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") { namefile = ""; 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 know the 90% mark
 252                 vector<unsigned long int> positions;
 253                 if (optimize.size() != 0) {  //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
 254                         //use the namefile to optimize correctly
 255                         if (namefile != "") { nameMap = m->readNames(namefile); }
 256                         getSummary(positions);
 257                 }
 258                 else {
 259                         positions = m->divideFile(fastafile, processors);
 260                         for (int i = 0; i < (positions.size()-1); i++) {
 261                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 262                         }
 263                 }
 264
 265                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 266                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 267
 268                 int numFastaSeqs = 0;
 269                 set<string> badSeqNames;
 270                 int start = time(NULL);
 271
 272 #ifdef USE_MPI
 273                         int pid, numSeqsPerProcessor;
 274                         int tag = 2001;
 275                         vector<unsigned long int> MPIPos;
 276
 277                         MPI_Status status;
 278                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 279                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 280
 281                         MPI_File inMPI;
 282                         MPI_File outMPIGood;
 283                         MPI_File outMPIBadAccnos;
 284
 285                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 286                         int inMode=MPI_MODE_RDONLY;
 287
 288                         char outGoodFilename[1024];
 289                         strcpy(outGoodFilename, goodSeqFile.c_str());
 290
 291                         char outBadAccnosFilename[1024];
 292                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 293
 294                         char inFileName[1024];
 295                         strcpy(inFileName, fastafile.c_str());
 296
 297                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 298                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 299                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 300
 301                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 302
 303                         if (pid == 0) { //you are the root process
 304
 305                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 306
 307                                 //send file positions to all processes
 308                                 for(int i = 1; i < processors; i++) {
 309                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 310                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 311                                 }
 312
 313                                 //figure out how many sequences you have to align
 314                                 numSeqsPerProcessor = numFastaSeqs / processors;
 315                                 int startIndex =  pid * numSeqsPerProcessor;
 316                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 317                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 318                                 //align your part
 319                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 320                 //cout << pid << " done" << endl;
 321                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 322
 323                                 for (int i = 1; i < processors; i++) {
 324
 325                                         //get bad lists
 326                                         int badSize;
 327                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 328                                         /*for (int j = 0; j < badSize; j++) {
 329                                                 int length;
 330                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 331                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 332                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 333
 334                                                 string tempBuf = buf2;
 335                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 336                                                 delete buf2;
 337
 338                                                 badSeqNames.insert(tempBuf);
 339                                         }*/
 340                                 }
 341                         }else{ //you are a child process
 342                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 343                                 MPIPos.resize(numFastaSeqs+1);
 344                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 345
 346                                 //figure out how many sequences you have to align
 347                                 numSeqsPerProcessor = numFastaSeqs / processors;
 348                                 int startIndex =  pid * numSeqsPerProcessor;
 349                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 350                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 351                                 //align your part
 352                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 353 //cout << pid << " done" << endl;
 354                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 355
 356                                 //send bad list
 357                                 int badSize = badSeqNames.size();
 358                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 359
 360                                 /*
 361                                 set<string>::iterator it;
 362                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 363                                         string name = *it;
 364                                         int length = name.length();
 365                                         char* buf2 = new char[length];
 366                                         memcpy(buf2, name.c_str(), length);
 367
 368                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 369                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 370                                 }*/
 371                         }
 372
 373                         //close files
 374                         MPI_File_close(&inMPI);
 375                         MPI_File_close(&outMPIGood);
 376                         MPI_File_close(&outMPIBadAccnos);
 377                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 378
 379 #else
 380
 381         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 382                         if(processors == 1){
 383                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 384
 385                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 386
 387                         }else{
 388                                 processIDS.resize(0);
 389
 390                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 391
 392                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 393                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 394
 395                                 //append alignment and report files
 396                                 for(int i=1;i<processors;i++){
 397                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 398                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 399
