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
 136                                         bool ignore = false;
 137                                         if (fastafileNames[i] == "current") {
 138                                                 fastafileNames[i] = m->getFastaFile();
 139                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 140                                                 else {
 141                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 142                                                         //erase from file list
 143                                                         fastafileNames.erase(fastafileNames.begin()+i);
 144                                                         i--;
 145                                                 }
 146                                         }
 147
 148                                         if (!ignore) {
 149                                                 if (inputDir != "") {
 150                                                         string path = m->hasPath(fastafileNames[i]);
 151                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 153                                                 }
 154
 155                                                 ifstream in;
 156                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 157
 158                                                 //if you can't open it, try default location
 159                                                 if (ableToOpen == 1) {
 160                                                         if (m->getDefaultPath() != "") { //default path is set
 161                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 162                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 163                                                                 ifstream in2;
 164                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 165                                                                 in2.close();
 166                                                                 fastafileNames[i] = tryPath;
 167                                                         }
 168                                                 }
 169
 170                                                 //if you can't open it, try default location
 171                                                 if (ableToOpen == 1) {
 172                                                         if (m->getOutputDir() != "") { //default path is set
 173                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 174                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 175                                                                 ifstream in2;
 176                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 177                                                                 in2.close();
 178                                                                 fastafileNames[i] = tryPath;
 179                                                         }
 180                                                 }
 181
 182                                                 in.close();
 183
 184                                                 if (ableToOpen == 1) {
 185                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 186                                                         //erase from file list
 187                                                         fastafileNames.erase(fastafileNames.begin()+i);
 188                                                         i--;
 189                                                 }else{
 190                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 191                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 192                                                 }
 193                                                 in.close();
 194                                         }
 195                                 }
 196
 197                                 //make sure there is at least one valid file left
 198                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 199                         }
 200
 201                         if (!abort) {
 202                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 203                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 204                                         outputDir = "";
 205                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 206                                 }
 207                         }
 208                         //check for optional parameter and set defaults
 209                         // ...at some point should added some additional type checking...
 210
 211                         string temp;
 212                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 213                         else if (hard == "not open") { hard = ""; abort = true; }
 214
 215                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 216                         trump = temp[0];
 217
 218                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 219                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 220
 221                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 222                         m->setProcessors(temp);
 223                         convert(temp, processors);
 224
 225                         vertical = validParameter.validFile(parameters, "vertical", false);
 226                         if (vertical == "not found") {
 227                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 228                                 else { vertical = "F";  }
 229                         }
 230
 231                         numSeqs = 0;
 232                 }
 233
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 237                 exit(1);
 238         }
 239 }
 240 /**************************************************************************************/
 241
 242 int FilterSeqsCommand::execute() {
 243         try {
 244
 245                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 246
 247                 ifstream inFASTA;
 248                 m->openInputFile(fastafileNames[0], inFASTA);
 249
 250                 Sequence testSeq(inFASTA);
 251                 alignmentLength = testSeq.getAlignLength();
 252                 inFASTA.close();
 253
 254                 ////////////create filter/////////////////
 255                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 256
 257                 filter = createFilter();
 258
 259                 m->mothurOutEndLine();  m->mothurOutEndLine();
 260
 261                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 262
 263                 #ifdef USE_MPI
 264                         int pid;
 265                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 266
 267                         if (pid == 0) { //only one process should output the filter
 268                 #endif
 269
 270                 ofstream outFilter;
 271
 272                 //prevent giantic file name
 273                 string filterFile;
 274                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 275                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 276
 277                 m->openOutputFile(filterFile, outFilter);
 278                 outFilter << filter << endl;
 279                 outFilter.close();
 280                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 281
 282                 #ifdef USE_MPI
 283                         }
 284                 #endif
 285
 286                 ////////////run filter/////////////////
 287
 288                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 289
 290                 filterSequences();
 291
 292                 m->mothurOutEndLine();  m->mothurOutEndLine();
 293
 294                 int filteredLength = 0;
 295                 for(int i=0;i<alignmentLength;i++){
 296                         if(filter[i] == '1'){   filteredLength++;       }
 297                 }
 298
 299                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 300
