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                 //set fasta file as new current fastafile
 489                 string current = "";
 490                 itTypes = outputTypes.find("fasta");
 491                 if (itTypes != outputTypes.end()) {
 492                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 493                 }
 494
 495                 itTypes = outputTypes.find("name");
 496                 if (itTypes != outputTypes.end()) {
 497                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 498                 }
 499
 500                 itTypes = outputTypes.find("group");
 501                 if (itTypes != outputTypes.end()) {
 502                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 503                 }
 504
 505                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 506                 m->mothurOutEndLine();
 507
 508                 return 0;
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 512                 exit(1);
 513         }
 514 }
 515
 516 //***************************************************************************************************************
 517
 518 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 519         try {
 520                 ifstream inputNames;
 521                 m->openInputFile(namefile, inputNames);
 522                 set<string> badSeqGroups;
 523                 string seqName, seqList, group;
 524                 set<string>::iterator it;
 525
 526                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 527                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 528
 529                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 530
 531                 while(!inputNames.eof()){
 532                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 533
 534                         inputNames >> seqName >> seqList;
 535                         it = badSeqNames.find(seqName);
 536
 537                         if(it != badSeqNames.end()){
 538                                 badSeqNames.erase(it);
 539
 540                                 if(namefile != ""){
 541                                         int start = 0;
 542                                         for(int i=0;i<seqList.length();i++){
 543                                                 if(seqList[i] == ','){
 544                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 545                                                         start = i+1;
 546                                                 }
 547                                         }
 548                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 549                                 }
 550                         }
 551                         else{
 552                                 goodNameOut << seqName << '\t' << seqList << endl;
 553                         }
 554                         m->gobble(inputNames);
 555                 }
 556                 inputNames.close();
 557                 goodNameOut.close();
 558
 559                 //we were unable to remove some of the bad sequences
 560                 if (badSeqNames.size() != 0) {
 561                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 562                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 563                                 m->mothurOutEndLine();
 564                         }
 565                 }
 566
 567                 if(groupfile != ""){
 568
 569                         ifstream inputGroups;
 570                         m->openInputFile(groupfile, inputGroups);
 571
 572                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 573                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 574
 575                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 576
 577                         while(!inputGroups.eof()){
 578                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 579
 580                                 inputGroups >> seqName >> group;
 581
 582                                 it = badSeqGroups.find(seqName);
 583
 584                                 if(it != badSeqGroups.end()){
 585                                         badSeqGroups.erase(it);
 586                                 }
 587                                 else{
 588                                         goodGroupOut << seqName << '\t' << group << endl;
 589                                 }
 590                                 m->gobble(inputGroups);
 591                         }
 592                         inputGroups.close();
 593                         goodGroupOut.close();
 594
 595                         //we were unable to remove some of the bad sequences
 596                         if (badSeqGroups.size() != 0) {
 597                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 598                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 599                                         m->mothurOutEndLine();
 600                                 }
 601                         }
 602                 }
 603
 604
 605                 return 0;
 606
 607         }
 608         catch(exception& e) {
 609                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 610                 exit(1);
 611         }
 612 }
 613 //***************************************************************************************************************
 614 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 615         try {
 616
 617                 vector<int> startPosition;
 618                 vector<int> endPosition;
 619                 vector<int> seqLength;
 620                 vector<int> ambigBases;
 621                 vector<int> longHomoPolymer;
 622
 623                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 624
 625                 for (int i = 0; i < (positions.size()-1); i++) {
 626                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 627                 }
 628
 629                 int numSeqs = 0;
 630                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 631                         if(processors == 1){
 632                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 633                         }else{
 634                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 635                         }
 636
 637                         if (m->control_pressed) {  return 0; }
 638                 #else
 639                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 640                         if (m->control_pressed) {  return 0; }
 641                 #endif
 642
 643                 sort(startPosition.begin(), startPosition.end());
 644                 sort(endPosition.begin(), endPosition.end());
 645                 sort(seqLength.begin(), seqLength.end());
 646                 sort(ambigBases.begin(), ambigBases.end());
 647                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 648
 649                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 650                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 651
 652                 for (int i = 0; i < optimize.size(); i++) {
 653                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 654                         else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
 655                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 656                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 657                         else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
 658                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 659                 }
 660
 661                 return 0;
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 665                 exit(1);
 666         }
 667 }
 668 /**************************************************************************************/
 669 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 670         try {
 671
 672                 ifstream in;
 673                 m->openInputFile(filename, in);
 674
 675                 in.seekg(filePos->start);
 676
 677                 bool done = false;
 678                 int count = 0;
 679
 680                 while (!done) {
 681
 682                         if (m->control_pressed) { in.close(); return 1; }
 683
 684                         Sequence current(in); m->gobble(in);
 685
 686                         if (current.getName() != "") {
 687                                 int num = 1;
 688                                 if (namefile != "") {
 689                                         //make sure this sequence is in the namefile, else error
 690                                         map<string, int>::iterator it = nameMap.find(current.getName());
 691
 692                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 693                                         else { num = it->second; }
 694                                 }
 695
 696                                 //for each sequence this sequence represents
 697                                 for (int i = 0; i < num; i++) {
 698                                         startPosition.push_back(current.getStartPos());