 400                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 401                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 402                                 }
 403
 404                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 405
 406                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 407                                 ifstream inBad;
 408                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 409
 410                                 if (ableToOpen == 0) {
 411                                         badSeqNames.clear();
 412                                         string tempName;
 413                                         while (!inBad.eof()) {
 414                                                 inBad >> tempName; m->gobble(inBad);
 415                                                 badSeqNames.insert(tempName);
 416                                         }
 417                                         inBad.close();
 418                                 }
 419                         }
 420         #else
 421                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 422
 423                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 424
 425         #endif
 426
 427 #endif
 428
 429                 #ifdef USE_MPI
 430                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 431
 432                         if (pid == 0) { //only one process should fix files
 433
 434                                 //read accnos file with all names in it, process 0 just has its names
 435                                 MPI_File inMPIAccnos;
 436                                 MPI_Offset size;
 437
 438                                 char inFileName[1024];
 439                                 strcpy(inFileName, badAccnosFile.c_str());
 440
 441                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 442                                 MPI_File_get_size(inMPIAccnos, &size);
 443
 444                                 char* buffer = new char[size];
 445                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 446
 447                                 string tempBuf = buffer;
 448                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 449                                 istringstream iss (tempBuf,istringstream::in);
 450
 451                                 delete buffer;
 452                                 MPI_File_close(&inMPIAccnos);
 453
 454                                 badSeqNames.clear();
 455                                 string tempName;
 456                                 while (!iss.eof()) {
 457                                         iss >> tempName; m->gobble(iss);
 458                                         badSeqNames.insert(tempName);
 459                                 }
 460                 #endif
 461
 462                 if(namefile != "" && groupfile != "")   {
 463                         screenNameGroupFile(badSeqNames);
 464                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 465                 }else if(namefile != "")        {
 466                         screenNameGroupFile(badSeqNames);
 467                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 468                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 469
 470                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 471
 472                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 473
 474                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 475
 476                 #ifdef USE_MPI
 477                         }
 478                 #endif
 479
 480                 m->mothurOutEndLine();
 481                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 482                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 483                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 484                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 485                 m->mothurOutEndLine();
 486                 m->mothurOutEndLine();
 487
 488                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 489                 m->mothurOutEndLine();
 490
 491                 return 0;
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 495                 exit(1);
 496         }
 497 }
 498
 499 //***************************************************************************************************************
 500
 501 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 502         try {
 503                 ifstream inputNames;
 504                 m->openInputFile(namefile, inputNames);
 505                 set<string> badSeqGroups;
 506                 string seqName, seqList, group;
 507                 set<string>::iterator it;
 508
 509                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 510                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 511
 512                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 513
 514                 while(!inputNames.eof()){
 515                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 516
 517                         inputNames >> seqName >> seqList;
 518                         it = badSeqNames.find(seqName);
 519
 520                         if(it != badSeqNames.end()){
 521                                 badSeqNames.erase(it);
 522
 523                                 if(namefile != ""){
 524                                         int start = 0;
 525                                         for(int i=0;i<seqList.length();i++){
 526                                                 if(seqList[i] == ','){
 527                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 528                                                         start = i+1;
 529                                                 }
 530                                         }
 531                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 532                                 }
 533                         }
 534                         else{
 535                                 goodNameOut << seqName << '\t' << seqList << endl;
 536                         }
 537                         m->gobble(inputNames);
 538                 }
 539                 inputNames.close();
 540                 goodNameOut.close();
 541
 542                 //we were unable to remove some of the bad sequences
 543                 if (badSeqNames.size() != 0) {
 544                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 545                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 546                                 m->mothurOutEndLine();
 547                         }
 548                 }
 549
 550                 if(groupfile != ""){
 551
 552                         ifstream inputGroups;
 553                         m->openInputFile(groupfile, inputGroups);
 554
 555                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 556                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 557
 558                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 559
 560                         while(!inputGroups.eof()){
 561                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 562
 563                                 inputGroups >> seqName >> group;
 564
 565                                 it = badSeqGroups.find(seqName);
 566
 567                                 if(it != badSeqGroups.end()){
 568                                         badSeqGroups.erase(it);
 569                                 }
 570                                 else{
 571                                         goodGroupOut << seqName << '\t' << group << endl;
 572                                 }
 573                                 m->gobble(inputGroups);
