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::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
  20                 CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  21                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  22                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  23                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  24                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  25                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  26                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  27                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  28                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string ScreenSeqsCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The screen.seqs command reads a fastafile and creates .....\n";
  46                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n";
  47                 helpString += "The fasta parameter is required.\n";
  48                 helpString += "The start parameter .... The default is -1.\n";
  49                 helpString += "The end parameter .... The default is -1.\n";
  50                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  51                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  52                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  53                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  54                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  55                 helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
  56                 helpString += "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";
  57                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  58                 helpString += "The screen.seqs command should be in the following format: \n";
  59                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  60                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  61                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  62                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
  63                 return helpString;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 ScreenSeqsCommand::ScreenSeqsCommand(){
  72         try {
  73                 abort = true; calledHelp = true;
  74                 setParameters();
  75                 vector<string> tempOutNames;
  76                 outputTypes["fasta"] = tempOutNames;
  77                 outputTypes["name"] = tempOutNames;
  78                 outputTypes["group"] = tempOutNames;
  79                 outputTypes["alignreport"] = tempOutNames;
  80                 outputTypes["accnos"] = tempOutNames;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
  84                 exit(1);
  85         }
  86 }
  87 //***************************************************************************************************************
  88
  89 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  90         try {
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95
  96                 else {
  97                         vector<string> myArray = setParameters();
  98
  99                         OptionParser parser(option);
 100                         map<string,string> parameters = parser.getParameters();
 101
 102                         ValidParameters validParameter("screen.seqs");
 103                         map<string,string>::iterator it;
 104
 105                         //check to make sure all parameters are valid for command
 106                         for (it = parameters.begin(); it != parameters.end(); it++) {
 107                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 108                         }
 109
 110                         //initialize outputTypes
 111                         vector<string> tempOutNames;
 112                         outputTypes["fasta"] = tempOutNames;
 113                         outputTypes["name"] = tempOutNames;
 114                         outputTypes["group"] = tempOutNames;
 115                         outputTypes["alignreport"] = tempOutNames;
 116                         outputTypes["accnos"] = tempOutNames;
 117
 118                         //if the user changes the input directory command factory will send this info to us in the output parameter
 119                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 120                         if (inputDir == "not found"){   inputDir = "";          }
 121                         else {
 122                                 string path;
 123                                 it = parameters.find("fasta");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 129                                 }
 130
 131                                 it = parameters.find("group");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 137                                 }
 138
 139                                 it = parameters.find("name");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 145                                 }
 146
 147                                 it = parameters.find("alignreport");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 153                                 }
 154                         }
 155
 156                         //check for required parameters
 157                         fastafile = validParameter.validFile(parameters, "fasta", true);
 158                         if (fastafile == "not found") {
 159                                 fastafile = m->getFastaFile();
 160                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 161                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 162                         }
 163                         else if (fastafile == "not open") { abort = true; }
 164
 165                         groupfile = validParameter.validFile(parameters, "group", true);
 166                         if (groupfile == "not open") { abort = true; }
 167                         else if (groupfile == "not found") { groupfile = ""; }
 168
 169                         namefile = validParameter.validFile(parameters, "name", true);
 170                         if (namefile == "not open") { namefile = ""; abort = true; }
 171                         else if (namefile == "not found") { namefile = ""; }
 172
 173                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 174                         if (alignreport == "not open") { abort = true; }
 175                         else if (alignreport == "not found") { alignreport = ""; }
 176
 177                         //if the user changes the output directory command factory will send this info to us in the output parameter
 178                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 179                                 outputDir = "";
 180                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 181                         }
 182
 183                         //check for optional parameter and set defaults
 184                         // ...at some point should added some additional type checking...
