filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> FilterSeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
  19                 CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
  20                 CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
  21                 CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "FilterSeqsCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string FilterSeqsCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
  40                 helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
  41                 helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
  42                 helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
  43                 helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
  44                 helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
  45                 helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
  46                 helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
  47                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  48                 helpString += "The filter.seqs command should be in the following format: \n";
  49                 helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
  50                 helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "FilterSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 FilterSeqsCommand::FilterSeqsCommand(){
  61         try {
  62                 abort = true; calledHelp = true;
  63                 setParameters();
  64                 vector<string> tempOutNames;
  65                 outputTypes["fasta"] = tempOutNames;
  66                 outputTypes["filter"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  70                 exit(1);
  71         }
  72 }
  73 /**************************************************************************************/
  74 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77                 filterFileName = "";
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter("filter.seqs");
  90                         map<string,string>::iterator it;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["fasta"] = tempOutNames;
 100                         outputTypes["filter"] = tempOutNames;
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106                                 string path;
 107                                 it = parameters.find("fasta");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 113                                 }
 114
 115                                 it = parameters.find("hard");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 121                                 }
 122                         }
 123
 124                         //check for required parameters
 125                         fasta = validParameter.validFile(parameters, "fasta", false);
 126                         if (fasta == "not found") {
 127                                 fasta = m->getFastaFile();
 128                                 if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 129                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 130                         }
 131                         else {
 132                                 m->splitAtDash(fasta, fastafileNames);
 133
 134                                 //go through files and make sure they are good, if not, then disregard them
 135                                 for (int i = 0; i < fastafileNames.size(); i++) {
 136
 137                                         bool ignore = false;
 138                                         if (fastafileNames[i] == "current") {
 139                                                 fastafileNames[i] = m->getFastaFile();
 140                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 141                                                 else {
 142                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 143                                                         //erase from file list
 144                                                         fastafileNames.erase(fastafileNames.begin()+i);
 145                                                         i--;
 146                                                 }
 147                                         }
 148
 149                                         if (!ignore) {
 150                                                 if (inputDir != "") {
 151                                                         string path = m->hasPath(fastafileNames[i]);
 152                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 154                                                 }
 155
 156                                                 ifstream in;
 157                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 158
 159                                                 //if you can't open it, try default location
 160                                                 if (ableToOpen == 1) {
 161                                                         if (m->getDefaultPath() != "") { //default path is set
 162                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 163                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 164                                                                 ifstream in2;
 165                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 166                                                                 in2.close();
 167                                                                 fastafileNames[i] = tryPath;
 168                                                         }
 169                                                 }
 170
 171                                                 //if you can't open it, try default location
 172                                                 if (ableToOpen == 1) {
 173                                                         if (m->getOutputDir() != "") { //default path is set
 174                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 175                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 176                                                                 ifstream in2;
 177                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 178                                                                 in2.close();
 179                                                                 fastafileNames[i] = tryPath;
 180                                                         }
 181                                                 }
 182
 183                                                 in.close();
 184
 185                                                 if (ableToOpen == 1) {
 186                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 187                                                         //erase from file list
 188                                                         fastafileNames.erase(fastafileNames.begin()+i);
 189                                                         i--;
 190                                                 }else{
 191                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 192                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 193                                                         m->setFastaFile(fastafileNames[i]);
 194                                                 }
 195                                                 in.close();
 196                                         }
 197                                 }
 198
 199                                 //make sure there is at least one valid file left
 200                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 201                         }
 202
 203                         if (!abort) {
 204                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 205                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 206                                         outputDir = "";
 207                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 208                                 }
 209                         }
 210                         //check for optional parameter and set defaults
 211                         // ...at some point should added some additional type checking...