 301
 302                 m->mothurOutEndLine();
 303                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 304                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 305                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 306                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 307
 308                 //set fasta file as new current fastafile
 309                 string current = "";
 310                 itTypes = outputTypes.find("fasta");
 311                 if (itTypes != outputTypes.end()) {
 312                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 313                 }
 314
 315                 m->mothurOutEndLine();
 316                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 317                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 318                 m->mothurOutEndLine();
 319
 320                 return 0;
 321
 322         }
 323         catch(exception& e) {
 324                 m->errorOut(e, "FilterSeqsCommand", "execute");
 325                 exit(1);
 326         }
 327 }
 328 /**************************************************************************************/
 329 int FilterSeqsCommand::filterSequences() {
 330         try {
 331
 332                 numSeqs = 0;
 333
 334                 for (int s = 0; s < fastafileNames.size(); s++) {
 335
 336                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 337
 338                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 339 #ifdef USE_MPI
 340                                 int pid, numSeqsPerProcessor, num;
 341                                 int tag = 2001;
 342                                 vector<unsigned long int>MPIPos;
 343
 344                                 MPI_Status status;
 345                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 346                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 347
 348                                 MPI_File outMPI;
 349                                 MPI_File inMPI;
 350                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 351                                 int inMode=MPI_MODE_RDONLY;
 352
 353                                 char outFilename[1024];
 354                                 strcpy(outFilename, filteredFasta.c_str());
 355
 356                                 char inFileName[1024];
 357                                 strcpy(inFileName, fastafileNames[s].c_str());
 358
 359                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 360                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 361
 362                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 363
 364                                 if (pid == 0) { //you are the root process
 365
 366                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 367                                         numSeqs += num;
 368
 369                                         //send file positions to all processes
 370                                         for(int i = 1; i < processors; i++) {
 371                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 372                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 373                                         }
 374
 375                                         //figure out how many sequences you have to do
 376                                         numSeqsPerProcessor = num / processors;
 377                                         int startIndex =  pid * numSeqsPerProcessor;
 378                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 379
 380
 381                                         //do your part
 382                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 383
 384                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 385
 386                                         //wait on chidren
 387                                         for(int i = 1; i < processors; i++) {
 388                                                 char buf[5];
 389                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 390                                         }
 391
 392                                 }else { //you are a child process
 393                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 394                                         MPIPos.resize(num+1);
 395                                         numSeqs += num;
 396                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 397
 398                                         //figure out how many sequences you have to align
 399                                         numSeqsPerProcessor = num / processors;
 400                                         int startIndex =  pid * numSeqsPerProcessor;
 401                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 402
 403
 404                                         //align your part
 405                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 406
 407                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 408
 409                                         char buf[5];
 410                                         strcpy(buf, "done");
 411
 412                                         //tell parent you are done.
 413                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 414                                 }
 415
 416                                 MPI_File_close(&outMPI);
 417                                 MPI_File_close(&inMPI);
 418                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 419
 420 #else
 421                         vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 422
 423                         for (int i = 0; i < (positions.size()-1); i++) {
 424                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 425                         }
 426                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 427                                 if(processors == 1){
 428                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 429                                         numSeqs += numFastaSeqs;
 430                                 }else{
 431                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 432                                         numSeqs += numFastaSeqs;
 433
 434                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 435
 436                                         //append fasta files
 437                                         for(int i=1;i<processors;i++){
 438                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 439                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 440                                         }
 441                                 }
 442
 443                                 if (m->control_pressed) {  return 1; }
 444                 #else
 445                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 446                                 numSeqs += numFastaSeqs;
 447
 448                                 if (m->control_pressed) {  return 1; }
 449                 #endif
 450 #endif
 451                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 452                 }
 453
 454                 return 0;
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 458                 exit(1);
 459         }
 460 }
 461 #ifdef USE_MPI
 462 /**************************************************************************************/
 463 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 464         try {
 465                 string outputString = "";
 466                 int count = 0;
 467                 MPI_Status status;
 468
 469                 for(int i=0;i<num;i++){
 470
 471                         if (m->control_pressed) { return 0; }
 472
 473                         //read next sequence
 474                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 475                         char* buf4 = new char[length];
 476                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 477
 478                         string tempBuf = buf4;
