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 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 filterFileName = "";
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("hard");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
  58                                 }
  59                         }
  60
  61                         //check for required parameters
  62                         fasta = validParameter.validFile(parameters, "fasta", false);
  63                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
  64                         else {
  65                                 splitAtDash(fasta, fastafileNames);
  66
  67                                 //go through files and make sure they are good, if not, then disregard them
  68                                 for (int i = 0; i < fastafileNames.size(); i++) {
  69                                         if (inputDir != "") {
  70                                                 string path = hasPath(fastafileNames[i]);
  71                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  72                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
  73                                         }
  74
  75                                         int ableToOpen;
  76                                         ifstream in;
  77                                         ableToOpen = openInputFile(fastafileNames[i], in);
  78                                         if (ableToOpen == 1) {
  79                                                 m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  80                                                 //erase from file list
  81                                                 fastafileNames.erase(fastafileNames.begin()+i);
  82                                                 i--;
  83                                         }else{
  84                                                 string simpleName = getSimpleName(fastafileNames[i]);
  85                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  86                                         }
  87                                         in.close();
  88                                 }
  89
  90                                 //make sure there is at least one valid file left
  91                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  92                         }
  93
  94                         if (!abort) {
  95                                 //if the user changes the output directory command factory will send this info to us in the output parameter
  96                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                         outputDir = "";
  98                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
  99                                 }
 100                         }
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103
 104                         string temp;
 105                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 106                         trump = temp[0];
 107
 108                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 109                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 110
 111                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 112                         convert(temp, processors);
 113
 114                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 115                         else if (hard == "not open") { abort = true; }
 116
 117                         vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
 118
 119                         numSeqs = 0;
 120
 121                 }
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 126                 exit(1);
 127         }
 128 }
 129
 130 //**********************************************************************************************************************
 131
 132 void FilterSeqsCommand::help(){
 133         try {
 134
 135                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 136                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 137                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 138                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 139                 m->mothurOut("The trump parameter .... The default is ...\n");
 140                 m->mothurOut("The soft parameter .... The default is ....\n");
 141                 m->mothurOut("The hard parameter .... The default is ....\n");
 142                 m->mothurOut("The vertical parameter .... The default is T.\n");
 143                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 144                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
 145                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
 146                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 147
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "FilterSeqsCommand", "help");
 151                 exit(1);
 152         }
 153 }
 154
 155 /**************************************************************************************/
 156
 157 int FilterSeqsCommand::execute() {
 158         try {
 159
 160                 if (abort == true) { return 0; }
 161
 162                 ifstream inFASTA;
 163                 openInputFile(fastafileNames[0], inFASTA);
 164
 165                 Sequence testSeq(inFASTA);
 166                 alignmentLength = testSeq.getAlignLength();
 167                 inFASTA.close();
 168
 169                 ////////////create filter/////////////////
 170
 171                 filter = createFilter();
 172
 173                 if (m->control_pressed) { return 0; }
 174
 175                 #ifdef USE_MPI
 176                         int pid;
 177                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 178
 179                         if (pid == 0) { //only one process should output the filter
 180                 #endif
 181
 182                 ofstream outFilter;
 183
 184                 string filterFile = outputDir + filterFileName + ".filter";
 185                 openOutputFile(filterFile, outFilter);
 186                 outFilter << filter << endl;
 187                 outFilter.close();
 188                 outputNames.push_back(filterFile);
 189
 190                 #ifdef USE_MPI
 191                         }
 192                 #endif
 193
 194                 ////////////run filter/////////////////
 195
 196                 filterSequences();
 197
 198                 int filteredLength = 0;
 199                 for(int i=0;i<alignmentLength;i++){
 200                         if(filter[i] == '1'){   filteredLength++;       }
 201                 }
 202
 203                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 204
 205
 206                 m->mothurOutEndLine();
 207                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 208                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 209                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 210                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 211
 212
 213                 m->mothurOutEndLine();
 214                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 215                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 216                 m->mothurOutEndLine();
 217
