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
  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 pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  20                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
  21                 CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
  22                 CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  23                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  24                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  25                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  26                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  27                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  28                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  29                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  30                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string ScreenSeqsCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The screen.seqs command reads a fastafile and creates .....\n";
  48                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
  49                 helpString += "The fasta parameter is required.\n";
  50                 helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
  51                 helpString += "The start parameter .... The default is -1.\n";
  52                 helpString += "The end parameter .... The default is -1.\n";
  53                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  54                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  55                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  56                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  57                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  58                 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";
  59                 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";
  60                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  61                 helpString += "The screen.seqs command should be in the following format: \n";
  62                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  63                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  64                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  65                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  66                 return helpString;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 string ScreenSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  75         try {
  76         string outputFileName = "";
  77                 map<string, vector<string> >::iterator it;
  78
  79         //is this a type this command creates
  80         it = outputTypes.find(type);
  81         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  82         else {
  83             if (type == "fasta")            {   outputFileName =  "good" + m->getExtension(inputName);   }
  84             else if (type == "taxonomy")    {   outputFileName =  "good" + m->getExtension(inputName);   }
  85             else if (type == "name")        {   outputFileName =  "good" + m->getExtension(inputName);   }
  86             else if (type == "group")       {   outputFileName =  "good" + m->getExtension(inputName);   }
  87             else if (type == "accnos")      {   outputFileName =  "bad.accnos";   }
  88             else if (type == "qfile")       {   outputFileName =  "good" + m->getExtension(inputName);   }
  89             else if (type == "alignreport") {   outputFileName =  "good.align.report";                   }
  90             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  91         }
  92         return outputFileName;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "ScreenSeqsCommand", "getOutputFileNameTag");
  96                 exit(1);
  97         }
  98 }
  99
 100 //**********************************************************************************************************************
 101 ScreenSeqsCommand::ScreenSeqsCommand(){
 102         try {
 103                 abort = true; calledHelp = true;
 104                 setParameters();
 105                 vector<string> tempOutNames;
 106                 outputTypes["fasta"] = tempOutNames;
 107                 outputTypes["name"] = tempOutNames;
 108                 outputTypes["group"] = tempOutNames;
 109                 outputTypes["alignreport"] = tempOutNames;
 110                 outputTypes["accnos"] = tempOutNames;
 111                 outputTypes["qfile"] = tempOutNames;
 112                 outputTypes["taxonomy"] = tempOutNames;
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 116                 exit(1);
 117         }
 118 }
 119 //***************************************************************************************************************
 120
 121 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
 122         try {
 123                 abort = false; calledHelp = false;
 124
 125                 //allow user to run help
 126                 if(option == "help") { help(); abort = true; calledHelp = true; }
 127                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 128
 129                 else {
 130                         vector<string> myArray = setParameters();
 131
 132                         OptionParser parser(option);
 133                         map<string,string> parameters = parser.getParameters();
 134
 135                         ValidParameters validParameter("screen.seqs");
 136                         map<string,string>::iterator it;
 137
 138                         //check to make sure all parameters are valid for command
 139                         for (it = parameters.begin(); it != parameters.end(); it++) {
 140                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 141                         }
 142
 143                         //initialize outputTypes
 144                         vector<string> tempOutNames;
 145                         outputTypes["fasta"] = tempOutNames;
 146                         outputTypes["name"] = tempOutNames;
 147                         outputTypes["group"] = tempOutNames;
 148                         outputTypes["alignreport"] = tempOutNames;
 149                         outputTypes["accnos"] = tempOutNames;
 150                         outputTypes["qfile"] = tempOutNames;
 151                         outputTypes["taxonomy"] = tempOutNames;
 152
 153                         //if the user changes the input directory command factory will send this info to us in the output parameter
 154                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 155                         if (inputDir == "not found"){   inputDir = "";          }
 156                         else {
 157                                 string path;
 158                                 it = parameters.find("fasta");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 164                                 }
 165
 166                                 it = parameters.find("group");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 172                                 }
 173
 174                                 it = parameters.find("name");
 175                                 //user has given a template file
 176                                 if(it != parameters.end()){
 177                                         path = m->hasPath(it->second);
 178                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 180                                 }
 181
 182                                 it = parameters.find("alignreport");
 183                                 //user has given a template file
 184                                 if(it != parameters.end()){
 185                                         path = m->hasPath(it->second);
 186                                         //if the user has not given a path then, add inputdir. else leave path alone.