 185                         string temp;
 186                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 187                         convert(temp, startPos);
 188
 189                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 190                         convert(temp, endPos);
 191
 192                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 193                         convert(temp, maxAmbig);
 194
 195                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 196                         convert(temp, maxHomoP);
 197
 198                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 199                         convert(temp, minLength);
 200
 201                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 202                         convert(temp, maxLength);
 203
 204                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 205                         m->setProcessors(temp);
 206                         convert(temp, processors);
 207
 208                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 209                         if (temp == "not found"){       temp = "none";          }
 210                         m->splitAtDash(temp, optimize);
 211
 212                         //check for invalid optimize options
 213                         set<string> validOptimizers;
 214                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 215                         for (int i = 0; i < optimize.size(); i++) {
 216                                 if (validOptimizers.count(optimize[i]) == 0) {
 217                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 218                                         optimize.erase(optimize.begin()+i);
 219                                         i--;
 220                                 }
 221                         }
 222
 223                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 224
 225                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 226                         convert(temp, criteria);
 227                 }
 228
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 232                 exit(1);
 233         }
 234 }
 235 //***************************************************************************************************************
 236
 237 int ScreenSeqsCommand::execute(){
 238         try{
 239
 240                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 241
 242                 //if the user want to optimize we need to know the 90% mark
 243                 vector<unsigned long int> positions;
 244                 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
 245                         //use the namefile to optimize correctly
 246                         if (namefile != "") { nameMap = m->readNames(namefile); }
 247                         getSummary(positions);
 248                 }
 249                 else {
 250                         positions = m->divideFile(fastafile, processors);
 251                         for (int i = 0; i < (positions.size()-1); i++) {
 252                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 253                         }
 254                 }
 255
 256                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 257                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 258
 259                 int numFastaSeqs = 0;
 260                 set<string> badSeqNames;
 261                 int start = time(NULL);
 262
 263 #ifdef USE_MPI
 264                         int pid, numSeqsPerProcessor;
 265                         int tag = 2001;
 266                         vector<unsigned long int> MPIPos;
 267
 268                         MPI_Status status;
 269                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 270                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 271
 272                         MPI_File inMPI;
 273                         MPI_File outMPIGood;
 274                         MPI_File outMPIBadAccnos;
 275
 276                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 277                         int inMode=MPI_MODE_RDONLY;
 278
 279                         char outGoodFilename[1024];
 280                         strcpy(outGoodFilename, goodSeqFile.c_str());
 281
 282                         char outBadAccnosFilename[1024];
 283                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 284
 285                         char inFileName[1024];
 286                         strcpy(inFileName, fastafile.c_str());
 287
 288                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 289                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 290                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 291
 292                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 293
 294                         if (pid == 0) { //you are the root process
 295
 296                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 297
 298                                 //send file positions to all processes
 299                                 for(int i = 1; i < processors; i++) {
 300                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 301                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 302                                 }
 303
 304                                 //figure out how many sequences you have to align
 305                                 numSeqsPerProcessor = numFastaSeqs / processors;
 306                                 int startIndex =  pid * numSeqsPerProcessor;
 307                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 308                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 309                                 //align your part
 310                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 311                 //cout << pid << " done" << endl;
 312                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 313
 314                                 for (int i = 1; i < processors; i++) {
 315
 316                                         //get bad lists
 317                                         int badSize;
 318                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 319                                         /*for (int j = 0; j < badSize; j++) {
 320                                                 int length;
 321                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 322                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 323                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 324
 325                                                 string tempBuf = buf2;
 326                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 327                                                 delete buf2;
 328
 329                                                 badSeqNames.insert(tempBuf);
 330                                         }*/
 331                                 }
 332                         }else{ //you are a child process
 333                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 334                                 MPIPos.resize(numFastaSeqs+1);
 335                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 336
 337                                 //figure out how many sequences you have to align
 338                                 numSeqsPerProcessor = numFastaSeqs / processors;
 339                                 int startIndex =  pid * numSeqsPerProcessor;
 340                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 341                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 342                                 //align your part
 343                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 344 //cout << pid << " done" << endl;
 345                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 346
 347                                 //send bad list
 348                                 int badSize = badSeqNames.size();
 349                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 350
 351                                 /*
 352                                 set<string>::iterator it;
 353                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 354                                         string name = *it;
