screenseqscommand.cpp

   1 /*
   2  *  screenseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/3/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "screenseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ScreenSeqsCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
  17                                                                         "name", "group", "alignreport","processors","outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "ScreenSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 ScreenSeqsCommand::ScreenSeqsCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["name"] = tempOutNames;
  34                 outputTypes["group"] = tempOutNames;
  35                 outputTypes["alignreport"] = tempOutNames;
  36                 outputTypes["accnos"] = tempOutNames;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 vector<string> ScreenSeqsCommand::getRequiredParameters(){
  45         try {
  46                 string Array[] =  {"fasta"};
  47                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "ScreenSeqsCommand", "getRequiredParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 vector<string> ScreenSeqsCommand::getRequiredFiles(){
  57         try {
  58                 vector<string> myArray;
  59                 return myArray;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "ScreenSeqsCommand", "getRequiredFiles");
  63                 exit(1);
  64         }
  65 }
  66 //***************************************************************************************************************
  67
  68 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  69         try {
  70                 abort = false;
  71
  72                 //allow user to run help
  73                 if(option == "help") { help(); abort = true; }
  74
  75                 else {
  76                         //valid paramters for this command
  77                         string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
  78                                                                         "name", "group", "alignreport","processors","outputdir","inputdir"};
  79                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  80
  81                         OptionParser parser(option);
  82                         map<string,string> parameters = parser.getParameters();
  83
  84                         ValidParameters validParameter("screen.seqs");
  85                         map<string,string>::iterator it;
  86
  87                         //check to make sure all parameters are valid for command
  88                         for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["fasta"] = tempOutNames;
  95                         outputTypes["name"] = tempOutNames;
  96                         outputTypes["group"] = tempOutNames;
  97                         outputTypes["alignreport"] = tempOutNames;
  98                         outputTypes["accnos"] = tempOutNames;
  99
 100                         //if the user changes the input directory command factory will send this info to us in the output parameter
 101                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 102                         if (inputDir == "not found"){   inputDir = "";          }
 103                         else {
 104                                 string path;
 105                                 it = parameters.find("fasta");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 111                                 }
 112
 113                                 it = parameters.find("group");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 119                                 }
 120
 121                                 it = parameters.find("name");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 127                                 }
 128
 129                                 it = parameters.find("alignreport");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 135                                 }
 136                         }
 137
 138                         //check for required parameters
 139                         fastafile = validParameter.validFile(parameters, "fasta", true);
 140                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
 141                         else if (fastafile == "not open") { abort = true; }
 142
 143                         groupfile = validParameter.validFile(parameters, "group", true);
 144                         if (groupfile == "not open") { abort = true; }
 145                         else if (groupfile == "not found") { groupfile = ""; }
 146
 147                         namefile = validParameter.validFile(parameters, "name", true);
 148                         if (namefile == "not open") { abort = true; }
 149                         else if (namefile == "not found") { namefile = ""; }
 150
 151                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 152                         if (alignreport == "not open") { abort = true; }
 153                         else if (alignreport == "not found") { alignreport = ""; }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 157                                 outputDir = "";
 158                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 159                         }
 160
 161                         //check for optional parameter and set defaults
 162                         // ...at some point should added some additional type checking...