 187                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 188                                 }
 189
 190                                 it = parameters.find("qfile");
 191                                 //user has given a template file
 192                                 if(it != parameters.end()){
 193                                         path = m->hasPath(it->second);
 194                                         //if the user has not given a path then, add inputdir. else leave path alone.
 195                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 196                                 }
 197
 198                                 it = parameters.find("taxonomy");
 199                                 //user has given a template file
 200                                 if(it != parameters.end()){
 201                                         path = m->hasPath(it->second);
 202                                         //if the user has not given a path then, add inputdir. else leave path alone.
 203                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 204                                 }
 205                         }
 206
 207                         //check for required parameters
 208                         fastafile = validParameter.validFile(parameters, "fasta", true);
 209                         if (fastafile == "not found") {
 210                                 fastafile = m->getFastaFile();
 211                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 212                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 213                         }
 214                         else if (fastafile == "not open") { abort = true; }
 215                         else { m->setFastaFile(fastafile); }
 216
 217                         groupfile = validParameter.validFile(parameters, "group", true);
 218                         if (groupfile == "not open") { abort = true; }
 219                         else if (groupfile == "not found") { groupfile = ""; }
 220                         else { m->setGroupFile(groupfile); }
 221
 222                         qualfile = validParameter.validFile(parameters, "qfile", true);
 223                         if (qualfile == "not open") { abort = true; }
 224                         else if (qualfile == "not found") { qualfile = ""; }
 225                         else { m->setQualFile(qualfile); }
 226
 227                         namefile = validParameter.validFile(parameters, "name", true);
 228                         if (namefile == "not open") { namefile = ""; abort = true; }
 229                         else if (namefile == "not found") { namefile = ""; }
 230                         else { m->setNameFile(namefile); }
 231
 232                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 233                         if (alignreport == "not open") { abort = true; }
 234                         else if (alignreport == "not found") { alignreport = ""; }
 235
 236                         taxonomy = validParameter.validFile(parameters, "taxonomy", true);
 237                         if (taxonomy == "not open") { abort = true; }
 238                         else if (taxonomy == "not found") { taxonomy = ""; }
 239
 240                         //if the user changes the output directory command factory will send this info to us in the output parameter
 241                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 242                                 outputDir = "";
 243                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 244                         }
 245
 246                         //check for optional parameter and set defaults
 247                         // ...at some point should added some additional type checking...
 248                         string temp;
 249                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 250                         m->mothurConvert(temp, startPos);
 251
 252                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 253                         m->mothurConvert(temp, endPos);
 254
 255                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 256                         m->mothurConvert(temp, maxAmbig);
 257
 258                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 259                         m->mothurConvert(temp, maxHomoP);
 260
 261                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 262                         m->mothurConvert(temp, minLength);
 263
 264                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 265                         m->mothurConvert(temp, maxLength);
 266
 267                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 268                         m->setProcessors(temp);
 269                         m->mothurConvert(temp, processors);
 270
 271                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 272                         if (temp == "not found"){       temp = "none";          }
 273                         m->splitAtDash(temp, optimize);
 274
 275                         //check for invalid optimize options
 276                         set<string> validOptimizers;
 277                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 278                         for (int i = 0; i < optimize.size(); i++) {
 279                                 if (validOptimizers.count(optimize[i]) == 0) {
 280                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 281                                         optimize.erase(optimize.begin()+i);
 282                                         i--;
 283                                 }
 284                         }
 285
 286                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 287
 288                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 289                         m->mothurConvert(temp, criteria);
 290
 291                         if (namefile == "") {
 292                                 vector<string> files; files.push_back(fastafile);
 293                                 parser.getNameFile(files);
 294                         }
 295                 }
 296
 297         }
 298         catch(exception& e) {
 299                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 300                 exit(1);
 301         }
 302 }
 303 //***************************************************************************************************************
 304
 305 int ScreenSeqsCommand::execute(){
 306         try{
 307
 308                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 309
 310                 //if the user want to optimize we need to know the 90% mark
 311                 vector<unsigned long long> positions;
 312                 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
 313                         //use the namefile to optimize correctly
 314                         if (namefile != "") { nameMap = m->readNames(namefile); }
 315                         getSummary(positions);
 316                 }
 317                 else {
 318                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 319                 positions = m->divideFile(fastafile, processors);
 320                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 321                         #else
 322                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 323                 else {
 324                     int numFastaSeqs = 0;
 325                     positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 326                     if (positions.size() < processors) { processors = positions.size(); }
 327
 328                     //figure out how many sequences you have to process
 329                     int numSeqsPerProcessor = numFastaSeqs / processors;
 330                     for (int i = 0; i < processors; i++) {
 331                         int startIndex =  i * numSeqsPerProcessor;
 332                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 333                         lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 334                     }
 335                 }
 336                         #endif
 337                 }
 338
 339                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 340                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