 355                                         int length = name.length();
 356                                         char* buf2 = new char[length];
 357                                         memcpy(buf2, name.c_str(), length);
 358
 359                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 360                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 361                                 }*/
 362                         }
 363
 364                         //close files
 365                         MPI_File_close(&inMPI);
 366                         MPI_File_close(&outMPIGood);
 367                         MPI_File_close(&outMPIBadAccnos);
 368                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 369
 370 #else
 371
 372         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 373                         if(processors == 1){
 374                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 375
 376                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 377
 378                         }else{
 379                                 processIDS.resize(0);
 380
 381                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 382
 383                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 384                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 385
 386                                 //append alignment and report files
 387                                 for(int i=1;i<processors;i++){
 388                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 389                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 390
 391                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 392                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 393                                 }
 394
 395                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 396
 397                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 398                                 ifstream inBad;
 399                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 400
 401                                 if (ableToOpen == 0) {
 402                                         badSeqNames.clear();
 403                                         string tempName;
 404                                         while (!inBad.eof()) {
 405                                                 inBad >> tempName; m->gobble(inBad);
 406                                                 badSeqNames.insert(tempName);
 407                                         }
 408                                         inBad.close();
 409                                 }
 410                         }
 411         #else
 412                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 413
 414                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 415
 416         #endif
 417
 418 #endif
 419
 420                 #ifdef USE_MPI
 421                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 422
 423                         if (pid == 0) { //only one process should fix files
 424
 425                                 //read accnos file with all names in it, process 0 just has its names
 426                                 MPI_File inMPIAccnos;
 427                                 MPI_Offset size;
 428
 429                                 char inFileName[1024];
 430                                 strcpy(inFileName, badAccnosFile.c_str());
 431
 432                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 433                                 MPI_File_get_size(inMPIAccnos, &size);
 434
 435                                 char* buffer = new char[size];
 436                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 437
 438                                 string tempBuf = buffer;
 439                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 440                                 istringstream iss (tempBuf,istringstream::in);
 441
 442                                 delete buffer;
 443                                 MPI_File_close(&inMPIAccnos);
 444
 445                                 badSeqNames.clear();
 446                                 string tempName;
 447                                 while (!iss.eof()) {
 448                                         iss >> tempName; m->gobble(iss);
 449                                         badSeqNames.insert(tempName);
 450                                 }
 451                 #endif
 452
 453                 if(namefile != "" && groupfile != "")   {
 454                         screenNameGroupFile(badSeqNames);
 455                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 456                 }else if(namefile != "")        {
 457                         screenNameGroupFile(badSeqNames);
 458                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 459                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 460
 461                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 462
 463                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 464
 465                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 466
 467                 #ifdef USE_MPI
 468                         }
 469                 #endif
 470
 471                 m->mothurOutEndLine();
 472                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 473                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 474                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 475                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 476                 m->mothurOutEndLine();
 477                 m->mothurOutEndLine();
 478
 479                 //set fasta file as new current fastafile
 480                 string current = "";
 481                 itTypes = outputTypes.find("fasta");
 482                 if (itTypes != outputTypes.end()) {
 483                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 484                 }
 485
 486                 itTypes = outputTypes.find("name");
 487                 if (itTypes != outputTypes.end()) {
 488                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 489                 }
 490
 491                 itTypes = outputTypes.find("group");
 492                 if (itTypes != outputTypes.end()) {
 493                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 494                 }
 495
 496                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 497                 m->mothurOutEndLine();
 498
 499                 return 0;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 503                 exit(1);
 504         }
 505 }
 506
 507 //***************************************************************************************************************
 508
 509 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 510         try {
 511                 ifstream inputNames;
 512                 m->openInputFile(namefile, inputNames);
 513                 set<string> badSeqGroups;
 514                 string seqName, seqList, group;
 515                 set<string>::iterator it;
 516
 517                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 518                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 519
 520                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 521
 522                 while(!inputNames.eof()){
 523                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 524
 525                         inputNames >> seqName >> seqList;
 526                         it = badSeqNames.find(seqName);
 527
 528                         if(it != badSeqNames.end()){
 529                                 badSeqNames.erase(it);
 530
 531                                 if(namefile != ""){
 532                                         int start = 0;
 533                                         for(int i=0;i<seqList.length();i++){
 534                                                 if(seqList[i] == ','){
 535                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 536                                                         start = i+1;
 537                                                 }
 538                                         }