 218                 return 0;
 219
 220         }
 221         catch(exception& e) {
 222                 m->errorOut(e, "FilterSeqsCommand", "execute");
 223                 exit(1);
 224         }
 225 }
 226 /**************************************************************************************/
 227 int FilterSeqsCommand::filterSequences() {
 228         try {
 229
 230                 numSeqs = 0;
 231
 232                 for (int s = 0; s < fastafileNames.size(); s++) {
 233
 234                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 235
 236                                 string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
 237 #ifdef USE_MPI
 238                                 int pid, start, end;
 239                                 int tag = 2001;
 240
 241                                 MPI_Status status;
 242                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 243                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 244
 245                                 MPI_File outMPI;
 246                                 MPI_File inMPI;
 247                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 248                                 int inMode=MPI_MODE_RDONLY;
 249
 250                                 char outFilename[filteredFasta.length()];
 251                                 strcpy(outFilename, filteredFasta.c_str());
 252
 253                                 char inFileName[fastafileNames[s].length()];
 254                                 strcpy(inFileName, fastafileNames[s].c_str());
 255
 256                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 257                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 258
 259                                 if (pid == 0) { //you are the root process
 260
 261                                         setLines(fastafileNames[s]);
 262
 263                                         char bufF[alignmentLength];
 264                                         strcpy(bufF, filter.c_str());
 265
 266                                         for (int j = 0; j < lines.size(); j++) { //each process
 267                                                 if (j != 0) { //don't send to yourself
 268                                                         MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
 269                                                         MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
 270                                                         MPI_Send(bufF, alignmentLength, MPI_CHAR, j, tag, MPI_COMM_WORLD);
 271                                                 }
 272                                         }
 273
 274                                         //read your peice of file
 275                                         char buf[bufferSizes[0]];
 276                                         MPI_File_read_at(inMPI, lines[0]->start, buf, bufferSizes[0], MPI_CHAR, &status);
 277                                         istringstream iss (buf,istringstream::in);
 278
 279                                         //do your part
 280                                         driverMPIRun(iss, outMPI);
 281
 282                                         //wait on chidren
 283                                         for(int i = 1; i < processors; i++) {
 284                                                 char buf[4];
 285                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 286                                         }
 287
 288                                 }else { //you are a child process
 289                                         //receive your section of file
 290                                         int startPos, bufferSize;
 291                                         char bufF[alignmentLength];
 292                                         MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 293                                         MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 294                                         MPI_Recv(bufF, alignmentLength, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
 295
 296                                         filter = bufF; //filter was made by process 0 so other processes need to get it
 297
 298                                         //read your peice of file
 299                                         char buf2[bufferSize];
 300                                         MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
 301                                         istringstream iss (buf2,istringstream::in);
 302
 303                                         //do your part
 304                                         driverMPIRun(iss, outMPI);
 305
 306                                         char buf[4];
 307                                         strcpy(buf, "done");
 308
 309                                         //tell parent you are done.
 310                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 311                                 }
 312
 313                                 MPI_File_close(&outMPI);
 314                                 MPI_File_close(&inMPI);
 315
 316 #else
 317                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 318                                 if(processors == 1){
 319                                         ifstream inFASTA;
 320                                         openInputFile(fastafileNames[s], inFASTA);
 321                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 322                                         inFASTA.close();
 323
 324                                         lines.push_back(new linePair(0, numFastaSeqs));
 325
 326                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 327                                 }else{
 328                                         setLines(fastafileNames[s]);
 329                                         createProcessesRunFilter(filter, fastafileNames[s]);
 330
 331                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 332
 333                                         //append fasta files
 334                                         for(int i=1;i<processors;i++){
 335                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 336                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 337                                         }
 338                                 }
 339
 340                                 if (m->control_pressed) {  return 1; }
 341                 #else
 342                                 ifstream inFASTA;
 343                                 openInputFile(fastafileNames[s], inFASTA);
 344                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 345                                 inFASTA.close();
 346
 347                                 lines.push_back(new linePair(0, numFastaSeqs));
 348
 349                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 350
 351                                 if (m->control_pressed) {  return 1; }
 352                 #endif
 353 #endif
 354                         outputNames.push_back(filteredFasta);
 355                 }
 356
 357                 return 0;
 358         }
 359         catch(exception& e) {
 360                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 361                 exit(1);