 341
 342                 int numFastaSeqs = 0;
 343                 set<string> badSeqNames;
 344                 int start = time(NULL);
 345
 346 #ifdef USE_MPI
 347                         int pid, numSeqsPerProcessor;
 348                         int tag = 2001;
 349                         vector<unsigned long long> MPIPos;
 350
 351                         MPI_Status status;
 352                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 353                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 354
 355                         MPI_File inMPI;
 356                         MPI_File outMPIGood;
 357                         MPI_File outMPIBadAccnos;
 358
 359                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 360                         int inMode=MPI_MODE_RDONLY;
 361
 362                         char outGoodFilename[1024];
 363                         strcpy(outGoodFilename, goodSeqFile.c_str());
 364
 365                         char outBadAccnosFilename[1024];
 366                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 367
 368                         char inFileName[1024];
 369                         strcpy(inFileName, fastafile.c_str());
 370
 371                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 372                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 373                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 374
 375                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 376
 377                         if (pid == 0) { //you are the root process
 378
 379                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 380
 381                                 //send file positions to all processes
 382                                 for(int i = 1; i < processors; i++) {
 383                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 384                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 385                                 }
 386
 387                                 //figure out how many sequences you have to align
 388                                 numSeqsPerProcessor = numFastaSeqs / processors;
 389                                 int startIndex =  pid * numSeqsPerProcessor;
 390                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 391
 392                                 //align your part
 393                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 394
 395                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 396
 397                                 for (int i = 1; i < processors; i++) {
 398                                         //get bad lists
 399                                         int badSize;
 400                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 401                                 }
 402                         }else{ //you are a child process
 403                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 404                                 MPIPos.resize(numFastaSeqs+1);
 405                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 406
 407                                 //figure out how many sequences you have to align
 408                                 numSeqsPerProcessor = numFastaSeqs / processors;
 409                                 int startIndex =  pid * numSeqsPerProcessor;
 410                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 411
 412                                 //align your part
 413                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 414
 415                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 416
 417                                 //send bad list
 418                                 int badSize = badSeqNames.size();
 419                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 420                         }
 421
 422                         //close files
 423                         MPI_File_close(&inMPI);
 424                         MPI_File_close(&outMPIGood);
 425                         MPI_File_close(&outMPIBadAccnos);
 426                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 427
 428 #else
 429         if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);       }
 430         else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
 431
 432         if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 433 #endif
 434
 435                 #ifdef USE_MPI
 436                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 437
 438                         if (pid == 0) { //only one process should fix files
 439
 440                                 //read accnos file with all names in it, process 0 just has its names
 441                                 MPI_File inMPIAccnos;
 442                                 MPI_Offset size;
 443
 444                                 char inFileName[1024];
 445                                 strcpy(inFileName, badAccnosFile.c_str());
 446
 447                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 448                                 MPI_File_get_size(inMPIAccnos, &size);
 449
 450                                 char* buffer = new char[size];
 451                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 452
 453                                 string tempBuf = buffer;
 454                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 455                                 istringstream iss (tempBuf,istringstream::in);
 456
 457                                 delete buffer;
 458                                 MPI_File_close(&inMPIAccnos);
 459
 460                                 badSeqNames.clear();
 461                                 string tempName;
 462                                 while (!iss.eof()) {
 463                                         iss >> tempName; m->gobble(iss);
 464                                         badSeqNames.insert(tempName);
 465                                 }
 466                 #endif
 467
 468                 if(namefile != "" && groupfile != "")   {
 469                         screenNameGroupFile(badSeqNames);
 470                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile); return 0; }
 471                 }else if(namefile != "")        {
 472                         screenNameGroupFile(badSeqNames);
 473                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile);  return 0; }
 474                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 475
 476                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 477
 478                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 479                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 480                 if(taxonomy != "")                                              {       screenTaxonomy(badSeqNames);            }
 481
 482                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 483
 484                 #ifdef USE_MPI
 485                         }
 486                 #endif
 487
 488                 m->mothurOutEndLine();
 489                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 490                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 491                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 492                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 493                 m->mothurOutEndLine();
 494                 m->mothurOutEndLine();
 495
 496                 //set fasta file as new current fastafile
 497                 string current = "";
 498                 itTypes = outputTypes.find("fasta");
 499                 if (itTypes != outputTypes.end()) {
 500                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 501                 }
 502
 503                 itTypes = outputTypes.find("name");
 504                 if (itTypes != outputTypes.end()) {
 505                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 506                 }
 507
 508                 itTypes = outputTypes.find("group");
 509                 if (itTypes != outputTypes.end()) {
 510                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 511                 }
 512
 513                 itTypes = outputTypes.find("qfile");
 514                 if (itTypes != outputTypes.end()) {
