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                 vector<string> outputNames;
 162
 163                 ifstream inFASTA;
 164                 openInputFile(fastafileNames[0], inFASTA);
 165
 166                 Sequence testSeq(inFASTA);
 167                 alignmentLength = testSeq.getAlignLength();
 168                 inFASTA.close();
 169
 170                 ////////////create filter/////////////////
 171
 172                 filter = createFilter();
 173
 174                 ofstream outFilter;
 175
 176                 string filterFile = outputDir + filterFileName + ".filter";
 177                 openOutputFile(filterFile, outFilter);
 178                 outFilter << filter << endl;
 179                 outFilter.close();
 180                 outputNames.push_back(filterFile);
 181
 182
 183                 ////////////run filter/////////////////
 184
 185                 numSeqs = 0;
 186                 for (int i = 0; i < fastafileNames.size(); i++) {
 187                         ifstream in;
 188                         openInputFile(fastafileNames[i], in);
 189                         string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
 190                         ofstream outFASTA;
 191                         openOutputFile(filteredFasta, outFASTA);
 192                         outputNames.push_back(filteredFasta);
 193
 194
 195                         while(!in.eof()){
 196                                 if (m->control_pressed) { in.close(); outFASTA.close(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 197
 198                                 Sequence seq(in);
 199                                 if (seq.getName() != "") {
 200                                         string align = seq.getAligned();
 201                                         string filterSeq = "";
 202
 203                                         for(int j=0;j<alignmentLength;j++){
 204                                                 if(filter[j] == '1'){
 205                                                         filterSeq += align[j];
 206                                                 }
 207                                         }
 208
 209                                         outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
 210                                         numSeqs++;
 211                                 }
 212                                 gobble(in);
 213                         }
 214                         outFASTA.close();
 215                         in.close();
 216                 }
 217
 218                 int filteredLength = 0;
 219                 for(int i=0;i<alignmentLength;i++){
 220                         if(filter[i] == '1'){   filteredLength++;       }
 221                 }
 222
 223                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 224
 225
 226                 m->mothurOutEndLine();
 227                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 228                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 229                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 230                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 231
 232
 233                 m->mothurOutEndLine();
 234                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 235                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 236                 m->mothurOutEndLine();
 237
 238                 return 0;
 239
 240         }
 241         catch(exception& e) {
 242                 m->errorOut(e, "FilterSeqsCommand", "execute");
 243                 exit(1);
 244         }
 245 }
 246 /**************************************************************************************/
 247 string FilterSeqsCommand::createFilter() {
 248         try {
 249                 string filterString = "";
 250
 251                 Filters F;
 252
 253                 if (soft != 0)                  {  F.setSoft(soft);             }
 254                 if (trump != '*')               {  F.setTrump(trump);   }
 255
 256                 F.setLength(alignmentLength);
 257
 258                 if(soft != 0 || isTrue(vertical)){
 259                         F.initialize();
 260                 }
 261
 262                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 263                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 264
 265                 numSeqs = 0;
 266
 267                 if(trump != '*' || isTrue(vertical) || soft != 0){
 268                         for (int s = 0; s < fastafileNames.size(); s++) {
 269
 270                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 271
 272 #ifdef USE_MPI
 273                                 int pid, rc, ierr;
 274                                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 275                                 int tag = 2001;
 276
 277                                 MPI_Status status;
 278                                 MPI_File in;
 279                                 rc = MPI_Comm_size(MPI_COMM_WORLD, &processors);
 280                                 rc = MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 281
 282
 283                                 char* tempFileName = new char(fastafileNames[s].length());
 284                                 tempFileName = &(fastafileNames[s][0]);
 285
 286                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &in);  //comm, filename, mode, info, filepointer
 287
 288                                 if (pid == 0) { //you are the root process
 289                                                 setLines(fastafileNames[s]);
 290
 291                                                 for (int j = 0; j < lines.size(); j++) { //each process
 292                                                         if (j != 0) { //don't send to yourself
 293                                                                 MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
 294                                                                 MPI_Send(&lines[j]->numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how many sequences we are sending
 295                                                                 MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
 296                                                         }
 297                                                 }
 298                                                 //cout << "done sending" << endl;
 299                                                 //cout << "parent = " << pid << " lines = " << lines[pid]->start << '\t' << lines[pid]->numSeqs << " size = " <<  lines.size() << endl;
 300