 163                         string temp;
 164                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 165                         convert(temp, startPos);
 166
 167                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 168                         convert(temp, endPos);
 169
 170                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 171                         convert(temp, maxAmbig);
 172
 173                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 174                         convert(temp, maxHomoP);
 175
 176                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 177                         convert(temp, minLength);
 178
 179                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 180                         convert(temp, maxLength);
 181
 182                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 183                         convert(temp, processors);
 184
 185                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 186                         if (temp == "not found"){       temp = "";              }
 187                         else {  m->splitAtDash(temp, optimize);         }
 188
 189                         //check for invalid optimize options
 190                         set<string> validOptimizers;
 191                         validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 192
 193                         for (int i = 0; i < optimize.size(); i++) {
 194                                 if (validOptimizers.count(optimize[i]) == 0) {
 195                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 196                                         optimize.erase(optimize.begin()+i);
 197                                         i--;
 198                                 }
 199                         }
 200
 201                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 202                         convert(temp, criteria);
 203                 }
 204
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 208                 exit(1);
 209         }
 210 }
 211 //**********************************************************************************************************************
 212
 213 void ScreenSeqsCommand::help(){
 214         try {
 215                 m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
 216                 m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n");
 217                 m->mothurOut("The fasta parameter is required.\n");
 218                 m->mothurOut("The start parameter .... The default is -1.\n");
 219                 m->mothurOut("The end parameter .... The default is -1.\n");
 220                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 221                 m->mothurOut("The maxhomop parameter .... The default is -1.\n");
 222                 m->mothurOut("The minlength parameter .... The default is -1.\n");
 223                 m->mothurOut("The maxlength parameter .... The default is -1.\n");
 224                 m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
 225                 m->mothurOut("The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n");
 226                 m->mothurOut("For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n");
 227                 m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
 228                 m->mothurOut("The screen.seqs command should be in the following format: \n");
 229                 m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n");
 230                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 231                 m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 232                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 233
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "ScreenSeqsCommand", "help");
 237                 exit(1);
 238         }
 239 }
 240
 241 //***************************************************************************************************************
 242
 243 ScreenSeqsCommand::~ScreenSeqsCommand(){        /*      do nothing      */      }
 244
 245 //***************************************************************************************************************
 246
 247 int ScreenSeqsCommand::execute(){
 248         try{
 249
 250                 if (abort == true) { return 0; }
 251
 252                 //if the user want to optimize we need to no the 90% mark
 253                 vector<unsigned long int> positions;
 254                 if (optimize.size() != 0) {  getSummary(positions); } //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
 255                 else {
 256                         positions = m->divideFile(fastafile, processors);
 257                         for (int i = 0; i < (positions.size()-1); i++) {
 258                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 259                         }
 260                 }
 261
 262                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 263                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 264
 265                 int numFastaSeqs = 0;
 266                 set<string> badSeqNames;
 267                 int start = time(NULL);
 268
 269 #ifdef USE_MPI
 270                         int pid, numSeqsPerProcessor;
 271                         int tag = 2001;
 272                         vector<unsigned long int> MPIPos;
 273
 274                         MPI_Status status;
 275                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 276                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 277
 278                         MPI_File inMPI;
 279                         MPI_File outMPIGood;
 280                         MPI_File outMPIBadAccnos;
 281
 282                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 283                         int inMode=MPI_MODE_RDONLY;
 284
 285                         char outGoodFilename[1024];
 286                         strcpy(outGoodFilename, goodSeqFile.c_str());
 287
 288                         char outBadAccnosFilename[1024];
 289                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 290
 291                         char inFileName[1024];
 292                         strcpy(inFileName, fastafile.c_str());
 293
 294                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 295                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 296                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 297
 298                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 299
 300                         if (pid == 0) { //you are the root process
 301
 302                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 303
 304                                 //send file positions to all processes
 305                                 for(int i = 1; i < processors; i++) {
 306                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 307                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 308                                 }
 309
 310                                 //figure out how many sequences you have to align
 311                                 numSeqsPerProcessor = numFastaSeqs / processors;
 312                                 int startIndex =  pid * numSeqsPerProcessor;
 313                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 314                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 315                                 //align your part
 316                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 317                 //cout << pid << " done" << endl;
 318                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 319
 320                                 for (int i = 1; i < processors; i++) {
 321
 322                                         //get bad lists
 323                                         int badSize;
 324                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 325                                         /*for (int j = 0; j < badSize; j++) {
 326                                                 int length;
 327                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 328                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 329                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 330