 515                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 516                 }
 517
 518                 itTypes = outputTypes.find("taxonomy");
 519                 if (itTypes != outputTypes.end()) {
 520                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 521                 }
 522
 523                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 524                 m->mothurOutEndLine();
 525
 526                 return 0;
 527         }
 528         catch(exception& e) {
 529                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 530                 exit(1);
 531         }
 532 }
 533
 534 //***************************************************************************************************************
 535
 536 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 537         try {
 538                 ifstream inputNames;
 539                 m->openInputFile(namefile, inputNames);
 540                 set<string> badSeqGroups;
 541                 string seqName, seqList, group;
 542                 set<string>::iterator it;
 543
 544                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 545                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 546
 547                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 548
 549                 while(!inputNames.eof()){
 550                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 551
 552                         inputNames >> seqName >> seqList;
 553                         it = badSeqNames.find(seqName);
 554
 555                         if(it != badSeqNames.end()){
 556                                 badSeqNames.erase(it);
 557
 558                                 if(namefile != ""){
 559                                         int start = 0;
 560                                         for(int i=0;i<seqList.length();i++){
 561                                                 if(seqList[i] == ','){
 562                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 563                                                         start = i+1;
 564                                                 }
 565                                         }
 566                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 567                                 }
 568                         }
 569                         else{
 570                                 goodNameOut << seqName << '\t' << seqList << endl;
 571                         }
 572                         m->gobble(inputNames);
 573                 }
 574                 inputNames.close();
 575                 goodNameOut.close();
 576
 577                 //we were unable to remove some of the bad sequences
 578                 if (badSeqNames.size() != 0) {
 579                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 580                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 581                                 m->mothurOutEndLine();
 582                         }
 583                 }
 584
 585                 if(groupfile != ""){
 586
 587                         ifstream inputGroups;
 588                         m->openInputFile(groupfile, inputGroups);
 589
 590                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 591                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 592
 593                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 594
 595                         while(!inputGroups.eof()){
 596                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 597
 598                                 inputGroups >> seqName >> group;
 599
 600                                 it = badSeqGroups.find(seqName);
 601
 602                                 if(it != badSeqGroups.end()){
 603                                         badSeqGroups.erase(it);
 604                                 }
 605                                 else{
 606                                         goodGroupOut << seqName << '\t' << group << endl;
 607                                 }
 608                                 m->gobble(inputGroups);
 609                         }
 610                         inputGroups.close();
 611                         goodGroupOut.close();
 612
 613                         //we were unable to remove some of the bad sequences
 614                         if (badSeqGroups.size() != 0) {
 615                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 616                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 617                                         m->mothurOutEndLine();
 618                                 }
 619                         }
 620                 }
 621
 622
 623                 return 0;
 624
 625         }
 626         catch(exception& e) {
 627                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 628                 exit(1);
 629         }
 630 }
 631 //***************************************************************************************************************
 632 int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 633         try {
 634
 635                 vector<int> startPosition;
 636                 vector<int> endPosition;
 637                 vector<int> seqLength;
 638                 vector<int> ambigBases;
 639                 vector<int> longHomoPolymer;
 640
 641         vector<unsigned long long> positions;
 642 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 643                 positions = m->divideFile(fastafile, processors);
 644                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 645 #else
 646                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 647         else {
 648             int numFastaSeqs = 0;
 649             positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 650             if (positions.size() < processors) { processors = positions.size(); }
 651
 652             //figure out how many sequences you have to process
 653             int numSeqsPerProcessor = numFastaSeqs / processors;
 654             for (int i = 0; i < processors; i++) {
 655                 int startIndex =  i * numSeqsPerProcessor;
 656                 if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 657                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 658             }
 659         }
 660 #endif
 661
 662 #ifdef USE_MPI
 663                 int pid;
 664                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 665
 666                 if (pid == 0) {
 667                         driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 668 #else
 669                 int numSeqs = 0;
 670                 //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 671                         if(processors == 1){
 672                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 673                         }else{
 674                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 675                         }
 676
 677                         if (m->control_pressed) {  return 0; }
 678                 //#else
 679                 //      numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 680                 //      if (m->control_pressed) {  return 0; }
 681                 //#endif
 682 #endif
 683                 sort(startPosition.begin(), startPosition.end());
 684                 sort(endPosition.begin(), endPosition.end());
 685                 sort(seqLength.begin(), seqLength.end());
 686                 sort(ambigBases.begin(), ambigBases.end());
 687                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 688
 689                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 690                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 691
 692                 for (int i = 0; i < optimize.size(); i++) {
 693                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 694                         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();}
 695                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 696                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 697                         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(); }
 698                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 699                 }
 700
 701 #ifdef USE_MPI