 539                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 540                                 }
 541                         }
 542                         else{
 543                                 goodNameOut << seqName << '\t' << seqList << endl;
 544                         }
 545                         m->gobble(inputNames);
 546                 }
 547                 inputNames.close();
 548                 goodNameOut.close();
 549
 550                 //we were unable to remove some of the bad sequences
 551                 if (badSeqNames.size() != 0) {
 552                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 553                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 554                                 m->mothurOutEndLine();
 555                         }
 556                 }
 557
 558                 if(groupfile != ""){
 559
 560                         ifstream inputGroups;
 561                         m->openInputFile(groupfile, inputGroups);
 562
 563                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 564                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 565
 566                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 567
 568                         while(!inputGroups.eof()){
 569                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 570
 571                                 inputGroups >> seqName >> group;
 572
 573                                 it = badSeqGroups.find(seqName);
 574
 575                                 if(it != badSeqGroups.end()){
 576                                         badSeqGroups.erase(it);
 577                                 }
 578                                 else{
 579                                         goodGroupOut << seqName << '\t' << group << endl;
 580                                 }
 581                                 m->gobble(inputGroups);
 582                         }
 583                         inputGroups.close();
 584                         goodGroupOut.close();
 585
 586                         //we were unable to remove some of the bad sequences
 587                         if (badSeqGroups.size() != 0) {
 588                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 589                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 590                                         m->mothurOutEndLine();
 591                                 }
 592                         }
 593                 }
 594
 595
 596                 return 0;
 597
 598         }
 599         catch(exception& e) {
 600                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 601                 exit(1);
 602         }
 603 }
 604 //***************************************************************************************************************
 605 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 606         try {
 607
 608                 vector<int> startPosition;
 609                 vector<int> endPosition;
 610                 vector<int> seqLength;
 611                 vector<int> ambigBases;
 612                 vector<int> longHomoPolymer;
 613
 614                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 615
 616                 for (int i = 0; i < (positions.size()-1); i++) {
 617                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 618                 }
 619
 620                 int numSeqs = 0;
 621                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 622                         if(processors == 1){
 623                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 624                         }else{
 625                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 626                         }
 627
 628                         if (m->control_pressed) {  return 0; }
 629                 #else
 630                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 631                         if (m->control_pressed) {  return 0; }
 632                 #endif
 633
 634                 sort(startPosition.begin(), startPosition.end());
 635                 sort(endPosition.begin(), endPosition.end());
 636                 sort(seqLength.begin(), seqLength.end());
 637                 sort(ambigBases.begin(), ambigBases.end());
 638                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 639
 640                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 641                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 642
 643                 for (int i = 0; i < optimize.size(); i++) {
 644                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 645                         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();}
 646                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 647                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 648                         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(); }
 649                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 650                 }
 651
 652                 return 0;
 653         }
 654         catch(exception& e) {
 655                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 656                 exit(1);
 657         }
 658 }
 659 /**************************************************************************************/
 660 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 661         try {
 662
 663                 ifstream in;
 664                 m->openInputFile(filename, in);
 665
 666                 in.seekg(filePos->start);
 667
 668                 bool done = false;
 669                 int count = 0;
 670
 671                 while (!done) {
 672
 673                         if (m->control_pressed) { in.close(); return 1; }
 674
 675                         Sequence current(in); m->gobble(in);
 676
 677                         if (current.getName() != "") {
 678                                 int num = 1;
 679                                 if (namefile != "") {
 680                                         //make sure this sequence is in the namefile, else error
 681                                         map<string, int>::iterator it = nameMap.find(current.getName());
 682
 683                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 684                                         else { num = it->second; }
 685                                 }
 686
 687                                 //for each sequence this sequence represents
 688                                 for (int i = 0; i < num; i++) {
 689                                         startPosition.push_back(current.getStartPos());
 690                                         endPosition.push_back(current.getEndPos());
 691                                         seqLength.push_back(current.getNumBases());
 692                                         ambigBases.push_back(current.getAmbigBases());
 693                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 694                                 }
 695
 696                                 count++;
 697                         }
 698
 699                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 700                                 unsigned long int pos = in.tellg();
 701                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 702                         #else
 703                                 if (in.eof()) { break; }
 704                         #endif
 705
 706                 }
 707
 708                 in.close();
 709
 710                 return count;
 711         }
 712         catch(exception& e) {
 713                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 714                 exit(1);
 715         }
 716 }
 717 /**************************************************************************************************/
 718 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 719         try {
 720 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 721                 int process = 1;
 722                 int num = 0;
 723                 processIDS.clear();
 724
 725                 //loop through and create all the processes you want
 726                 while (process != processors) {
 727                         int pid = fork();
 728
 729                         if (pid > 0) {
 730                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 731                                 process++;