 301                                 cout << "parent =  " << pid << " address of Filter " << &F << " address of FilterString  " << &filterString << " address of numSeqs = " << &numSeqs << " address of soft = " << &soft << endl;
 302
 303                                                 char* buf = new char(bufferSizes[0]);
 304                         //cout << pid << '\t' << bufferSizes[0] << " line 1 start pos = " << lines[1]->start   << " buffer size 0 " << bufferSizes[0] << " buffer size 1 " << bufferSizes[1] << endl;
 305                                                 MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status);
 306
 307                 cout << pid << " done reading " << &buf <<  endl;
 308                                                 string tempBuf = buf;
 309                                                 delete buf;
 310                         //cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl;
 311
 312                                                 //parse buffer
 313                                                 istringstream iss (tempBuf,istringstream::in);
 314                                                 string name, seqstring;
 315                                                 vector<string> seqs;
 316
 317                                                 while (iss) {
 318
 319                                                         if (m->control_pressed) { return filterString; }
 320                                                         cout << "here" << endl;
 321                                                         Sequence seq(iss);
 322                                                         cout << "here1" << endl;
 323                                                         gobble(iss);
 324                                                         cout << seq.getName() << endl;
 325                                                         if (seq.getName() != "") {
 326                                                                 seqs.push_back(seq.getAligned());
 327                                                         }
 328
 329                                                 }
 330
 331                                                 for(int i=0;i<seqs.size();i++){
 332
 333                                                         if (m->control_pressed) { return filterString; }
 334
 335                                                         Sequence seq("", seqs[i]);
 336
 337                                                         if(trump != '*'){       F.doTrump(seq); }
 338                                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 339                                                         cout.flush();
 340
 341                                                         //report progress
 342                                                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 343                                                 }
 344
 345                                                 //report progress
 346                                                 if((seqs.size()) % 100 != 0){   m->mothurOut(toString(seqs.size())); m->mothurOutEndLine();             }
 347
 348                                                 //do your part
 349                                                 //MPICreateFilter(F, seqs);
 350
 351                                                 vector<int> temp; temp.resize(alignmentLength);
 352
 353                                                 //get the frequencies from the child processes
 354                                                 for(int i = 0; i < ((processors-1)*5); i++) {
 355                                 cout << "i = " << i << endl;
 356                                                         int ierr = MPI_Recv(&temp, alignmentLength, MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
 357
 358                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 359
 360                                                         int sender = status.MPI_SOURCE;
 361
 362                                                         if (receiveTag == Atag) { //you are recieveing the A frequencies
 363                                                                 for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 364                                                         }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 365                                                                 for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 366                                                         }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 367                                                                 for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 368                                                         }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 369                                                                 for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 370                                                         }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 371                                                                 for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 372                                                         }
 373
 374                                                         m->mothurOut("receive tag = " + toString(receiveTag) + " " + toString(sender) + " is complete."); m->mothurOutEndLine();
 375                                                 }
 376
 377
 378                                 }else { //i am the child process
 379                                         int startPos, numLines, bufferSize;
 380                                 cout << "child = " << pid << " address of Filter " << &F << " address of FilterString  " << &filterString << " address of numSeqs = " << &numSeqs << " address of soft = " << &soft<< endl;
 381                                         ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 382                                         ierr = MPI_Recv(&numLines, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 383                                         ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 384                                 //cout << "child = " << pid << " done recv messages startpos = " << startPos << " numLines = " << numLines << " buffersize = " << bufferSize << endl;
 385
 386
 387                                         //send freqs
 388                                         char* buf2 = new char(bufferSize);
 389                                         MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status);