 574                         }
 575                         inputGroups.close();
 576                         goodGroupOut.close();
 577
 578                         //we were unable to remove some of the bad sequences
 579                         if (badSeqGroups.size() != 0) {
 580                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 581                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 582                                         m->mothurOutEndLine();
 583                                 }
 584                         }
 585                 }
 586
 587
 588                 return 0;
 589
 590         }
 591         catch(exception& e) {
 592                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 593                 exit(1);
 594         }
 595 }
 596 //***************************************************************************************************************
 597 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 598         try {
 599
 600                 vector<int> startPosition;
 601                 vector<int> endPosition;
 602                 vector<int> seqLength;
 603                 vector<int> ambigBases;
 604                 vector<int> longHomoPolymer;
 605
 606                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 607
 608                 for (int i = 0; i < (positions.size()-1); i++) {
 609                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 610                 }
 611
 612                 int numSeqs = 0;
 613                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 614                         if(processors == 1){
 615                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 616                         }else{
 617                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 618                         }
 619
 620                         if (m->control_pressed) {  return 0; }
 621                 #else
 622                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 623                         if (m->control_pressed) {  return 0; }
 624                 #endif
 625
 626                 sort(startPosition.begin(), startPosition.end());
 627                 sort(endPosition.begin(), endPosition.end());
 628                 sort(seqLength.begin(), seqLength.end());
 629                 sort(ambigBases.begin(), ambigBases.end());
 630                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 631
 632                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 633                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 634
 635                 for (int i = 0; i < optimize.size(); i++) {
 636                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 637                         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();}
 638                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 639                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 640                         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(); }
 641                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 642                 }
 643
 644                 return 0;
 645         }
 646         catch(exception& e) {
 647                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 648                 exit(1);
 649         }
 650 }
 651 /**************************************************************************************/
 652 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 653         try {
 654
 655                 ifstream in;
 656                 m->openInputFile(filename, in);
 657
 658                 in.seekg(filePos->start);
 659
 660                 bool done = false;
 661                 int count = 0;
 662
 663                 while (!done) {
 664
 665                         if (m->control_pressed) { in.close(); return 1; }
 666
 667                         Sequence current(in); m->gobble(in);
 668
 669                         if (current.getName() != "") {
 670                                 int num = 1;
 671                                 if (namefile != "") {
 672                                         //make sure this sequence is in the namefile, else error
 673                                         map<string, int>::iterator it = nameMap.find(current.getName());
 674
 675                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 676                                         else { num = it->second; }
 677                                 }
 678
 679                                 //for each sequence this sequence represents
 680                                 for (int i = 0; i < num; i++) {
 681                                         startPosition.push_back(current.getStartPos());
 682                                         endPosition.push_back(current.getEndPos());
 683                                         seqLength.push_back(current.getNumBases());
 684                                         ambigBases.push_back(current.getAmbigBases());
 685                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 686                                 }
 687
 688                                 count++;
 689                         }
 690
 691                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 692                                 unsigned long int pos = in.tellg();
 693                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 694                         #else
 695                                 if (in.eof()) { break; }
 696                         #endif
 697
 698                 }
 699
 700                 in.close();
 701
 702                 return count;
 703         }
 704         catch(exception& e) {
 705                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 706                 exit(1);
 707         }
 708 }
 709 /**************************************************************************************************/
 710 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 711         try {
 712 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 713                 int process = 1;
 714                 int num = 0;
 715                 processIDS.clear();
 716
 717                 //loop through and create all the processes you want
 718                 while (process != processors) {
 719                         int pid = fork();
 720
 721                         if (pid > 0) {
 722                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 723                                 process++;
 724                         }else if (pid == 0){
 725                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 726
 727                                 //pass numSeqs to parent
 728                                 ofstream out;
 729                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 730                                 m->openOutputFile(tempFile, out);
 731
 732                                 out << num << endl;
 733                                 out << startPosition.size() << endl;
 734                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 735                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 736                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 737                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 738                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 739
 740                                 out.close();
 741
 742                                 exit(0);
 743                         }else {
 744                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 745                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 746                                 exit(0);