 212
 213                         string temp;
 214                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 215                         else if (hard == "not open") { hard = ""; abort = true; }
 216
 217                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 218                         trump = temp[0];
 219
 220                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 221                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 222
 223                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 224                         m->setProcessors(temp);
 225                         convert(temp, processors);
 226
 227                         vertical = validParameter.validFile(parameters, "vertical", false);
 228                         if (vertical == "not found") {
 229                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 230                                 else { vertical = "F";  }
 231                         }
 232
 233                         numSeqs = 0;
 234                 }
 235
 236         }
 237         catch(exception& e) {
 238                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 239                 exit(1);
 240         }
 241 }
 242 /**************************************************************************************/
 243
 244 int FilterSeqsCommand::execute() {
 245         try {
 246
 247                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 248
 249                 ifstream inFASTA;
 250                 m->openInputFile(fastafileNames[0], inFASTA);
 251
 252                 Sequence testSeq(inFASTA);
 253                 alignmentLength = testSeq.getAlignLength();
 254                 inFASTA.close();
 255
 256                 ////////////create filter/////////////////
 257                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 258
 259                 filter = createFilter();
 260
 261                 m->mothurOutEndLine();  m->mothurOutEndLine();
 262
 263                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 264
 265                 #ifdef USE_MPI
 266                         int pid;
 267                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 268
 269                         if (pid == 0) { //only one process should output the filter
 270                 #endif
 271
 272                 ofstream outFilter;
 273
 274                 //prevent giantic file name
 275                 string filterFile;
 276                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 277                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 278
 279                 m->openOutputFile(filterFile, outFilter);
 280                 outFilter << filter << endl;
 281                 outFilter.close();
 282                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 283
 284                 #ifdef USE_MPI
 285                         }
 286                 #endif
 287
 288                 ////////////run filter/////////////////
 289
 290                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 291
 292                 filterSequences();
 293
 294                 m->mothurOutEndLine();  m->mothurOutEndLine();
 295
 296                 int filteredLength = 0;
 297                 for(int i=0;i<alignmentLength;i++){
 298                         if(filter[i] == '1'){   filteredLength++;       }
 299                 }
 300
 301                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 302
 303
 304                 m->mothurOutEndLine();
 305                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 306                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 307                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 308                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 309
 310                 //set fasta file as new current fastafile
 311                 string current = "";
 312                 itTypes = outputTypes.find("fasta");
 313                 if (itTypes != outputTypes.end()) {
 314                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 315                 }
 316
 317                 m->mothurOutEndLine();
 318                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 319                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 320                 m->mothurOutEndLine();
 321
 322                 return 0;
 323
 324         }
 325         catch(exception& e) {
 326                 m->errorOut(e, "FilterSeqsCommand", "execute");
 327                 exit(1);
 328         }
 329 }
 330 /**************************************************************************************/
 331 int FilterSeqsCommand::filterSequences() {
 332         try {
 333
 334                 numSeqs = 0;
 335
 336                 for (int s = 0; s < fastafileNames.size(); s++) {
 337
 338                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 339
 340                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 341 #ifdef USE_MPI
 342                                 int pid, numSeqsPerProcessor, num;
 343                                 int tag = 2001;
 344                                 vector<unsigned long long>MPIPos;
 345
 346                                 MPI_Status status;
 347                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 348                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 349
 350                                 MPI_File outMPI;
 351                                 MPI_File inMPI;
 352                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 353                                 int inMode=MPI_MODE_RDONLY;
 354
 355                                 char outFilename[1024];
 356                                 strcpy(outFilename, filteredFasta.c_str());
 357
 358                                 char inFileName[1024];
 359                                 strcpy(inFileName, fastafileNames[s].c_str());
 360
 361                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 362                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 363
 364                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 365
 366                                 if (pid == 0) { //you are the root process
 367
 368                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 369                                         numSeqs += num;
 370
 371                                         //send file positions to all processes
 372                                         for(int i = 1; i < processors; i++) {
 373                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 374                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 375                                         }
 376
 377                                         //figure out how many sequences you have to do
 378                                         numSeqsPerProcessor = num / processors;
 379                                         int startIndex =  pid * numSeqsPerProcessor;
 380                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 381
 382
 383                                         //do your part
 384                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 385
 386                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 387
 388                                         //wait on chidren
 389                                         for(int i = 1; i < processors; i++) {
 390                                                 char buf[5];
 391                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 392                                         }
 393
 394                                 }else { //you are a child process
 395                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 396                                         MPIPos.resize(num+1);
 397                                         numSeqs += num;
 398                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 399
 400                                         //figure out how many sequences you have to align
 401                                         numSeqsPerProcessor = num / processors;
 402                                         int startIndex =  pid * numSeqsPerProcessor;
 403                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 404
 405
 406                                         //align your part
 407                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 408
 409                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 410
 411                                         char buf[5];
 412                                         strcpy(buf, "done");
 413
 414                                         //tell parent you are done.