 362         }
 363 }
 364 /**************************************************************************************/
 365 int FilterSeqsCommand::driverMPIRun(istringstream& in, MPI_File& outMPI) {
 366         try {
 367                 string outputString = "";
 368                 int count = 0;
 369                 MPI_Status status;
 370
 371                 while (!in.eof()) {
 372
 373                         Sequence seq(in); gobble(in);
 374
 375                         if (seq.getName() != "") {
 376                                 string align = seq.getAligned();
 377                                 string filterSeq = "";
 378
 379                                 for(int j=0;j<alignmentLength;j++){
 380                                         if(filter[j] == '1'){
 381                                                 filterSeq += align[j];
 382                                         }
 383                                 }
 384
 385                                 count++;
 386                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 387
 388                                 if(count % 10 == 0){ //output to file
 389                                         //send results to parent
 390                                         int length = outputString.length();
 391                                         char buf[length];
 392                                         strcpy(buf, outputString.c_str());
 393
 394                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 395                                         outputString = "";
 396                                 }
 397
 398                         }
 399                 }
 400
 401                 if(outputString != ""){ //output to file
 402                         //send results to parent
 403                         int length = outputString.length();
 404                         char buf[length];
 405                         strcpy(buf, outputString.c_str());
 406
 407                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 408                         outputString = "";
 409                 }
 410
 411
 412                 return 0;
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 416                 exit(1);
 417         }
 418 }
 419 /**************************************************************************************/
 420 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 421         try {
 422                 ofstream out;
 423                 openOutputFile(outputFilename, out);
 424
 425                 ifstream in;
 426                 openInputFile(inputFilename, in);
 427
 428                 in.seekg(line->start);
 429
 430                 for(int i=0;i<line->num;i++){
 431
 432                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 433
 434                                 Sequence seq(in);
 435                                 if (seq.getName() != "") {
 436                                         string align = seq.getAligned();
 437                                         string filterSeq = "";
 438
 439                                         for(int j=0;j<alignmentLength;j++){
 440                                                 if(filter[j] == '1'){
 441                                                         filterSeq += align[j];
 442                                                 }
 443                                         }
 444
 445                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 446                                 }
 447                                 gobble(in);
 448                 }
 449                 out.close();
 450                 in.close();
 451
 452                 return 0;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 456                 exit(1);
 457         }
 458 }
 459 /**************************************************************************************************/
 460
 461 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 462         try {
 463 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 464                 int process = 0;
 465                 int exitCommand = 1;
 466                 processIDS.clear();
 467
 468                 //loop through and create all the processes you want
 469                 while (process != processors) {
 470                         int pid = fork();
 471
 472                         if (pid > 0) {
 473                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 474                                 process++;
 475                         }else if (pid == 0){
 476                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 477                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 478                                 exit(0);
 479                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 480                 }
 481
 482                 //force parent to wait until all the processes are done
 483                 for (int i=0;i<processors;i++) {
 484                         int temp = processIDS[i];
 485                         wait(&temp);
 486                 }
 487
 488                 return exitCommand;
 489 #endif
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 493                 exit(1);
 494         }
 495 }
 496 /**************************************************************************************/
 497 string FilterSeqsCommand::createFilter() {
 498         try {
 499                 string filterString = "";
 500                 Filters F;
 501
 502                 if (soft != 0)                  {  F.setSoft(soft);             }
 503                 if (trump != '*')               {  F.setTrump(trump);   }
 504
 505                 F.setLength(alignmentLength);
 506
 507                 if(soft != 0 || isTrue(vertical)){
 508                         F.initialize();
 509                 }
 510
 511                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 512                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 513
 514                 numSeqs = 0;
 515                 if(trump != '*' || isTrue(vertical) || soft != 0){
 516                         for (int s = 0; s < fastafileNames.size(); s++) {
 517
 518                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 519
 520 #ifdef USE_MPI
 521                                 int pid;
 522                                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 523                                 int tag = 2001;
 524
 525                                 MPI_Status status;
 526                                 MPI_File inMPI;
 527                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 528                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 529
 530                                 char* tempFileName = new char(fastafileNames[s].length());
 531                                 tempFileName = &(fastafileNames[s][0]);
 532
 533                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 534
 535                                 if (pid == 0) { //you are the root process
 536                                                 setLines(fastafileNames[s]);
 537
 538                                                 for (int j = 0; j < lines.size(); j++) { //each process
 539                                                         if (j != 0) { //don't send to yourself
