 892                 for(int i=0;i<num;i++){
 893
 894                         if (m->control_pressed) { return 0; }
 895
 896                         //read next sequence
 897                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 898
 899                         char* buf4 = new char[length];
 900                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 901
 902                         string tempBuf = buf4;
 903                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 904                         istringstream iss (tempBuf,istringstream::in);
 905                         delete buf4;
 906
 907                         Sequence seq(iss);
 908
 909                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 910
 911                         if(trump != '*'){       F.doTrump(seq); }
 912                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 913                         cout.flush();
 914
 915                         //report progress
 916                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 917                 }
 918
 919                 //report progress
 920                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 921
 922                 return 0;
 923         }
 924         catch(exception& e) {
 925                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 926                 exit(1);
 927         }
 928 }
 929 #endif
 930 /**************************************************************************************************/
 931
 932 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 933         try {
 934 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 935                 int process = 1;
 936                 int num = 0;
 937                 processIDS.clear();
 938
 939                 //loop through and create all the processes you want
 940                 while (process != processors) {
 941                         int pid = fork();
 942
 943                         if (pid > 0) {
 944                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 945                                 process++;
 946                         }else if (pid == 0){
 947                                 //reset child's filter counts to 0;
 948                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 949                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 950                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 951                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 952                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 953
 954                                 num = driverCreateFilter(F, filename, lines[process]);
 955
 956                                 //write out filter counts to file
 957                                 filename += toString(getpid()) + "filterValues.temp";
 958                                 ofstream out;
 959                                 m->openOutputFile(filename, out);
 960
 961                                 out << num << endl;
 962                                 out << F.getFilter() << endl;
 963                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 964                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 965                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 966                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 967                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 968
 969                                 //cout << F.getFilter() << endl;
 970                                 out.close();
 971
 972                                 exit(0);
 973                         }else {
 974                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 975                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 976                                 exit(0);
 977                         }
 978                 }
 979
 980                 //parent do your part
 981                 num = driverCreateFilter(F, filename, lines[0]);
 982
 983                 //force parent to wait until all the processes are done
 984                 for (int i=0;i<(processors-1);i++) {
 985                         int temp = processIDS[i];
 986                         wait(&temp);
 987                 }
 988
 989                 //parent reads in and combines Filter info
 990                 for (int i = 0; i < processIDS.size(); i++) {
 991                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
 992                         ifstream in;
 993                         m->openInputFile(tempFilename, in);
 994
 995                         int temp, tempNum;
 996                         string tempFilterString;
 997
 998                         in >> tempNum; m->gobble(in); num += tempNum;
 999
1000                         in >> tempFilterString;
1001                         F.mergeFilter(tempFilterString);
1002
1003                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1004                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1005                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1006                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1007                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1008
1009                         in.close();
1010                         remove(tempFilename.c_str());
1011                 }
1012
1013                 return num;
1014 #endif
1015         }
1016         catch(exception& e) {
1017                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1018                 exit(1);
1019         }
1020 }
1021 /**************************************************************************************/