 479                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 480                         istringstream iss (tempBuf,istringstream::in);
 481                         delete buf4;
 482
 483                         Sequence seq(iss);  m->gobble(iss);
 484
 485                         if (seq.getName() != "") {
 486                                 string align = seq.getAligned();
 487                                 string filterSeq = "";
 488
 489                                 for(int j=0;j<alignmentLength;j++){
 490                                         if(filter[j] == '1'){
 491                                                 filterSeq += align[j];
 492                                         }
 493                                 }
 494
 495                                 count++;
 496                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 497
 498                                 if(count % 10 == 0){ //output to file
 499                                         //send results to parent
 500                                         int length = outputString.length();
 501                                         char* buf = new char[length];
 502                                         memcpy(buf, outputString.c_str(), length);
 503
 504                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 505                                         outputString = "";
 506                                         delete buf;
 507                                 }
 508
 509                         }
 510
 511                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 512                 }
 513
 514                 if(outputString != ""){ //output to file
 515                         //send results to parent
 516                         int length = outputString.length();
 517                         char* buf = new char[length];
 518                         memcpy(buf, outputString.c_str(), length);
 519
 520                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 521                         outputString = "";
 522                         delete buf;
 523                 }
 524
 525                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 526
 527                 return 0;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 531                 exit(1);
 532         }
 533 }
 534 #endif
 535 /**************************************************************************************/
 536 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 537         try {
 538                 ofstream out;
 539                 m->openOutputFile(outputFilename, out);
 540
 541                 ifstream in;
 542                 m->openInputFile(inputFilename, in);
 543
 544                 in.seekg(filePos->start);
 545
 546                 bool done = false;
 547                 int count = 0;
 548
 549                 while (!done) {
 550
 551                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 552
 553                                 Sequence seq(in); m->gobble(in);
 554                                 if (seq.getName() != "") {
 555                                         string align = seq.getAligned();
 556                                         string filterSeq = "";
 557
 558                                         for(int j=0;j<alignmentLength;j++){
 559                                                 if(filter[j] == '1'){
 560                                                         filterSeq += align[j];
 561                                                 }
 562                                         }
 563
 564                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 565                                 count++;
 566                         }
 567
 568                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 569                                 unsigned long int pos = in.tellg();
 570                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 571                         #else
 572                                 if (in.eof()) { break; }
 573                         #endif
 574
 575                         //report progress
 576                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 577                 }
 578                 //report progress
 579                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 580
 581
 582                 out.close();
 583                 in.close();
 584
 585                 return count;
 586         }
 587         catch(exception& e) {
 588                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 589                 exit(1);
 590         }
 591 }
 592 /**************************************************************************************************/
 593
 594 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 595         try {
 596 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 597                 int process = 0;
 598                 int num = 0;
 599                 processIDS.clear();
 600
 601                 //loop through and create all the processes you want
 602                 while (process != processors) {
 603                         int pid = fork();
 604
 605                         if (pid > 0) {
 606                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 607                                 process++;
 608                         }else if (pid == 0){
 609                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 610                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 611
 612                                 //pass numSeqs to parent
 613                                 ofstream out;
 614                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 615                                 m->openOutputFile(tempFile, out);
 616                                 out << num << endl;
 617                                 out.close();
 618
 619                                 exit(0);
 620                         }else {
 621                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 622                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 623                                 exit(0);
 624                         }
 625                 }
 626
 627                 //force parent to wait until all the processes are done
 628                 for (int i=0;i<processors;i++) {
 629                         int temp = processIDS[i];
 630                         wait(&temp);
 631                 }
 632
 633                 for (int i = 0; i < processIDS.size(); i++) {
 634                         ifstream in;
 635                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 636                         m->openInputFile(tempFile, in);
 637                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 638                         in.close(); remove(tempFile.c_str());
 639                 }
 640
 641
 642                 return num;
 643 #endif
 644         }
 645         catch(exception& e) {
 646                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 647                 exit(1);
 648         }
 649 }
 650 /**************************************************************************************/
 651 string FilterSeqsCommand::createFilter() {
 652         try {
 653                 string filterString = "";
 654                 Filters F;
 655
 656                 if (soft != 0)                  {  F.setSoft(soft);             }
 657                 if (trump != '*')               {  F.setTrump(trump);   }
 658
 659                 F.setLength(alignmentLength);
 660
 661                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 662                         F.initialize();
 663                 }
 664
 665                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 666                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 667
 668                 numSeqs = 0;
 669                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 670                         for (int s = 0; s < fastafileNames.size(); s++) {
 671
 672                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 673
 674 #ifdef USE_MPI
 675                                 int pid, numSeqsPerProcessor, num;