 747                         }
 748                 }
 749
 750                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 751
 752                 //force parent to wait until all the processes are done
 753                 for (int i=0;i<processIDS.size();i++) {
 754                         int temp = processIDS[i];
 755                         wait(&temp);
 756                 }
 757
 758                 //parent reads in and combine Filter info
 759                 for (int i = 0; i < processIDS.size(); i++) {
 760                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 761                         ifstream in;
 762                         m->openInputFile(tempFilename, in);
 763
 764                         int temp, tempNum;
 765                         in >> tempNum; m->gobble(in); num += tempNum;
 766                         in >> tempNum; m->gobble(in);
 767                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 768                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 769                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 770                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 771                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 772
 773                         in.close();
 774                         remove(tempFilename.c_str());
 775                 }
 776
 777                 return num;
 778 #endif
 779         }
 780         catch(exception& e) {
 781                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 782                 exit(1);
 783         }
 784 }
 785
 786 //***************************************************************************************************************
 787
 788 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 789         try {
 790                 ifstream inputGroups;
 791                 m->openInputFile(groupfile, inputGroups);
 792                 string seqName, group;
 793                 set<string>::iterator it;
 794
 795                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 796                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 797                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 798
 799                 while(!inputGroups.eof()){
 800                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 801
 802                         inputGroups >> seqName >> group;
 803                         it = badSeqNames.find(seqName);
 804
 805                         if(it != badSeqNames.end()){
 806                                 badSeqNames.erase(it);
 807                         }
 808                         else{
 809                                 goodGroupOut << seqName << '\t' << group << endl;
 810                         }
 811                         m->gobble(inputGroups);
 812                 }
 813
 814                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 815
 816                 //we were unable to remove some of the bad sequences
 817                 if (badSeqNames.size() != 0) {
 818                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 819                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 820                                 m->mothurOutEndLine();
 821                         }
 822                 }
 823
 824                 inputGroups.close();
 825                 goodGroupOut.close();
 826
 827                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 828
 829                 return 0;
 830
 831         }
 832         catch(exception& e) {
 833                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 834                 exit(1);
 835         }
 836 }
 837
 838 //***************************************************************************************************************
 839
 840 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 841         try {
 842                 ifstream inputAlignReport;
 843                 m->openInputFile(alignreport, inputAlignReport);
 844                 string seqName, group;
 845                 set<string>::iterator it;
 846
 847                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 848                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 849                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 850
 851                 while (!inputAlignReport.eof()) {               //      need to copy header
 852                         char c = inputAlignReport.get();
 853                         goodAlignReportOut << c;
 854                         if (c == 10 || c == 13){        break;  }
 855                 }
 856
 857                 while(!inputAlignReport.eof()){
 858                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 859
 860                         inputAlignReport >> seqName;
 861                         it = badSeqNames.find(seqName);
 862                         string line;
 863                         while (!inputAlignReport.eof()) {               //      need to copy header
 864                                 char c = inputAlignReport.get();
 865                                 line += c;
 866                                 if (c == 10 || c == 13){        break;  }
 867                         }
 868
 869                         if(it != badSeqNames.end()){
 870                                 badSeqNames.erase(it);
 871                         }
 872                         else{
 873                                 goodAlignReportOut << seqName << '\t' << line;
 874                         }
 875                         m->gobble(inputAlignReport);
 876                 }
 877
 878                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 879
 880                 //we were unable to remove some of the bad sequences
 881                 if (badSeqNames.size() != 0) {
 882                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 883                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 884                                 m->mothurOutEndLine();
 885                         }
 886                 }
 887
 888                 inputAlignReport.close();
 889                 goodAlignReportOut.close();
 890
 891                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 892
 893                 return 0;
 894
 895         }
 896         catch(exception& e) {
 897                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 898                 exit(1);
 899         }
 900
 901 }
 902 //**********************************************************************************************************************
 903
 904 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 905         try {
 906                 ofstream goodFile;
 907                 m->openOutputFile(goodFName, goodFile);
 908
 909                 ofstream badAccnosFile;
 910                 m->openOutputFile(badAccnosFName, badAccnosFile);
 911
 912                 ifstream inFASTA;
 913                 m->openInputFile(filename, inFASTA);
 914
 915                 inFASTA.seekg(filePos->start);
 916
 917                 bool done = false;
 918                 int count = 0;
 919
 920                 while (!done) {
 921
 922                         if (m->control_pressed) {  return 0; }
 923
 924                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 925                         if (currSeq.getName() != "") {
 926                                 bool goodSeq = 1;               //      innocent until proven guilty
 927                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 928                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 929                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 930                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 931                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 932                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 933