 390                                 cout << pid << " done reading " << &buf2 <<  endl;
 391
 392                                         string tempBuf = buf2;
 393                                         delete buf2;
 394                 //      cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl;
 395                                         istringstream iss (tempBuf,istringstream::in);
 396
 397                                         string name, seqstring;
 398                                         vector<string> seqs;
 399
 400                                         while (iss) {
 401
 402                                                 if (m->control_pressed) { return filterString; }
 403                                                 cout << "here" << endl;
 404                                                 Sequence seq(iss);
 405                                                 cout << "here1" << endl;
 406                                                 gobble(iss);
 407                                                 cout << seq.getName() << endl;
 408
 409                                                 if (seq.getName() != "") {
 410                                                         seqs.push_back(seq.getAligned());
 411                                                 }
 412                                         }
 413
 414                                         for(int i=0;i<seqs.size();i++){
 415
 416                                                 if (m->control_pressed) { return filterString; }
 417
 418                                                 Sequence seq("", seqs[i]);
 419
 420                                                 if(trump != '*'){       F.doTrump(seq); }
 421                                                 if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 422                                                 cout.flush();
 423
 424                                                 //report progress
 425                                                 if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 426                                         }
 427
 428                                         //report progress
 429                                         if((seqs.size()) % 100 != 0){   m->mothurOut(toString(seqs.size())); m->mothurOutEndLine();             }
 430
 431                                         //MPICreateFilter(F, seqs);
 432
 433                                         //send my fequency counts
 434                                         F.a.push_back(Atag);
 435                                         int ierr = MPI_Send( &F.a[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
 436                                         F.t.push_back(Ttag);
 437                                         ierr = MPI_Send( &F.t[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
 438                                         F.c.push_back(Ctag);
 439                                         ierr = MPI_Send( &F.c[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
 440                                         F.g.push_back(Gtag);
 441                                         ierr = MPI_Send( &F.g[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
 442                                         F.gap.push_back(Gaptag);
 443                                         ierr = MPI_Send( &F.gap[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
 444
 445                                         cout << "child " << pid << " done sending counts" << endl;
 446                                 }
 447
 448                                 MPI_Barrier(MPI_COMM_WORLD);
 449
 450 #else
 451                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 452                                 if(processors == 1){
 453                                         ifstream inFASTA;
 454                                         openInputFile(fastafileNames[s], inFASTA);
 455                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 456                                         inFASTA.close();
 457
 458                                         numSeqs += numFastaSeqs;
 459
 460                                         lines.push_back(new linePair(0, numFastaSeqs));
 461
 462                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 463                                 }else{
 464
 465                                         setLines(fastafileNames[s]);
 466                                         createProcessesCreateFilter(F, fastafileNames[s]);
 467                                 }
 468                 #else
 469                                 ifstream inFASTA;
 470                                 openInputFile(fastafileNames[s], inFASTA);
 471                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 472                                 inFASTA.close();
 473
 474                                 numSeqs += numFastaSeqs;
 475
 476                                 lines.push_back(new linePair(0, numFastaSeqs));
 477
 478                                 driverCreateFilter(F, lines[0], fastafileNames[s]);
 479                 #endif
 480 #endif
 481
 482                         }
 483                 }
 484
 485 #ifdef USE_MPI
 486
 487 //merge all frequency data and create filter string
 488                                         //int pid;
 489                                         //MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 490
 491                                         //if (pid == 0) { //only one process should output to screen
 492 #endif
 493
 494         cout << "made it here" << endl;
 495                 F.setNumSeqs(numSeqs);
 496
 497                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 498                 if(soft != 0)                           {       F.doSoft();             }
 499 //cout << "Filter String = " << F.getFilter() << endl;
 500                 filterString = F.getFilter();
 501
 502                 return filterString;
 503         }
 504         catch(exception& e) {
 505                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 506                 exit(1);
 507         }
 508 }
 509 /**************************************************************************************/
 510 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 511         try {
 512
 513                 ifstream in;
 514                 openInputFile(filename, in);
 515
 516                 in.seekg(line->start);
 517
 518                 for(int i=0;i<line->numSeqs;i++){
 519
 520                         if (m->control_pressed) { in.close(); return 1; }
 521
 522                         Sequence seq(in);
 523                         if (seq.getName() != "") {