 415                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 416                                 }
 417
 418                                 MPI_File_close(&outMPI);
 419                                 MPI_File_close(&inMPI);
 420                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 421
 422 #else
 423
 424                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 425                         vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 426
 427                         for (int i = 0; i < (positions.size()-1); i++) {
 428                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 429                         }
 430
 431                                 if(processors == 1){
 432                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 433                                         numSeqs += numFastaSeqs;
 434                                 }else{
 435                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
 436                                         numSeqs += numFastaSeqs;
 437
 438                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 439
 440                                         //append fasta files
 441                                         for(int i=1;i<processors;i++){
 442                                                 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 443                                                 m->mothurRemove((fastafileNames[s] + toString(processIDS[i]) + ".temp"));
 444                                         }
 445                                 }
 446
 447                                 if (m->control_pressed) {  return 1; }
 448                 #else
 449                                 lines.push_back(new linePair(0, 1000));
 450                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 451                                 numSeqs += numFastaSeqs;
 452
 453                                 if (m->control_pressed) {  return 1; }
 454                 #endif
 455 #endif
 456                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 457                 }
 458
 459                 return 0;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 463                 exit(1);
 464         }
 465 }
 466 #ifdef USE_MPI
 467 /**************************************************************************************/
 468 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
 469         try {
 470                 string outputString = "";
 471                 int count = 0;
 472                 MPI_Status status;
 473
 474                 for(int i=0;i<num;i++){
 475
 476                         if (m->control_pressed) { return 0; }
 477
 478                         //read next sequence
 479                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 480                         char* buf4 = new char[length];
 481                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 482
 483                         string tempBuf = buf4;
 484                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 485                         istringstream iss (tempBuf,istringstream::in);
 486                         delete buf4;
 487
 488                         Sequence seq(iss);  m->gobble(iss);
 489
 490                         if (seq.getName() != "") {
 491                                 string align = seq.getAligned();
 492                                 string filterSeq = "";
 493
 494                                 for(int j=0;j<alignmentLength;j++){
 495                                         if(filter[j] == '1'){
 496                                                 filterSeq += align[j];
 497                                         }
 498                                 }
 499
 500                                 count++;
 501                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 502
 503                                 if(count % 10 == 0){ //output to file
 504                                         //send results to parent
 505                                         int length = outputString.length();
 506                                         char* buf = new char[length];
 507                                         memcpy(buf, outputString.c_str(), length);
 508
 509                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 510                                         outputString = "";
 511                                         delete buf;
 512                                 }
 513
 514                         }
 515
 516                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 517                 }
 518
 519                 if(outputString != ""){ //output to file
 520                         //send results to parent
 521                         int length = outputString.length();
 522                         char* buf = new char[length];
 523                         memcpy(buf, outputString.c_str(), length);
 524
 525                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 526                         outputString = "";
 527                         delete buf;
 528                 }
 529
 530                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 531
 532                 return 0;
 533         }
 534         catch(exception& e) {
 535                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 536                 exit(1);
 537         }
 538 }
 539 #endif
 540 /**************************************************************************************/
 541 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 542         try {
 543                 ofstream out;
 544                 m->openOutputFile(outputFilename, out);
 545
 546                 ifstream in;
 547                 m->openInputFile(inputFilename, in);
 548
 549                 in.seekg(filePos->start);
 550
 551                 bool done = false;
 552                 int count = 0;
 553
 554                 while (!done) {
 555
 556                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 557
 558                                 Sequence seq(in); m->gobble(in);
 559                                 if (seq.getName() != "") {
 560                                         string align = seq.getAligned();
 561                                         string filterSeq = "";
 562
 563                                         for(int j=0;j<alignmentLength;j++){
 564                                                 if(filter[j] == '1'){
 565                                                         filterSeq += align[j];
 566                                                 }
 567                                         }
 568
 569                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 570                                 count++;
 571                         }
 572
 573                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 574                                 unsigned long long pos = in.tellg();