 676                                 int tag = 2001;
 677                                 vector<unsigned long int> MPIPos;
 678
 679                                 MPI_Status status;
 680                                 MPI_File inMPI;
 681                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 682                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 683
 684                                 //char* tempFileName = new char(fastafileNames[s].length());
 685                                 //tempFileName = &(fastafileNames[s][0]);
 686
 687                                 char tempFileName[1024];
 688                                 strcpy(tempFileName, fastafileNames[s].c_str());
 689
 690                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 691
 692                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 693
 694                                 if (pid == 0) { //you are the root process
 695                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 696                                                 numSeqs += num;
 697
 698                                                 //send file positions to all processes
 699                                                 for(int i = 1; i < processors; i++) {
 700                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 701                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 702                                                 }
 703
 704                                                 //figure out how many sequences you have to do
 705                                                 numSeqsPerProcessor = num / processors;
 706                                                 int startIndex =  pid * numSeqsPerProcessor;
 707                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 708
 709
 710                                                 //do your part
 711                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 712
 713                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 714
 715                                 }else { //i am the child process
 716                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 717                                         MPIPos.resize(num+1);
 718                                         numSeqs += num;
 719                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 720
 721                                         //figure out how many sequences you have to align
 722                                         numSeqsPerProcessor = num / processors;
 723                                         int startIndex =  pid * numSeqsPerProcessor;
 724                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 725
 726
 727                                         //do your part
 728                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 729
 730                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 731                                 }
 732
 733                                 MPI_File_close(&inMPI);
 734                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 735
 736 #else
 737                 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 738
 739                 for (int i = 0; i < (positions.size()-1); i++) {
 740                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 741                 }
 742                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 743                                 if(processors == 1){
 744                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 745                                         numSeqs += numFastaSeqs;
 746                                 }else{
 747                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 748                                         numSeqs += numFastaSeqs;
 749                                 }
 750
 751                                 if (m->control_pressed) {  return filterString; }
 752                 #else
 753                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 754                                 numSeqs += numFastaSeqs;
 755                                 if (m->control_pressed) {  return filterString; }
 756                 #endif
 757 #endif
 758
 759                         }
 760                 }
 761
 762
 763 #ifdef USE_MPI
 764                 int pid;
 765                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 766                 MPI_Status status;
 767
 768                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 769
 770                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 771
 772                         if (pid == 0) { //only one process should output the filter
 773
 774                                 vector<int> temp; temp.resize(alignmentLength+1);
 775
 776                                 //get the frequencies from the child processes
 777                                 for(int i = 1; i < processors; i++) {
 778
 779                                         for (int j = 0; j < 5; j++) {
 780
 781                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 782                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 783
 784                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 785                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 786                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 787                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 788                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 789                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 790                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 791                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 792                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 793                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 794                                                 }
 795                                         }
 796                                 }
 797                         }else{
 798
 799                                 //send my fequency counts
 800                                 F.a.push_back(Atag);
 801                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 802                                 F.t.push_back(Ttag);
 803                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 804                                 F.c.push_back(Ctag);
 805                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 806                                 F.g.push_back(Gtag);
 807                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 808                                 F.gap.push_back(Gaptag);
 809                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 810                         }
 811
 812                 }
 813
 814                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 815
 816                 if (pid == 0) { //only one process should output the filter
 817 #endif
 818
 819                 F.setNumSeqs(numSeqs);
 820                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 821                 if(soft != 0)                           {       F.doSoft();             }
 822                 filterString = F.getFilter();
 823
 824 #ifdef USE_MPI
 825                 //send filter string to kids
 826                 //for(int i = 1; i < processors; i++) {
 827                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 828                 //}
 829                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 830         }else{
 831                 //recieve filterString
 832                 char* tempBuf = new char[alignmentLength];
 833                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 834                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 835
 836                 filterString = tempBuf;
 837                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 838                 delete tempBuf;
 839         }
 840
 841         MPI_Barrier(MPI_COMM_WORLD);
 842 #endif
 843