 331                                                 string tempBuf = buf2;
 332                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 333                                                 delete buf2;
 334
 335                                                 badSeqNames.insert(tempBuf);
 336                                         }*/
 337                                 }
 338                         }else{ //you are a child process
 339                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 340                                 MPIPos.resize(numFastaSeqs+1);
 341                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 342
 343                                 //figure out how many sequences you have to align
 344                                 numSeqsPerProcessor = numFastaSeqs / processors;
 345                                 int startIndex =  pid * numSeqsPerProcessor;
 346                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 347                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 348                                 //align your part
 349                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 350 //cout << pid << " done" << endl;
 351                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 352
 353                                 //send bad list
 354                                 int badSize = badSeqNames.size();
 355                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 356
 357                                 /*
 358                                 set<string>::iterator it;
 359                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 360                                         string name = *it;
 361                                         int length = name.length();
 362                                         char* buf2 = new char[length];
 363                                         memcpy(buf2, name.c_str(), length);
 364
 365                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 366                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 367                                 }*/
 368                         }
 369
 370                         //close files
 371                         MPI_File_close(&inMPI);
 372                         MPI_File_close(&outMPIGood);
 373                         MPI_File_close(&outMPIBadAccnos);
 374                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 375
 376 #else
 377
 378         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 379                         if(processors == 1){
 380                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 381
 382                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 383
 384                         }else{
 385                                 processIDS.resize(0);
 386
 387                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 388
 389                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 390                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 391
 392                                 //append alignment and report files
 393                                 for(int i=1;i<processors;i++){
 394                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 395                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 396
 397                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 398                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 399                                 }
 400
 401                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 402
 403                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 404                                 ifstream inBad;
 405                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 406
 407                                 if (ableToOpen == 0) {
 408                                         badSeqNames.clear();
 409                                         string tempName;
 410                                         while (!inBad.eof()) {
 411                                                 inBad >> tempName; m->gobble(inBad);
 412                                                 badSeqNames.insert(tempName);
 413                                         }
 414                                         inBad.close();
 415                                 }
 416                         }
 417         #else
 418                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 419
 420                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 421
 422         #endif
 423
 424 #endif
 425
 426                 #ifdef USE_MPI
 427                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 428
 429                         if (pid == 0) { //only one process should fix files
 430
 431                                 //read accnos file with all names in it, process 0 just has its names
 432                                 MPI_File inMPIAccnos;
 433                                 MPI_Offset size;
 434
 435                                 char inFileName[1024];
 436                                 strcpy(inFileName, badAccnosFile.c_str());
 437
 438                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 439                                 MPI_File_get_size(inMPIAccnos, &size);
 440
 441                                 char* buffer = new char[size];
 442                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 443
 444                                 string tempBuf = buffer;
 445                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 446                                 istringstream iss (tempBuf,istringstream::in);
 447
 448                                 delete buffer;
 449                                 MPI_File_close(&inMPIAccnos);
 450
 451                                 badSeqNames.clear();
 452                                 string tempName;
 453                                 while (!iss.eof()) {
 454                                         iss >> tempName; m->gobble(iss);
 455                                         badSeqNames.insert(tempName);
 456                                 }
 457                 #endif
 458
 459                 if(namefile != "" && groupfile != "")   {
 460                         screenNameGroupFile(badSeqNames);
 461                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 462                 }else if(namefile != "")        {
 463                         screenNameGroupFile(badSeqNames);
 464                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 465                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 466
 467                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 468
 469                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 470
 471                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 472
 473                 #ifdef USE_MPI
 474                         }
 475                 #endif
 476
 477                 m->mothurOutEndLine();
 478                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 479                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 480                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 481                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 482                 m->mothurOutEndLine();
 483                 m->mothurOutEndLine();
 484
 485                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 486                 m->mothurOutEndLine();
 487
 488                 return 0;
 489         }
 490         catch(exception& e) {
 491                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 492                 exit(1);
 493         }
 494 }
 495
 496 //***************************************************************************************************************
 497
 498 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 499         try {
 500                 ifstream inputNames;
 501                 m->openInputFile(namefile, inputNames);
 502                 set<string> badSeqGroups;
 503                 string seqName, seqList, group;
 504                 set<string>::iterator it;
 505
 506                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 507                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 508