 575                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 576                         #else
 577                                 if (in.eof()) { break; }
 578                         #endif
 579
 580                         //report progress
 581                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 582                 }
 583                 //report progress
 584                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 585
 586
 587                 out.close();
 588                 in.close();
 589
 590                 return count;
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 594                 exit(1);
 595         }
 596 }
 597 /**************************************************************************************************/
 598
 599 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 600         try {
 601 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 602                 int process = 0;
 603                 int num = 0;
 604                 processIDS.clear();
 605
 606                 //loop through and create all the processes you want
 607                 while (process != processors) {
 608                         int pid = fork();
 609
 610                         if (pid > 0) {
 611                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 612                                 process++;
 613                         }else if (pid == 0){
 614                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 615                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 616
 617                                 //pass numSeqs to parent
 618                                 ofstream out;
 619                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 620                                 m->openOutputFile(tempFile, out);
 621                                 out << num << endl;
 622                                 out.close();
 623
 624                                 exit(0);
 625                         }else {
 626                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 627                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 628                                 exit(0);
 629                         }
 630                 }
 631
 632                 //force parent to wait until all the processes are done
 633                 for (int i=0;i<processors;i++) {
 634                         int temp = processIDS[i];
 635                         wait(&temp);
 636                 }
 637
 638                 for (int i = 0; i < processIDS.size(); i++) {
 639                         ifstream in;
 640                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 641                         m->openInputFile(tempFile, in);
 642                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 643                         in.close(); m->mothurRemove(tempFile);
 644                 }
 645
 646
 647                 return num;
 648 #endif
 649         }
 650         catch(exception& e) {
 651                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 652                 exit(1);
 653         }
 654 }
 655 /**************************************************************************************/
 656 string FilterSeqsCommand::createFilter() {
 657         try {
 658                 string filterString = "";
 659                 Filters F;
 660
 661                 if (soft != 0)                  {  F.setSoft(soft);             }
 662                 if (trump != '*')               {  F.setTrump(trump);   }
 663
 664                 F.setLength(alignmentLength);
 665
 666                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 667                         F.initialize();
 668                 }
 669
 670                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 671                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 672
 673                 numSeqs = 0;
 674                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 675                         for (int s = 0; s < fastafileNames.size(); s++) {
 676
 677                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 678
 679 #ifdef USE_MPI
 680                                 int pid, numSeqsPerProcessor, num;
 681                                 int tag = 2001;
 682                                 vector<unsigned long long> MPIPos;
 683
 684                                 MPI_Status status;
 685                                 MPI_File inMPI;
 686                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 687                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 688
 689                                 //char* tempFileName = new char(fastafileNames[s].length());
 690                                 //tempFileName = &(fastafileNames[s][0]);
 691
 692                                 char tempFileName[1024];
 693                                 strcpy(tempFileName, fastafileNames[s].c_str());
 694
 695                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 696
 697                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 698
 699                                 if (pid == 0) { //you are the root process
 700                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 701                                                 numSeqs += num;
 702
 703                                                 //send file positions to all processes
 704                                                 for(int i = 1; i < processors; i++) {
 705                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 706                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 707                                                 }
 708
 709                                                 //figure out how many sequences you have to do
 710                                                 numSeqsPerProcessor = num / processors;
 711                                                 int startIndex =  pid * numSeqsPerProcessor;
 712                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 713
 714
 715                                                 //do your part
 716                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 717
 718                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 719
 720                                 }else { //i am the child process
 721                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 722                                         MPIPos.resize(num+1);
 723                                         numSeqs += num;
 724                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 725
 726                                         //figure out how many sequences you have to align
 727                                         numSeqsPerProcessor = num / processors;
 728                                         int startIndex =  pid * numSeqsPerProcessor;