 699                                         endPosition.push_back(current.getEndPos());
 700                                         seqLength.push_back(current.getNumBases());
 701                                         ambigBases.push_back(current.getAmbigBases());
 702                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 703                                 }
 704
 705                                 count++;
 706                         }
 707
 708                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 709                                 unsigned long int pos = in.tellg();
 710                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 711                         #else
 712                                 if (in.eof()) { break; }
 713                         #endif
 714
 715                 }
 716
 717                 in.close();
 718
 719                 return count;
 720         }
 721         catch(exception& e) {
 722                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 723                 exit(1);
 724         }
 725 }
 726 /**************************************************************************************************/
 727 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 728         try {
 729 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 730                 int process = 1;
 731                 int num = 0;
 732                 processIDS.clear();
 733
 734                 //loop through and create all the processes you want
 735                 while (process != processors) {
 736                         int pid = fork();
 737
 738                         if (pid > 0) {
 739                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 740                                 process++;
 741                         }else if (pid == 0){
 742                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 743
 744                                 //pass numSeqs to parent
 745                                 ofstream out;
 746                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 747                                 m->openOutputFile(tempFile, out);
 748
 749                                 out << num << endl;
 750                                 out << startPosition.size() << endl;
 751                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 752                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 753                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 754                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 755                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 756
 757                                 out.close();
 758
 759                                 exit(0);
 760                         }else {
 761                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 762                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 763                                 exit(0);
 764                         }
 765                 }
 766
 767                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 768
 769                 //force parent to wait until all the processes are done
 770                 for (int i=0;i<processIDS.size();i++) {
 771                         int temp = processIDS[i];
 772                         wait(&temp);
 773                 }
 774
 775                 //parent reads in and combine Filter info
 776                 for (int i = 0; i < processIDS.size(); i++) {
 777                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 778                         ifstream in;
 779                         m->openInputFile(tempFilename, in);
 780
 781                         int temp, tempNum;
 782                         in >> tempNum; m->gobble(in); num += tempNum;
 783                         in >> tempNum; m->gobble(in);
 784                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 785                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 786                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 787                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 788                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 789
 790                         in.close();
 791                         remove(tempFilename.c_str());
 792                 }
 793
 794                 return num;
 795 #endif
 796         }
 797         catch(exception& e) {
 798                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 799                 exit(1);
 800         }
 801 }
 802
 803 //***************************************************************************************************************
 804
 805 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 806         try {
 807                 ifstream inputGroups;
 808                 m->openInputFile(groupfile, inputGroups);
 809                 string seqName, group;
 810                 set<string>::iterator it;
 811
 812                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 813                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 814                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 815
 816                 while(!inputGroups.eof()){
 817                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 818
 819                         inputGroups >> seqName >> group;
 820                         it = badSeqNames.find(seqName);
 821
 822                         if(it != badSeqNames.end()){
 823                                 badSeqNames.erase(it);
 824                         }
 825                         else{
 826                                 goodGroupOut << seqName << '\t' << group << endl;
 827                         }
 828                         m->gobble(inputGroups);
 829                 }
 830
 831                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 832
 833                 //we were unable to remove some of the bad sequences
 834                 if (badSeqNames.size() != 0) {
 835                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 836                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 837                                 m->mothurOutEndLine();
 838                         }
 839                 }
 840
 841                 inputGroups.close();
 842                 goodGroupOut.close();
 843
 844                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 845
 846                 return 0;
 847
 848         }
 849         catch(exception& e) {
 850                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 851                 exit(1);
 852         }
 853 }
 854
 855 //***************************************************************************************************************
 856
 857 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 858         try {
 859                 ifstream inputAlignReport;
 860                 m->openInputFile(alignreport, inputAlignReport);
 861                 string seqName, group;
 862                 set<string>::iterator it;
 863
 864                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 865                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 866                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 867
 868                 while (!inputAlignReport.eof()) {               //      need to copy header
 869                         char c = inputAlignReport.get();
 870                         goodAlignReportOut << c;
 871                         if (c == 10 || c == 13){        break;  }
 872                 }
 873
 874                 while(!inputAlignReport.eof()){
 875                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 876
 877                         inputAlignReport >> seqName;
 878                         it = badSeqNames.find(seqName);
 879                         string line;
 880                         while (!inputAlignReport.eof()) {               //      need to copy header
 881                                 char c = inputAlignReport.get();
 882                                 line += c;
 883                                 if (c == 10 || c == 13){        break;  }
 884                         }
 885
 886                         if(it != badSeqNames.end()){
 887                                 badSeqNames.erase(it);
 888                         }
 889                         else{
 890                                 goodAlignReportOut << seqName << '\t' << line;
 891                         }
 892                         m->gobble(inputAlignReport);
 893                 }
 894
 895                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 896
 897                 //we were unable to remove some of the bad sequences
 898                 if (badSeqNames.size() != 0) {
 899                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 900                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 901                                 m->mothurOutEndLine();
 902                         }
 903                 }
 904
 905                 inputAlignReport.close();
 906                 goodAlignReportOut.close();
 907
 908                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 909