 732                         }else if (pid == 0){
 733                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 734
 735                                 //pass numSeqs to parent
 736                                 ofstream out;
 737                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 738                                 m->openOutputFile(tempFile, out);
 739
 740                                 out << num << endl;
 741                                 out << startPosition.size() << endl;
 742                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 743                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 744                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 745                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 746                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 747
 748                                 out.close();
 749
 750                                 exit(0);
 751                         }else {
 752                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 753                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 754                                 exit(0);
 755                         }
 756                 }
 757
 758                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 759
 760                 //force parent to wait until all the processes are done
 761                 for (int i=0;i<processIDS.size();i++) {
 762                         int temp = processIDS[i];
 763                         wait(&temp);
 764                 }
 765
 766                 //parent reads in and combine Filter info
 767                 for (int i = 0; i < processIDS.size(); i++) {
 768                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 769                         ifstream in;
 770                         m->openInputFile(tempFilename, in);
 771
 772                         int temp, tempNum;
 773                         in >> tempNum; m->gobble(in); num += tempNum;
 774                         in >> tempNum; m->gobble(in);
 775                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 776                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 777                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 778                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 779                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 780
 781                         in.close();
 782                         remove(tempFilename.c_str());
 783                 }
 784
 785                 return num;
 786 #endif
 787         }
 788         catch(exception& e) {
 789                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 790                 exit(1);
 791         }
 792 }
 793
 794 //***************************************************************************************************************
 795
 796 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 797         try {
 798                 ifstream inputGroups;
 799                 m->openInputFile(groupfile, inputGroups);
 800                 string seqName, group;
 801                 set<string>::iterator it;
 802
 803                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 804                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 805                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 806
 807                 while(!inputGroups.eof()){
 808                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 809
 810                         inputGroups >> seqName >> group;
 811                         it = badSeqNames.find(seqName);
 812
 813                         if(it != badSeqNames.end()){
 814                                 badSeqNames.erase(it);
 815                         }
 816                         else{
 817                                 goodGroupOut << seqName << '\t' << group << endl;
 818                         }
 819                         m->gobble(inputGroups);
 820                 }
 821
 822                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 823
 824                 //we were unable to remove some of the bad sequences
 825                 if (badSeqNames.size() != 0) {
 826                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 827                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 828                                 m->mothurOutEndLine();
 829                         }
 830                 }
 831
 832                 inputGroups.close();
 833                 goodGroupOut.close();
 834
 835                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 836
 837                 return 0;
 838
 839         }
 840         catch(exception& e) {
 841                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 842                 exit(1);
 843         }
 844 }
 845
 846 //***************************************************************************************************************
 847
 848 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 849         try {
 850                 ifstream inputAlignReport;
 851                 m->openInputFile(alignreport, inputAlignReport);
 852                 string seqName, group;
 853                 set<string>::iterator it;
 854
 855                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 856                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 857                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 858
 859                 while (!inputAlignReport.eof()) {               //      need to copy header
 860                         char c = inputAlignReport.get();
 861                         goodAlignReportOut << c;
 862                         if (c == 10 || c == 13){        break;  }
 863                 }
 864
 865                 while(!inputAlignReport.eof()){
 866                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 867
 868                         inputAlignReport >> seqName;
 869                         it = badSeqNames.find(seqName);
 870                         string line;
 871                         while (!inputAlignReport.eof()) {               //      need to copy header
 872                                 char c = inputAlignReport.get();
 873                                 line += c;
 874                                 if (c == 10 || c == 13){        break;  }
 875                         }
 876
 877                         if(it != badSeqNames.end()){
 878                                 badSeqNames.erase(it);
 879                         }
 880                         else{
 881                                 goodAlignReportOut << seqName << '\t' << line;
 882                         }
 883                         m->gobble(inputAlignReport);
 884                 }
 885
 886                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 887
 888                 //we were unable to remove some of the bad sequences
 889                 if (badSeqNames.size() != 0) {
 890                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 891                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 892                                 m->mothurOutEndLine();
 893                         }
 894                 }
 895
 896                 inputAlignReport.close();
 897                 goodAlignReportOut.close();
 898
 899                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 900
 901                 return 0;
 902
 903         }
 904         catch(exception& e) {
 905                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 906                 exit(1);
 907         }
 908
 909 }
 910 //**********************************************************************************************************************
 911
 912 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 913         try {
 914                 ofstream goodFile;
 915                 m->openOutputFile(goodFName, goodFile);
 916
 917                 ofstream badAccnosFile;
 918                 m->openOutputFile(badAccnosFName, badAccnosFile);
 919
 920                 ifstream inFASTA;
 921                 m->openInputFile(filename, inFASTA);
 922
 923                 inFASTA.seekg(filePos->start);
 924
 925                 bool done = false;