 729                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 730
 731
 732                                         //do your part
 733                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 734
 735                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 736                                 }
 737
 738                                 MPI_File_close(&inMPI);
 739                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 740
 741 #else
 742
 743
 744                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 745                                 vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 746                                 for (int i = 0; i < (positions.size()-1); i++) {
 747                                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 748                                 }
 749
 750                                 if(processors == 1){
 751                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 752                                         numSeqs += numFastaSeqs;
 753                                 }else{
 754                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 755                                         numSeqs += numFastaSeqs;
 756                                 }
 757
 758                                 if (m->control_pressed) {  return filterString; }
 759                 #else
 760                                 lines.push_back(new linePair(0, 1000));
 761                                 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 762                                 numSeqs += numFastaSeqs;
 763                                 if (m->control_pressed) {  return filterString; }
 764                 #endif
 765 #endif
 766
 767                         }
 768                 }
 769
 770
 771 #ifdef USE_MPI
 772                 int pid;
 773                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 774                 MPI_Status status;
 775
 776                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 777
 778                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 779
 780                         if (pid == 0) { //only one process should output the filter
 781
 782                                 vector<int> temp; temp.resize(alignmentLength+1);
 783
 784                                 //get the frequencies from the child processes
 785                                 for(int i = 1; i < processors; i++) {
 786
 787                                         for (int j = 0; j < 5; j++) {
 788
 789                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 790                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 791
 792                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 793                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 794                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 795                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 796                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 797                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 798                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 799                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 800                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 801                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 802                                                 }
 803                                         }
 804                                 }
 805                         }else{
 806
 807                                 //send my fequency counts
 808                                 F.a.push_back(Atag);
 809                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 810                                 F.t.push_back(Ttag);
 811                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 812                                 F.c.push_back(Ctag);
 813                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 814                                 F.g.push_back(Gtag);
 815                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 816                                 F.gap.push_back(Gaptag);
 817                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 818                         }
 819
 820                 }
 821
 822                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 823
 824                 if (pid == 0) { //only one process should output the filter
 825 #endif
 826
 827                 F.setNumSeqs(numSeqs);
 828                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 829                 if(soft != 0)                           {       F.doSoft();             }
 830                 filterString = F.getFilter();
 831
 832 #ifdef USE_MPI
 833                 //send filter string to kids
 834                 //for(int i = 1; i < processors; i++) {
 835                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 836                 //}
 837                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 838         }else{
 839                 //recieve filterString
 840                 char* tempBuf = new char[alignmentLength];
 841                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 842                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 843
 844                 filterString = tempBuf;
 845                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 846                 delete tempBuf;
 847         }
 848
 849         MPI_Barrier(MPI_COMM_WORLD);
 850 #endif
 851
 852                 return filterString;
 853         }
 854         catch(exception& e) {
 855                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 856                 exit(1);
 857         }
 858 }
 859 /**************************************************************************************/
 860 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 861         try {
 862
 863                 ifstream in;
 864                 m->openInputFile(filename, in);
 865
 866                 in.seekg(filePos->start);
 867
 868                 bool done = false;
 869                 int count = 0;
 870
 871                 while (!done) {
 872
 873                         if (m->control_pressed) { in.close(); return 1; }
 874
 875                         Sequence seq(in); m->gobble(in);
 876                         if (seq.getName() != "") {
 877                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 878
 879                                         if(trump != '*')                        {       F.doTrump(seq);         }
 880                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 881                                         cout.flush();
 882                                         count++;
 883                         }
 884