 702                 }
 703
 704                 MPI_Status status;
 705                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 706                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 707
 708                 if (pid == 0) {
 709                         //send file positions to all processes
 710                         for(int i = 1; i < processors; i++) {
 711                                 MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 712                                 MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 713                                 MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 714                                 MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 715                                 MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 716                                 MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 717                         }
 718                 }else {
 719                         MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 720                         MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 721                         MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 722                         MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 723                         MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 724                         MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 725                 }
 726                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 727 #endif
 728                 return 0;
 729         }
 730         catch(exception& e) {
 731                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 732                 exit(1);
 733         }
 734 }
 735 /**************************************************************************************/
 736 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair filePos) {
 737         try {
 738
 739                 ifstream in;
 740                 m->openInputFile(filename, in);
 741
 742                 in.seekg(filePos.start);
 743
 744                 bool done = false;
 745                 int count = 0;
 746
 747                 while (!done) {
 748
 749                         if (m->control_pressed) { in.close(); return 1; }
 750
 751                         Sequence current(in); m->gobble(in);
 752
 753                         if (current.getName() != "") {
 754                                 int num = 1;
 755                                 if (namefile != "") {
 756                                         //make sure this sequence is in the namefile, else error
 757                                         map<string, int>::iterator it = nameMap.find(current.getName());
 758
 759                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 760                                         else { num = it->second; }
 761                                 }
 762
 763                                 //for each sequence this sequence represents
 764                                 for (int i = 0; i < num; i++) {
 765                                         startPosition.push_back(current.getStartPos());
 766                                         endPosition.push_back(current.getEndPos());
 767                                         seqLength.push_back(current.getNumBases());
 768                                         ambigBases.push_back(current.getAmbigBases());
 769                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 770                                 }
 771
 772                                 count++;
 773                         }
 774                         //if((count) % 100 == 0){       m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();         }
 775                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 776                                 unsigned long long pos = in.tellg();
 777                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
 778                         #else
 779                                 if (in.eof()) { break; }
 780                         #endif
 781
 782                 }
 783
 784                 in.close();
 785
 786                 return count;
 787         }
 788         catch(exception& e) {
 789                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 790                 exit(1);
 791         }
 792 }
 793 /**************************************************************************************************/
 794 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 795         try {
 796
 797         int process = 1;
 798                 int num = 0;
 799                 vector<int> processIDS;
 800
 801 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 802
 803                 //loop through and create all the processes you want
 804                 while (process != processors) {
 805                         int pid = fork();
 806
 807                         if (pid > 0) {
 808                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 809                                 process++;
 810                         }else if (pid == 0){
 811                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 812
 813                                 //pass numSeqs to parent
 814                                 ofstream out;
 815                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 816                                 m->openOutputFile(tempFile, out);
 817
 818                                 out << num << endl;
 819                                 out << startPosition.size() << endl;
 820                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 821                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 822                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 823                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 824                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 825
 826                                 out.close();
 827
 828                                 exit(0);
 829                         }else {
 830                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 831                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 832                                 exit(0);
 833                         }
 834                 }
 835
 836                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 837
 838                 //force parent to wait until all the processes are done
 839                 for (int i=0;i<processIDS.size();i++) {
 840                         int temp = processIDS[i];
 841                         wait(&temp);
 842                 }
 843
 844                 //parent reads in and combine Filter info
 845                 for (int i = 0; i < processIDS.size(); i++) {
 846                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 847                         ifstream in;
 848                         m->openInputFile(tempFilename, in);
 849
 850                         int temp, tempNum;
 851                         in >> tempNum; m->gobble(in); num += tempNum;
 852                         in >> tempNum; m->gobble(in);
 853                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 854                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 855                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 856                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 857                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 858
 859                         in.close();
 860                         m->mothurRemove(tempFilename);
 861                 }
 862
 863
 864 #else
 865         //////////////////////////////////////////////////////////////////////////////////////////////////////
 866                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 867                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 868                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 869                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 870
 871                 vector<sumData*> pDataArray;
 872                 DWORD   dwThreadIdArray[processors-1];
 873                 HANDLE  hThreadArray[processors-1];
 874
 875                 //Create processor worker threads.