 540                                                                 MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
 541                                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 542                                                                 MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
 543                                                         }
 544                                                 }
 545
 546                                                 char buf[bufferSizes[0]];
 547                                                 MPI_File_read_at(inMPI, 0, buf, bufferSizes[0], MPI_CHAR, &status);
 548
 549                                                 string tempBuf = buf;
 550                                                 if (tempBuf.length() > bufferSizes[0]) { tempBuf = tempBuf.substr(0, bufferSizes[0]); }
 551
 552                                                 MPICreateFilter(F, tempBuf);
 553
 554                                                 if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
 555
 556                                                 vector<int> temp; temp.resize(alignmentLength+1);
 557
 558                                                 //get the frequencies from the child processes
 559                                                 for(int i = 0; i < ((processors-1)*5); i++) {
 560                                                         MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
 561                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 562
 563                                                         if (receiveTag == Atag) { //you are recieveing the A frequencies
 564                                                                 for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 565                                                         }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 566                                                                 for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 567                                                         }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 568                                                                 for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 569                                                         }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 570                                                                 for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 571                                                         }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 572                                                                 for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 573                                                         }
 574                                                 }
 575
 576
 577                                 }else { //i am the child process
 578
 579                                         int startPos, bufferSize;
 580                                         MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 581                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 582                                         MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 583
 584                                         //send freqs
 585                                         char buf2[bufferSize];
 586                                         MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
 587
 588                                         string tempBuf = buf2;
 589                                         if (tempBuf.length() > bufferSize) { tempBuf = tempBuf.substr(0, bufferSize); }
 590
 591                                         MPICreateFilter(F, tempBuf);
 592
 593                                         if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
 594
 595                                         //send my fequency counts
 596                                         F.a.push_back(Atag);
 597                                         int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 598                                         F.t.push_back(Ttag);
 599                                         ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 600                                         F.c.push_back(Ctag);
 601                                         ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 602                                         F.g.push_back(Gtag);
 603                                         ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 604                                         F.gap.push_back(Gaptag);
 605                                         ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 606                                 }
 607
 608                                 MPI_Barrier(MPI_COMM_WORLD);
 609                                 MPI_File_close(&inMPI);
 610
 611 #else
 612                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 613                                 if(processors == 1){
 614                                         ifstream inFASTA;
 615                                         openInputFile(fastafileNames[s], inFASTA);
 616                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 617                                         inFASTA.close();
 618
 619                                         numSeqs += numFastaSeqs;
 620
 621                                         lines.push_back(new linePair(0, numFastaSeqs));
 622
 623                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 624                                 }else{
 625                                         setLines(fastafileNames[s]);
 626                                         createProcessesCreateFilter(F, fastafileNames[s]);
 627                                 }
 628
 629                                 if (m->control_pressed) {  return filterString; }
 630                 #else
 631                                 ifstream inFASTA;
 632                                 openInputFile(fastafileNames[s], inFASTA);
 633                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 634                                 inFASTA.close();
 635
 636                                 numSeqs += numFastaSeqs;
 637
 638                                 lines.push_back(new linePair(0, numFastaSeqs));
 639
 640                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 641                                 if (m->control_pressed) {  return filterString; }
 642                 #endif
 643 #endif
 644
 645                         }
 646                 }
 647
 648                 F.setNumSeqs(numSeqs);
 649
 650                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 651                 if(soft != 0)                           {       F.doSoft();             }
 652
 653                 filterString = F.getFilter();
 654
 655                 return filterString;
 656         }
 657         catch(exception& e) {
 658                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 659                 exit(1);
 660         }
 661 }
 662 /**************************************************************************************/
 663 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 664         try {