 885                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 886                                 unsigned long long pos = in.tellg();
 887                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 888                         #else
 889                                 if (in.eof()) { break; }
 890                         #endif
 891
 892                         //report progress
 893                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 894                 }
 895                 //report progress
 896                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 897                 in.close();
 898
 899                 return count;
 900         }
 901         catch(exception& e) {
 902                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 903                 exit(1);
 904         }
 905 }
 906 #ifdef USE_MPI
 907 /**************************************************************************************/
 908 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
 909         try {
 910
 911                 MPI_Status status;
 912                 int pid;
 913                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 914
 915                 for(int i=0;i<num;i++){
 916
 917                         if (m->control_pressed) { return 0; }
 918
 919                         //read next sequence
 920                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 921
 922                         char* buf4 = new char[length];
 923                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 924
 925                         string tempBuf = buf4;
 926                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 927                         istringstream iss (tempBuf,istringstream::in);
 928                         delete buf4;
 929
 930                         Sequence seq(iss);
 931
 932                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 933
 934                         if(trump != '*'){       F.doTrump(seq); }
 935                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
 936                         cout.flush();
 937
 938                         //report progress
 939                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 940                 }
 941
 942                 //report progress
 943                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 944
 945                 return 0;
 946         }
 947         catch(exception& e) {
 948                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 949                 exit(1);
 950         }
 951 }
 952 #endif
 953 /**************************************************************************************************/
 954
 955 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 956         try {
 957 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 958                 int process = 1;
 959                 int num = 0;
 960                 processIDS.clear();
 961
 962                 //loop through and create all the processes you want
 963                 while (process != processors) {
 964                         int pid = fork();
 965
 966                         if (pid > 0) {
 967                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 968                                 process++;
 969                         }else if (pid == 0){
 970                                 //reset child's filter counts to 0;
 971                                 F.a.clear(); F.a.resize(alignmentLength, 0);
 972                                 F.t.clear(); F.t.resize(alignmentLength, 0);
 973                                 F.g.clear(); F.g.resize(alignmentLength, 0);
 974                                 F.c.clear(); F.c.resize(alignmentLength, 0);
 975                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
 976
 977                                 num = driverCreateFilter(F, filename, lines[process]);
 978
 979                                 //write out filter counts to file
 980                                 filename += toString(getpid()) + "filterValues.temp";
 981                                 ofstream out;
 982                                 m->openOutputFile(filename, out);
 983
 984                                 out << num << endl;
 985                                 out << F.getFilter() << endl;
 986                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
 987                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
 988                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
 989                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
 990                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
 991
 992                                 //cout << F.getFilter() << endl;
 993                                 out.close();
 994
 995                                 exit(0);
 996                         }else {
 997                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 998                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 999                                 exit(0);
1000                         }
1001                 }
1002
1003                 //parent do your part
1004                 num = driverCreateFilter(F, filename, lines[0]);
1005
1006                 //force parent to wait until all the processes are done
1007                 for (int i=0;i<(processors-1);i++) {
1008                         int temp = processIDS[i];
1009                         wait(&temp);
1010                 }
1011
1012                 //parent reads in and combines Filter info
1013                 for (int i = 0; i < processIDS.size(); i++) {
1014                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1015                         ifstream in;
1016                         m->openInputFile(tempFilename, in);
1017
1018                         int temp, tempNum;
1019                         string tempFilterString;
1020
1021                         in >> tempNum; m->gobble(in); num += tempNum;
1022
1023                         in >> tempFilterString;
1024                         F.mergeFilter(tempFilterString);
1025
1026                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1027                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1028                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1029                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1030                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1031
1032                         in.close();
1033                         m->mothurRemove(tempFilename);
1034                 }
1035
1036                 return num;
1037 #endif
1038         }
1039         catch(exception& e) {
1040                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1041                 exit(1);
1042         }
1043 }
1044 /**************************************************************************************/