 876                 for( int i=0; i<processors-1; i++ ){
 877
 878                         // Allocate memory for thread data.
 879                         sumData* tempSum = new sumData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
 880                         pDataArray.push_back(tempSum);
 881
 882                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 883                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 884                         hThreadArray[i] = CreateThread(NULL, 0, MySumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 885                 }
 886
 887         //do your part
 888                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[processors-1]);
 889
 890                 //Wait until all threads have terminated.
 891                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 892
 893                 //Close all thread handles and free memory allocations.
 894                 for(int i=0; i < pDataArray.size(); i++){
 895                         num += pDataArray[i]->count;
 896             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 897                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 898             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 899             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 900             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 901                         CloseHandle(hThreadArray[i]);
 902                         delete pDataArray[i];
 903                 }
 904
 905 #endif
 906         return num;
 907         }
 908         catch(exception& e) {
 909                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 910                 exit(1);
 911         }
 912 }
 913
 914 //***************************************************************************************************************
 915
 916 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 917         try {
 918                 ifstream inputGroups;
 919                 m->openInputFile(groupfile, inputGroups);
 920                 string seqName, group;
 921                 set<string>::iterator it;
 922
 923                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 924         outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 925                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 926
 927                 while(!inputGroups.eof()){
 928                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 929
 930                         inputGroups >> seqName >> group;
 931                         it = badSeqNames.find(seqName);
 932
 933                         if(it != badSeqNames.end()){
 934                                 badSeqNames.erase(it);
 935                         }
 936                         else{
 937                                 goodGroupOut << seqName << '\t' << group << endl;
 938                         }
 939                         m->gobble(inputGroups);
 940                 }
 941
 942                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
 943
 944                 //we were unable to remove some of the bad sequences
 945                 if (badSeqNames.size() != 0) {
 946                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 947                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 948                                 m->mothurOutEndLine();
 949                         }
 950                 }
 951
 952                 inputGroups.close();
 953                 goodGroupOut.close();
 954
 955                 if (m->control_pressed) { m->mothurRemove(goodGroupFile);   }
 956
 957                 return 0;
 958
 959         }
 960         catch(exception& e) {
 961                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 962                 exit(1);
 963         }
 964 }
 965
 966 //***************************************************************************************************************
 967
 968 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 969         try {
 970                 ifstream inputAlignReport;
 971                 m->openInputFile(alignreport, inputAlignReport);
 972                 string seqName, group;
 973                 set<string>::iterator it;
 974
 975                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
 976                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 977                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 978
 979                 while (!inputAlignReport.eof()) {               //      need to copy header
 980                         char c = inputAlignReport.get();
 981                         goodAlignReportOut << c;
 982                         if (c == 10 || c == 13){        break;  }
 983                 }
 984
 985                 while(!inputAlignReport.eof()){
 986                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
 987
 988                         inputAlignReport >> seqName;
 989                         it = badSeqNames.find(seqName);
 990                         string line;
 991                         while (!inputAlignReport.eof()) {               //      need to copy header
 992                                 char c = inputAlignReport.get();
 993                                 line += c;
 994                                 if (c == 10 || c == 13){        break;  }
 995                         }
 996
 997                         if(it != badSeqNames.end()){
 998                                 badSeqNames.erase(it);
 999                         }
1000                         else{
1001                                 goodAlignReportOut << seqName << '\t' << line;
1002                         }
1003                         m->gobble(inputAlignReport);
1004                 }
1005