 910                 return 0;
 911
 912         }
 913         catch(exception& e) {
 914                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 915                 exit(1);
 916         }
 917
 918 }
 919 //**********************************************************************************************************************
 920
 921 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 922         try {
 923                 ofstream goodFile;
 924                 m->openOutputFile(goodFName, goodFile);
 925
 926                 ofstream badAccnosFile;
 927                 m->openOutputFile(badAccnosFName, badAccnosFile);
 928
 929                 ifstream inFASTA;
 930                 m->openInputFile(filename, inFASTA);
 931
 932                 inFASTA.seekg(filePos->start);
 933
 934                 bool done = false;
 935                 int count = 0;
 936
 937                 while (!done) {
 938
 939                         if (m->control_pressed) {  return 0; }
 940
 941                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 942                         if (currSeq.getName() != "") {
 943                                 bool goodSeq = 1;               //      innocent until proven guilty
 944                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 945                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 946                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 947                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 948                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 949                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 950
 951                                 if(goodSeq == 1){
 952                                         currSeq.printSequence(goodFile);
 953                                 }
 954                                 else{
 955                                         badAccnosFile << currSeq.getName() << endl;
 956                                         badSeqNames.insert(currSeq.getName());
 957                                 }
 958                         count++;
 959                         }
 960
 961                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 962                                 unsigned long int pos = inFASTA.tellg();
 963                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 964                         #else
 965                                 if (inFASTA.eof()) { break; }
 966                         #endif
 967
 968                         //report progress
 969                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 970                 }
 971                 //report progress
 972                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 973
 974
 975                 goodFile.close();
 976                 inFASTA.close();
 977                 badAccnosFile.close();
 978
 979                 return count;
 980         }
 981         catch(exception& e) {
 982                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 983                 exit(1);
 984         }
 985 }
 986 //**********************************************************************************************************************
 987 #ifdef USE_MPI
 988 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
 989         try {
 990                 string outputString = "";
 991                 MPI_Status statusGood;
 992                 MPI_Status statusBadAccnos;
 993                 MPI_Status status;
 994                 int pid;
 995                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 996
 997                 for(int i=0;i<num;i++){
 998
 999                         if (m->control_pressed) {  return 0; }
1000
1001                         //read next sequence
1002                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1003
1004                         char* buf4 = new char[length];
1005                         memcpy(buf4, outputString.c_str(), length);
1006
1007                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1008
1009                         string tempBuf = buf4;  delete buf4;
1010                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1011                         istringstream iss (tempBuf,istringstream::in);
1012
1013                         Sequence currSeq(iss);
1014
1015                         //process seq
1016                         if (currSeq.getName() != "") {
1017                                 bool goodSeq = 1;               //      innocent until proven guilty
1018                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1019                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1020                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1021                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1022                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1023                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1024
1025                                 if(goodSeq == 1){
1026                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1027
1028                                         //print good seq
1029                                         length = outputString.length();
1030                                         char* buf2 = new char[length];
1031                                         memcpy(buf2, outputString.c_str(), length);
1032
1033                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1034                                         delete buf2;
1035                                 }
1036                                 else{
1037
1038                                         badSeqNames.insert(currSeq.getName());
1039
1040                                         //write to bad accnos file
1041                                         outputString = currSeq.getName() + "\n";
1042
1043                                         length = outputString.length();
1044                                         char* buf3 = new char[length];
1045                                         memcpy(buf3, outputString.c_str(), length);
1046
1047                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1048                                         delete buf3;
1049                                 }
1050                         }
1051
1052                         //report progress
1053                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1054                 }
1055
1056                 return 1;
1057         }
1058         catch(exception& e) {
1059                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1060                 exit(1);
1061         }
1062 }
1063 #endif
1064 /**************************************************************************************************/
1065
1066 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1067         try {
1068 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1069                 int process = 0;
1070                 int num = 0;
1071
1072                 //loop through and create all the processes you want
1073                 while (process != processors) {
1074                         int pid = fork();
1075
1076                         if (pid > 0) {
1077                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1078                                 process++;
1079                         }else if (pid == 0){
1080                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1081
1082                                 //pass numSeqs to parent
1083                                 ofstream out;
1084                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1085                                 m->openOutputFile(tempFile, out);
1086                                 out << num << endl;
1087                                 out.close();
1088
1089                                 exit(0);
1090                         }else {
1091                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1092                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1093                                 exit(0);
1094                         }
1095                 }
1096
1097                 //force parent to wait until all the processes are done
1098                 for (int i=0;i<processors;i++) {
1099                         int temp = processIDS[i];
1100                         wait(&temp);
1101                 }
1102
1103                 for (int i = 0; i < processIDS.size(); i++) {
1104                         ifstream in;
1105                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1106                         m->openInputFile(tempFile, in);
1107                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1108                         in.close(); remove(tempFile.c_str());
1109                 }
1110
1111                 return num;
1112 #endif
1113         }
1114         catch(exception& e) {
1115                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1116                 exit(1);
1117         }
1118 }
1119
1120 //***************************************************************************************************************
1121
1122