 844                 return filterString;
 845         }
 846         catch(exception& e) {
 847                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 848                 exit(1);
 849         }
 850 }
 851 /**************************************************************************************/
 852 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 853         try {
 854
 855                 ifstream in;
 856                 m->openInputFile(filename, in);
 857
 858                 in.seekg(filePos->start);
 859
 860                 bool done = false;
 861                 int count = 0;
 862
 863                 while (!done) {
 864
 865                         if (m->control_pressed) { in.close(); return 1; }
 866
 867                         Sequence seq(in); m->gobble(in);
 868                         if (seq.getName() != "") {
 869                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 870
 871                                         if(trump != '*')                        {       F.doTrump(seq);         }
 872                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 873                                         cout.flush();
 874                                         count++;
 875                         }
 876
 877                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 878                                 unsigned long int pos = in.tellg();
 879                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 880                         #else
 881                                 if (in.eof()) { break; }
 882                         #endif
 883
 884                         //report progress
 885                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 886                 }
 887                 //report progress
 888                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 889                 in.close();
 890
 891                 return count;
 892         }
 893         catch(exception& e) {
 894                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 895                 exit(1);
 896         }
 897 }
 898 #ifdef USE_MPI
 899 /**************************************************************************************/
 900 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
 901         try {
 902
 903                 MPI_Status status;
 904                 int pid;
 905                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 906
 907                 for(int i=0;i<num;i++){
 908
 909                         if (m->control_pressed) { return 0; }
 910
 911                         //read next sequence
 912                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 913
 914                         char* buf4 = new char[length];
 915                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 916
 917                         string tempBuf = buf4;
 918                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 919                         istringstream iss (tempBuf,istringstream::in);
 920                         delete buf4;
 921
 922                         Sequence seq(iss);
 923
 924                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 925
 926                         if(trump != '*'){       F.doTrump(seq); }
 927                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 928                         cout.flush();
 929
 930                         //report progress
 931                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 932                 }
 933
 934                 //report progress
 935                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 936
 937                 return 0;
 938         }
 939         catch(exception& e) {
 940                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 941                 exit(1);
 942         }
 943 }
 944 #endif
 945 /**************************************************************************************************/
 946
 947 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 948         try {
 949 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 950                 int process = 1;
 951                 int num = 0;
 952                 processIDS.clear();
 953
 954                 //loop through and create all the processes you want
 955                 while (process != processors) {
 956                         int pid = fork();
 957
 958                         if (pid > 0) {
 959                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 960                                 process++;
 961                         }else if (pid == 0){
 962                                 //reset child's filter counts to 0;
 963                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 964                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 965                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 966                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 967                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 968
 969                                 num = driverCreateFilter(F, filename, lines[process]);
 970
 971                                 //write out filter counts to file
 972                                 filename += toString(getpid()) + "filterValues.temp";
 973                                 ofstream out;
 974                                 m->openOutputFile(filename, out);
 975
 976                                 out << num << endl;
 977                                 out << F.getFilter() << endl;
 978                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 979                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 980                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 981                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 982                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 983
 984                                 //cout << F.getFilter() << endl;
 985                                 out.close();
 986
 987                                 exit(0);
 988                         }else {
 989                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 990                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 991                                 exit(0);
 992                         }
 993                 }
 994
 995                 //parent do your part
 996                 num = driverCreateFilter(F, filename, lines[0]);
 997
 998                 //force parent to wait until all the processes are done
 999                 for (int i=0;i<(processors-1);i++) {
1000                         int temp = processIDS[i];
1001                         wait(&temp);
1002                 }
1003
1004                 //parent reads in and combines Filter info
1005                 for (int i = 0; i < processIDS.size(); i++) {
1006                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1007                         ifstream in;
1008                         m->openInputFile(tempFilename, in);
1009
1010                         int temp, tempNum;
1011                         string tempFilterString;
1012
1013                         in >> tempNum; m->gobble(in); num += tempNum;
1014
1015                         in >> tempFilterString;
1016                         F.mergeFilter(tempFilterString);
1017
1018                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1019                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1020                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1021                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1022                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1023
1024                         in.close();
1025                         remove(tempFilename.c_str());
1026                 }
1027
1028                 return num;
1029 #endif
1030         }
1031         catch(exception& e) {
1032                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1033                 exit(1);
1034         }
1035 }
1036 /**************************************************************************************/