 665
 666                 ifstream in;
 667                 openInputFile(filename, in);
 668
 669                 in.seekg(line->start);
 670
 671                 for(int i=0;i<line->num;i++){
 672
 673                         if (m->control_pressed) { in.close(); return 1; }
 674
 675                         Sequence seq(in);
 676                         if (seq.getName() != "") {
 677                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 678
 679                                         if(trump != '*'){       F.doTrump(seq); }
 680                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 681                                         cout.flush();
 682                         }
 683
 684                         //report progress
 685                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 686                 }
 687
 688                 //report progress
 689                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 690
 691                 in.close();
 692
 693                 return 0;
 694         }
 695         catch(exception& e) {
 696                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 697                 exit(1);
 698         }
 699 }
 700 /**************************************************************************************/
 701 int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {
 702         try {
 703
 704                 vector<string> seqStrings;
 705                 parseBuffer(input, seqStrings);
 706
 707                 for(int i=0;i<seqStrings.size();i++){
 708
 709                         if (seqStrings[i].length() != alignmentLength) {  cout << i << '\t' << seqStrings[i].length() << "Sequences are not all the same length, please correct." << endl; m->control_pressed = true;  }
 710
 711                         if (m->control_pressed) { return 1; }
 712
 713                         Sequence seq("", seqStrings[i]);
 714
 715                         if(trump != '*'){       F.doTrump(seq); }
 716                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 717                         cout.flush();
 718
 719                         //report progress
 720                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 721                 }
 722
 723                 //report progress
 724                 if((seqStrings.size()) % 100 != 0){     m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine();               }
 725
 726                 return 0;
 727         }
 728         catch(exception& e) {
 729                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 730                 exit(1);
 731         }
 732 }
 733
 734 /**************************************************************************************************/
 735
 736 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 737         try {
 738 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 739                 int process = 0;
 740                 int exitCommand = 1;
 741                 processIDS.clear();
 742
 743                 //loop through and create all the processes you want
 744                 while (process != processors) {
 745                         int pid = vfork();
 746
 747                         if (pid > 0) {
 748                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 749                                 process++;
 750                         }else if (pid == 0){
 751                                 driverCreateFilter(F, filename, lines[process]);
 752                                 exit(0);
 753                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 754                 }
 755
 756                 //force parent to wait until all the processes are done
 757                 for (int i=0;i<processors;i++) {
 758                         int temp = processIDS[i];
 759                         wait(&temp);
 760                 }
 761
 762                 return exitCommand;
 763 #endif
 764         }
 765         catch(exception& e) {
 766                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 767                 exit(1);
 768         }
 769 }
 770 /**************************************************************************************************/
 771
 772 int FilterSeqsCommand::setLines(string filename) {
 773         try {
 774
 775                 vector<long int> positions;
 776                 bufferSizes.clear();
 777
 778                 ifstream inFASTA;
 779                 openInputFile(filename, inFASTA);
 780
 781                 string input;
 782                 while(!inFASTA.eof()){
 783                         input = getline(inFASTA);
 784
 785                         if (input.length() != 0) {
 786                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 787                         }
 788                 }
 789                 inFASTA.close();
 790
 791                 int numFastaSeqs = positions.size();
 792
 793                 FILE * pFile;
 794                 long size;
 795
 796                 //get num bytes in file
 797                 pFile = fopen (filename.c_str(),"rb");
 798                 if (pFile==NULL) perror ("Error opening file");
 799                 else{
 800                         fseek (pFile, 0, SEEK_END);
 801                         size=ftell (pFile);
 802                         fclose (pFile);
 803                 }
 804
 805                 numSeqs += numFastaSeqs;
 806
 807                 int numSeqsPerProcessor = numFastaSeqs / processors;
 808
 809                 for (int i = 0; i < processors; i++) {
 810
 811                         long int startPos = positions[ i * numSeqsPerProcessor ];
 812                         if(i == processors - 1){
 813                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 814                                 bufferSizes.push_back(size - startPos);
 815                         }else{
 816                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 817                                 bufferSizes.push_back(myEnd-startPos);
 818                         }
 819                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 820                 }
 821
 822                 return 0;
 823         }
 824         catch(exception& e) {
 825                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 826                 exit(1);
 827         }
 828 }
 829 /**************************************************************************************************/
 830 int FilterSeqsCommand::parseBuffer(string file, vector<string>& seqs) {
 831         try {
 832                 istringstream iss (file); //,istringstream::in
 833                 string name, seqstring;
 834
 835                 while (!iss.eof()) {
 836
 837                         if (m->control_pressed) { return 0; }
 838
 839                         Sequence seq(iss); gobble(iss);
 840
 841                         if (seq.getName() != "") {
 842                                 seqs.push_back(seq.getAligned());
 843                         }
 844                 }
 845
 846                 return 0;
 847         }
 848         catch(exception& e) {
 849                 m->errorOut(e, "FilterSeqsCommand", "parseBuffer");
 850                 exit(1);
 851         }
 852 }
 853 /**************************************************************************************/