 509                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 510
 511                 while(!inputNames.eof()){
 512                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 513
 514                         inputNames >> seqName >> seqList;
 515                         it = badSeqNames.find(seqName);
 516
 517                         if(it != badSeqNames.end()){
 518                                 badSeqNames.erase(it);
 519
 520                                 if(namefile != ""){
 521                                         int start = 0;
 522                                         for(int i=0;i<seqList.length();i++){
 523                                                 if(seqList[i] == ','){
 524                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 525                                                         start = i+1;
 526                                                 }
 527                                         }
 528                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 529                                 }
 530                         }
 531                         else{
 532                                 goodNameOut << seqName << '\t' << seqList << endl;
 533                         }
 534                         m->gobble(inputNames);
 535                 }
 536                 inputNames.close();
 537                 goodNameOut.close();
 538
 539                 //we were unable to remove some of the bad sequences
 540                 if (badSeqNames.size() != 0) {
 541                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 542                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 543                                 m->mothurOutEndLine();
 544                         }
 545                 }
 546
 547                 if(groupfile != ""){
 548
 549                         ifstream inputGroups;
 550                         m->openInputFile(groupfile, inputGroups);
 551
 552                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 553                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 554
 555                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 556
 557                         while(!inputGroups.eof()){
 558                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 559
 560                                 inputGroups >> seqName >> group;
 561
 562                                 it = badSeqGroups.find(seqName);
 563
 564                                 if(it != badSeqGroups.end()){
 565                                         badSeqGroups.erase(it);
 566                                 }
 567                                 else{
 568                                         goodGroupOut << seqName << '\t' << group << endl;
 569                                 }
 570                                 m->gobble(inputGroups);
 571                         }
 572                         inputGroups.close();
 573                         goodGroupOut.close();
 574
 575                         //we were unable to remove some of the bad sequences
 576                         if (badSeqGroups.size() != 0) {
 577                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 578                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 579                                         m->mothurOutEndLine();
 580                                 }
 581                         }
 582                 }
 583
 584
 585                 return 0;
 586
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 590                 exit(1);
 591         }
 592 }
 593 //***************************************************************************************************************
 594 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 595         try {
 596
 597                 vector<int> startPosition;
 598                 vector<int> endPosition;
 599                 vector<int> seqLength;
 600                 vector<int> ambigBases;
 601                 vector<int> longHomoPolymer;
 602
 603                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 604
 605                 for (int i = 0; i < (positions.size()-1); i++) {
 606                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 607                 }
 608
 609                 int numSeqs = 0;
 610                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 611                         if(processors == 1){
 612                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 613                         }else{
 614                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 615                         }
 616
 617                         if (m->control_pressed) {  return 0; }
 618                 #else
 619                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 620                         if (m->control_pressed) {  return 0; }
 621                 #endif
 622
 623                 sort(startPosition.begin(), startPosition.end());
 624                 sort(endPosition.begin(), endPosition.end());
 625                 sort(seqLength.begin(), seqLength.end());
 626                 sort(ambigBases.begin(), ambigBases.end());
 627                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 628
 629                 int criteriaPercentile  = int(numSeqs * (criteria / (float) 100));
 630
 631                 for (int i = 0; i < optimize.size(); i++) {
 632                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 633                         else if (optimize[i] == "end") { int endcriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
 634                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 635                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 636                         else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
 637                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 638                 }
 639
 640                 return 0;
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 644                 exit(1);
 645         }
 646 }
 647 /**************************************************************************************/
 648 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 649         try {
 650
 651                 ifstream in;
 652                 m->openInputFile(filename, in);
 653
 654                 in.seekg(filePos->start);
 655
 656                 bool done = false;
 657                 int count = 0;
 658
 659                 while (!done) {
 660
 661                         if (m->control_pressed) { in.close(); return 1; }
 662
 663                         Sequence current(in); m->gobble(in);
 664
 665                         if (current.getName() != "") {
 666                                 startPosition.push_back(current.getStartPos());
 667                                 endPosition.push_back(current.getEndPos());
 668                                 seqLength.push_back(current.getNumBases());
 669                                 ambigBases.push_back(current.getAmbigBases());
 670                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 671                                 count++;
 672                         }
 673
 674                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 675                                 unsigned long int pos = in.tellg();
 676                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 677                         #else
 678                                 if (in.eof()) { break; }
 679                         #endif
 680
 681                 }
 682
 683                 in.close();
 684
 685                 return count;
 686         }
 687         catch(exception& e) {
 688                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 689                 exit(1);
 690         }
 691 }
 692 /**************************************************************************************************/
 693 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 694         try {
 695 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 696                 int process = 1;
 697                 int num = 0;
 698                 processIDS.clear();
 699
 700                 //loop through and create all the processes you want
 701                 while (process != processors) {
 702                         int pid = fork();