 926                 int count = 0;
 927
 928                 while (!done) {
 929
 930                         if (m->control_pressed) {  return 0; }
 931
 932                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 933                         if (currSeq.getName() != "") {
 934                                 bool goodSeq = 1;               //      innocent until proven guilty
 935                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 936                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 937                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 938                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 939                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 940                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 941
 942                                 if(goodSeq == 1){
 943                                         currSeq.printSequence(goodFile);
 944                                 }
 945                                 else{
 946                                         badAccnosFile << currSeq.getName() << endl;
 947                                         badSeqNames.insert(currSeq.getName());
 948                                 }
 949                         count++;
 950                         }
 951
 952                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 953                                 unsigned long int pos = inFASTA.tellg();
 954                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 955                         #else
 956                                 if (inFASTA.eof()) { break; }
 957                         #endif
 958
 959                         //report progress
 960                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 961                 }
 962                 //report progress
 963                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 964
 965
 966                 goodFile.close();
 967                 inFASTA.close();
 968                 badAccnosFile.close();
 969
 970                 return count;
 971         }
 972         catch(exception& e) {
 973                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 974                 exit(1);
 975         }
 976 }
 977 //**********************************************************************************************************************
 978 #ifdef USE_MPI
 979 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
 980         try {
 981                 string outputString = "";
 982                 MPI_Status statusGood;
 983                 MPI_Status statusBadAccnos;
 984                 MPI_Status status;
 985                 int pid;
 986                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 987
 988                 for(int i=0;i<num;i++){
 989
 990                         if (m->control_pressed) {  return 0; }
 991
 992                         //read next sequence
 993                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 994
 995                         char* buf4 = new char[length];
 996                         memcpy(buf4, outputString.c_str(), length);
 997
 998                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 999
1000                         string tempBuf = buf4;  delete buf4;
1001                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1002                         istringstream iss (tempBuf,istringstream::in);
1003
1004                         Sequence currSeq(iss);
1005
1006                         //process seq
1007                         if (currSeq.getName() != "") {
1008                                 bool goodSeq = 1;               //      innocent until proven guilty
1009                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1010                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1011                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1012                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1013                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1014                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1015
1016                                 if(goodSeq == 1){
1017                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1018
1019                                         //print good seq
1020                                         length = outputString.length();
1021                                         char* buf2 = new char[length];
1022                                         memcpy(buf2, outputString.c_str(), length);
1023
1024                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1025                                         delete buf2;
1026                                 }
1027                                 else{
1028
1029                                         badSeqNames.insert(currSeq.getName());
1030
1031                                         //write to bad accnos file
1032                                         outputString = currSeq.getName() + "\n";
1033
1034                                         length = outputString.length();
1035                                         char* buf3 = new char[length];
1036                                         memcpy(buf3, outputString.c_str(), length);
1037
1038                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1039                                         delete buf3;
1040                                 }
1041                         }
1042
1043                         //report progress
1044                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1045                 }
1046
1047                 return 1;
1048         }
1049         catch(exception& e) {
1050                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1051                 exit(1);
1052         }
1053 }
1054 #endif
1055 /**************************************************************************************************/
1056
1057 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1058         try {
1059 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1060                 int process = 0;
1061                 int num = 0;
1062
1063                 //loop through and create all the processes you want
1064                 while (process != processors) {
1065                         int pid = fork();
1066
1067                         if (pid > 0) {
1068                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1069                                 process++;
1070                         }else if (pid == 0){
1071                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1072
1073                                 //pass numSeqs to parent
1074                                 ofstream out;
1075                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1076                                 m->openOutputFile(tempFile, out);
1077                                 out << num << endl;
1078                                 out.close();
1079
1080                                 exit(0);
1081                         }else {
1082                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1083                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1084                                 exit(0);
1085                         }
1086                 }
1087
1088                 //force parent to wait until all the processes are done
1089                 for (int i=0;i<processors;i++) {
1090                         int temp = processIDS[i];
1091                         wait(&temp);
1092                 }
1093
1094                 for (int i = 0; i < processIDS.size(); i++) {
1095                         ifstream in;
1096                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1097                         m->openInputFile(tempFile, in);
1098                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1099                         in.close(); remove(tempFile.c_str());
1100                 }
1101
1102                 return num;
1103 #endif
1104         }
1105         catch(exception& e) {
1106                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1107                 exit(1);
1108         }
1109 }
1110
1111 //***************************************************************************************************************
1112
1113