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