 703
 704                         if (pid > 0) {
 705                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 706                                 process++;
 707                         }else if (pid == 0){
 708                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 709
 710                                 //pass numSeqs to parent
 711                                 ofstream out;
 712                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 713                                 m->openOutputFile(tempFile, out);
 714
 715                                 out << num << endl;
 716                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 717                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 718                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 719                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 720                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 721
 722                                 out.close();
 723
 724                                 exit(0);
 725                         }else {
 726                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 727                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 728                                 exit(0);
 729                         }
 730                 }
 731
 732                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 733
 734                 //force parent to wait until all the processes are done
 735                 for (int i=0;i<processIDS.size();i++) {
 736                         int temp = processIDS[i];
 737                         wait(&temp);
 738                 }
 739
 740                 //parent reads in and combine Filter info
 741                 for (int i = 0; i < processIDS.size(); i++) {
 742                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 743                         ifstream in;
 744                         m->openInputFile(tempFilename, in);
 745
 746                         int temp, tempNum;
 747                         in >> tempNum; m->gobble(in); num += tempNum;
 748                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 749                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 750                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 751                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 752                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 753
 754                         in.close();
 755                         remove(tempFilename.c_str());
 756                 }
 757
 758                 return num;
 759 #endif
 760         }
 761         catch(exception& e) {
 762                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 763                 exit(1);
 764         }
 765 }
 766
 767 //***************************************************************************************************************
 768
 769 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 770         try {
 771                 ifstream inputGroups;
 772                 m->openInputFile(groupfile, inputGroups);
 773                 string seqName, group;
 774                 set<string>::iterator it;
 775
 776                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 777                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 778                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 779
 780                 while(!inputGroups.eof()){
 781                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 782
 783                         inputGroups >> seqName >> group;
 784                         it = badSeqNames.find(seqName);
 785
 786                         if(it != badSeqNames.end()){
 787                                 badSeqNames.erase(it);
 788                         }
 789                         else{
 790                                 goodGroupOut << seqName << '\t' << group << endl;
 791                         }
 792                         m->gobble(inputGroups);
 793                 }
 794
 795                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 796
 797                 //we were unable to remove some of the bad sequences
 798                 if (badSeqNames.size() != 0) {
 799                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 800                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 801                                 m->mothurOutEndLine();
 802                         }
 803                 }
 804
 805                 inputGroups.close();
 806                 goodGroupOut.close();
 807
 808                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 809
 810                 return 0;
 811
 812         }
 813         catch(exception& e) {
 814                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 815                 exit(1);
 816         }
 817 }
 818
 819 //***************************************************************************************************************
 820
 821 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 822         try {
 823                 ifstream inputAlignReport;
 824                 m->openInputFile(alignreport, inputAlignReport);
 825                 string seqName, group;
 826                 set<string>::iterator it;
 827
 828                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 829                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 830                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 831
 832                 while (!inputAlignReport.eof()) {               //      need to copy header
 833                         char c = inputAlignReport.get();
 834                         goodAlignReportOut << c;
 835                         if (c == 10 || c == 13){        break;  }
 836                 }
 837
 838                 while(!inputAlignReport.eof()){
 839                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 840
 841                         inputAlignReport >> seqName;
 842                         it = badSeqNames.find(seqName);
 843                         string line;
 844                         while (!inputAlignReport.eof()) {               //      need to copy header
 845                                 char c = inputAlignReport.get();
 846                                 line += c;
 847                                 if (c == 10 || c == 13){        break;  }
 848                         }
 849
 850                         if(it != badSeqNames.end()){
 851                                 badSeqNames.erase(it);
 852                         }
 853                         else{
 854                                 goodAlignReportOut << seqName << '\t' << line;
 855                         }
 856                         m->gobble(inputAlignReport);
 857                 }
 858
 859                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 860
 861                 //we were unable to remove some of the bad sequences
 862                 if (badSeqNames.size() != 0) {
 863                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 864                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 865                                 m->mothurOutEndLine();
 866                         }
 867                 }
 868
 869                 inputAlignReport.close();
 870                 goodAlignReportOut.close();
 871
 872                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 873
 874                 return 0;
 875
 876         }
 877         catch(exception& e) {
 878                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 879                 exit(1);
 880         }
 881
 882 }
 883 //**********************************************************************************************************************
 884
 885 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 886         try {
 887                 ofstream goodFile;
 888                 m->openOutputFile(goodFName, goodFile);
 889
 890                 ofstream badAccnosFile;
 891                 m->openOutputFile(badAccnosFName, badAccnosFile);
 892
 893                 ifstream inFASTA;
 894                 m->openInputFile(filename, inFASTA);
 895
 896                 inFASTA.seekg(filePos->start);
 897
 898                 bool done = false;