 524                                         if(trump != '*'){       F.doTrump(seq); }
 525                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 526                                         cout.flush();
 527                         }
 528
 529                         //report progress
 530                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 531                 }
 532
 533                 //report progress
 534                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 535
 536                 in.close();
 537
 538                 return 0;
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 542                 exit(1);
 543         }
 544 }
 545 /**************************************************************************************/
 546 int FilterSeqsCommand::MPICreateFilter(Filters& F, vector<string>& seqStrings) {
 547         try {
 548
 549                 for(int i=0;i<seqStrings.size();i++){
 550
 551                         if (m->control_pressed) { return 1; }
 552
 553                         Sequence seq("", seqStrings[0]);
 554
 555                         if(trump != '*'){       F.doTrump(seq); }
 556                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 557                         cout.flush();
 558
 559                         //report progress
 560                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 561                 }
 562
 563                 //report progress
 564                 if((seqStrings.size()) % 100 != 0){     m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine();               }
 565
 566                 return 0;
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 570                 exit(1);
 571         }
 572 }
 573
 574 /**************************************************************************************************/
 575
 576 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 577         try {
 578 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 579                 int process = 0;
 580                 int exitCommand = 1;
 581                 vector<int> processIDS;
 582
 583                 //loop through and create all the processes you want
 584                 while (process != processors) {
 585                         int pid = vfork();
 586
 587                         if (pid > 0) {
 588                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 589                                 process++;
 590                         }else if (pid == 0){
 591                                 driverCreateFilter(F, filename, lines[process]);
 592                                 exit(0);
 593                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 594                 }
 595
 596                 //force parent to wait until all the processes are done
 597                 for (int i=0;i<processors;i++) {
 598                         int temp = processIDS[i];
 599                         wait(&temp);
 600                 }
 601
 602                 return exitCommand;
 603 #endif
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 607                 exit(1);
 608         }
 609 }
 610 /**************************************************************************************************/
 611
 612 int FilterSeqsCommand::setLines(string filename) {
 613         try {
 614                 vector<int> positions;
 615                 map<int, int> buf;
 616                 bufferSizes.clear();
 617
 618                 int pid;
 619                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 620
 621                 ifstream inFASTA;
 622                 openInputFile(filename, inFASTA);
 623
 624                 string input;
 625                 int numbuf = 0;
 626                 while(!inFASTA.eof()){
 627                         input = getline(inFASTA);
 628
 629                         if (input.length() != 0) {
 630                                 numbuf += input.length();
 631                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  buf[(pos - input.length() - 1)] = numbuf; }
 632                         }
 633                 }
 634
 635                 inFASTA.close();
 636
 637                 int numFastaSeqs = positions.size();
 638
 639                 numSeqs += numFastaSeqs;
 640
 641                 int numSeqsPerProcessor = numFastaSeqs / processors;
 642
 643                 for (int i = 0; i < processors; i++) {
 644
 645                         long int startPos = positions[ i * numSeqsPerProcessor ];
 646                         if(i == processors - 1){
 647                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 648                                 bufferSizes.push_back(numbuf-buf[startPos]);
 649                         }else{
 650                                 int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 651                                 bufferSizes.push_back(buf[myEnd]-buf[startPos]);
 652                         }
 653                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 654                 }
 655
 656                 return 0;
 657         }
 658         catch(exception& e) {
 659                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 660                 exit(1);
 661         }
 662 }
 663 /**************************************************************************************************/
 664 int FilterSeqsCommand::parseBuffer(string file, vector<string>& seqs) {
 665         try {
 666
 667                 istringstream iss (file,istringstream::in);
 668                 string name, seqstring;
 669 int pid;
 670 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 671         Sequence* seq34 = new Sequence();
 672 cout << "address of new sequence " << pid << '\t' << seq34 << endl;
 673 cout << "address of seqStrings " << pid << '\t' << &seqs << endl;
 674
 675                 while (iss) {
 676
 677                         if (m->control_pressed) { return 0; }
 678                 cout << "here" << endl;
 679                         Sequence* seq = new Sequence(iss);
 680         cout << "here1" << endl;
 681                         gobble(iss);
 682         cout << seq->getName() << endl;
 683                         if (seq->getName() != "") {
 684                                 seqs.push_back(seq->getAligned());
 685                         }
 686                         delete seq;
 687                 }
 688
 689                 return 0;
 690         }
 691         catch(exception& e) {
 692                 m->errorOut(e, "FilterSeqsCommand", "parseBuffer");
 693                 exit(1);
 694         }
 695 }
 696 /**************************************************************************************/