 934                                 if(goodSeq == 1){
 935                                         currSeq.printSequence(goodFile);
 936                                 }
 937                                 else{
 938                                         badAccnosFile << currSeq.getName() << endl;
 939                                         badSeqNames.insert(currSeq.getName());
 940                                 }
 941                         count++;
 942                         }
 943
 944                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 945                                 unsigned long int pos = inFASTA.tellg();
 946                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 947                         #else
 948                                 if (inFASTA.eof()) { break; }
 949                         #endif
 950
 951                         //report progress
 952                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 953                 }
 954                 //report progress
 955                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 956
 957
 958                 goodFile.close();
 959                 inFASTA.close();
 960                 badAccnosFile.close();
 961
 962                 return count;
 963         }
 964         catch(exception& e) {
 965                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 966                 exit(1);
 967         }
 968 }
 969 //**********************************************************************************************************************
 970 #ifdef USE_MPI
 971 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
 972         try {
 973                 string outputString = "";
 974                 MPI_Status statusGood;
 975                 MPI_Status statusBadAccnos;
 976                 MPI_Status status;
 977                 int pid;
 978                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 979
 980                 for(int i=0;i<num;i++){
 981
 982                         if (m->control_pressed) {  return 0; }
 983
 984                         //read next sequence
 985                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 986
 987                         char* buf4 = new char[length];
 988                         memcpy(buf4, outputString.c_str(), length);
 989
 990                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 991
 992                         string tempBuf = buf4;  delete buf4;
 993                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 994                         istringstream iss (tempBuf,istringstream::in);
 995
 996                         Sequence currSeq(iss);
 997
 998                         //process seq
 999                         if (currSeq.getName() != "") {
1000                                 bool goodSeq = 1;               //      innocent until proven guilty
1001                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1002                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1003                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1004                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1005                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1006                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1007
1008                                 if(goodSeq == 1){
1009                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1010
1011                                         //print good seq
1012                                         length = outputString.length();
1013                                         char* buf2 = new char[length];
1014                                         memcpy(buf2, outputString.c_str(), length);
1015
1016                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1017                                         delete buf2;
1018                                 }
1019                                 else{
1020
1021                                         badSeqNames.insert(currSeq.getName());
1022
1023                                         //write to bad accnos file
1024                                         outputString = currSeq.getName() + "\n";
1025
1026                                         length = outputString.length();
1027                                         char* buf3 = new char[length];
1028                                         memcpy(buf3, outputString.c_str(), length);
1029
1030                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1031                                         delete buf3;
1032                                 }
1033                         }
1034
1035                         //report progress
1036                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1037                 }
1038
1039                 return 1;
1040         }
1041         catch(exception& e) {
1042                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1043                 exit(1);
1044         }
1045 }
1046 #endif
1047 /**************************************************************************************************/
1048
1049 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1050         try {
1051 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1052                 int process = 0;
1053                 int num = 0;
1054
1055                 //loop through and create all the processes you want
1056                 while (process != processors) {
1057                         int pid = fork();
1058
1059                         if (pid > 0) {
1060                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1061                                 process++;
1062                         }else if (pid == 0){
1063                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1064
1065                                 //pass numSeqs to parent
1066                                 ofstream out;
1067                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1068                                 m->openOutputFile(tempFile, out);
1069                                 out << num << endl;
1070                                 out.close();
1071
1072                                 exit(0);
1073                         }else {
1074                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1075                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1076                                 exit(0);
1077                         }
1078                 }
1079
1080                 //force parent to wait until all the processes are done
1081                 for (int i=0;i<processors;i++) {
1082                         int temp = processIDS[i];
1083                         wait(&temp);
1084                 }
1085
1086                 for (int i = 0; i < processIDS.size(); i++) {
1087                         ifstream in;
1088                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1089                         m->openInputFile(tempFile, in);
1090                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1091                         in.close(); remove(tempFile.c_str());
1092                 }
1093
1094                 return num;
1095 #endif
1096         }
1097         catch(exception& e) {
1098                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1099                 exit(1);
1100         }
1101 }
1102
1103 //***************************************************************************************************************
1104
1105