 899                 int count = 0;
 900
 901                 while (!done) {
 902
 903                         if (m->control_pressed) {  return 0; }
 904
 905                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 906                         if (currSeq.getName() != "") {
 907                                 bool goodSeq = 1;               //      innocent until proven guilty
 908                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 909                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 910                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 911                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 912                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 913                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 914
 915                                 if(goodSeq == 1){
 916                                         currSeq.printSequence(goodFile);
 917                                 }
 918                                 else{
 919                                         badAccnosFile << currSeq.getName() << endl;
 920                                         badSeqNames.insert(currSeq.getName());
 921                                 }
 922                         count++;
 923                         }
 924
 925                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 926                                 unsigned long int pos = inFASTA.tellg();
 927                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 928                         #else
 929                                 if (inFASTA.eof()) { break; }
 930                         #endif
 931
 932                         //report progress
 933                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 934                 }
 935                 //report progress
 936                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 937
 938
 939                 goodFile.close();
 940                 inFASTA.close();
 941                 badAccnosFile.close();
 942
 943                 return count;
 944         }
 945         catch(exception& e) {
 946                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 947                 exit(1);
 948         }
 949 }
 950 //**********************************************************************************************************************
 951 #ifdef USE_MPI
 952 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
 953         try {
 954                 string outputString = "";
 955                 MPI_Status statusGood;
 956                 MPI_Status statusBadAccnos;
 957                 MPI_Status status;
 958                 int pid;
 959                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 960
 961                 for(int i=0;i<num;i++){
 962
 963                         if (m->control_pressed) {  return 0; }
 964
 965                         //read next sequence
 966                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 967
 968                         char* buf4 = new char[length];
 969                         memcpy(buf4, outputString.c_str(), length);
 970
 971                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 972
 973                         string tempBuf = buf4;  delete buf4;
 974                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 975                         istringstream iss (tempBuf,istringstream::in);
 976
 977                         Sequence currSeq(iss);
 978
 979                         //process seq
 980                         if (currSeq.getName() != "") {
 981                                 bool goodSeq = 1;               //      innocent until proven guilty
 982                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 983                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 984                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 985                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 986                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 987                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 988
 989                                 if(goodSeq == 1){
 990                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 991
 992                                         //print good seq
 993                                         length = outputString.length();
 994                                         char* buf2 = new char[length];
 995                                         memcpy(buf2, outputString.c_str(), length);
 996
 997                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
 998                                         delete buf2;
 999                                 }
1000                                 else{
1001
1002                                         badSeqNames.insert(currSeq.getName());
1003
1004                                         //write to bad accnos file
1005                                         outputString = currSeq.getName() + "\n";
1006
1007                                         length = outputString.length();
1008                                         char* buf3 = new char[length];
1009                                         memcpy(buf3, outputString.c_str(), length);
1010
1011                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1012                                         delete buf3;
1013                                 }
1014                         }
1015
1016                         //report progress
1017                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1018                 }
1019
1020                 return 1;
1021         }
1022         catch(exception& e) {
1023                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1024                 exit(1);
1025         }
1026 }
1027 #endif
1028 /**************************************************************************************************/
1029
1030 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1031         try {
1032 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1033                 int process = 0;
1034                 int num = 0;
1035
1036                 //loop through and create all the processes you want
1037                 while (process != processors) {
1038                         int pid = fork();
1039
1040                         if (pid > 0) {
1041                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1042                                 process++;
1043                         }else if (pid == 0){
1044                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1045
1046                                 //pass numSeqs to parent
1047                                 ofstream out;
1048                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1049                                 m->openOutputFile(tempFile, out);
1050                                 out << num << endl;
1051                                 out.close();
1052
1053                                 exit(0);
1054                         }else {
1055                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1056                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1057                                 exit(0);
1058                         }
1059                 }
1060
1061                 //force parent to wait until all the processes are done
1062                 for (int i=0;i<processors;i++) {
1063                         int temp = processIDS[i];
1064                         wait(&temp);
1065                 }
1066
1067                 for (int i = 0; i < processIDS.size(); i++) {
1068                         ifstream in;
1069                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1070                         m->openInputFile(tempFile, in);
1071                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1072                         in.close(); remove(tempFile.c_str());
1073                 }
1074
1075                 return num;
1076 #endif
1077         }
1078         catch(exception& e) {
1079                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1080                 exit(1);
1081         }
1082 }
1083
1084 //***************************************************************************************************************
1085
1086