1006                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); m->mothurRemove(goodAlignReportFile);  return 0; }
1007
1008                 //we were unable to remove some of the bad sequences
1009                 if (badSeqNames.size() != 0) {
1010                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1011                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
1012                                 m->mothurOutEndLine();
1013                         }
1014                 }
1015
1016                 inputAlignReport.close();
1017                 goodAlignReportOut.close();
1018
1019                 if (m->control_pressed) {  m->mothurRemove(goodAlignReportFile);  return 0; }
1020
1021                 return 0;
1022
1023         }
1024         catch(exception& e) {
1025                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
1026                 exit(1);
1027         }
1028
1029 }
1030 //***************************************************************************************************************
1031
1032 int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
1033         try {
1034                 ifstream input;
1035                 m->openInputFile(taxonomy, input);
1036                 string seqName, tax;
1037                 set<string>::iterator it;
1038
1039                 string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
1040                 outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
1041                 ofstream goodTaxOut;    m->openOutputFile(goodTaxFile, goodTaxOut);
1042
1043                 while(!input.eof()){
1044                         if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1045
1046                         input >> seqName >> tax;
1047                         it = badSeqNames.find(seqName);
1048
1049                         if(it != badSeqNames.end()){ badSeqNames.erase(it); }
1050                         else{
1051                                 goodTaxOut << seqName << '\t' << tax << endl;
1052                         }
1053                         m->gobble(input);
1054                 }
1055
1056                 if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1057
1058                 //we were unable to remove some of the bad sequences
1059                 if (badSeqNames.size() != 0) {
1060                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1061                                 m->mothurOut("Your taxonomy file does not include the sequence " + *it + " please correct.");
1062                                 m->mothurOutEndLine();
1063                         }
1064                 }
1065
1066                 input.close();
1067                 goodTaxOut.close();
1068
1069                 if (m->control_pressed) {  m->mothurRemove(goodTaxFile);  return 0; }
1070
1071                 return 0;
1072
1073         }
1074         catch(exception& e) {
1075                 m->errorOut(e, "ScreenSeqsCommand", "screenTaxonomy");
1076                 exit(1);
1077         }
1078
1079 }
1080 //***************************************************************************************************************
1081
1082 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
1083         try {
1084                 ifstream in;
1085                 m->openInputFile(qualfile, in);
1086                 set<string>::iterator it;
1087
1088                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
1089                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
1090                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
1091
1092                 while(!in.eof()){
1093
1094                         if (m->control_pressed) { goodQual.close(); in.close(); m->mothurRemove(goodQualFile); return 0; }
1095
1096                         string saveName = "";
1097                         string name = "";
1098                         string scores = "";
1099
1100                         in >> name;
1101
1102                         if (name.length() != 0) {
1103                                 saveName = name.substr(1);
1104                                 while (!in.eof())       {
1105                                         char c = in.get();
1106                                         if (c == 10 || c == 13){        break;  }
1107                                         else { name += c; }
1108                                 }
1109                                 m->gobble(in);
1110                         }
1111
1112                         while(in){
1113                                 char letter= in.get();
1114                                 if(letter == '>'){      in.putback(letter);     break;  }
1115                                 else{ scores += letter; }
1116                         }
1117
1118                         m->gobble(in);
1119
1120                         it = badSeqNames.find(saveName);
1121
1122                         if(it != badSeqNames.end()){
1123                                 badSeqNames.erase(it);
1124                         }else{
1125                                 goodQual << name << endl << scores;
1126                         }
1127
1128                         m->gobble(in);
1129                 }
1130
1131                 in.close();
1132                 goodQual.close();
1133
1134                 //we were unable to remove some of the bad sequences
1135                 if (badSeqNames.size() != 0) {
1136                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1137                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
1138                                 m->mothurOutEndLine();
1139                         }
1140                 }
1141
1142                 if (m->control_pressed) {  m->mothurRemove(goodQualFile);  return 0; }
1143
1144                 return 0;
1145
1146         }
1147         catch(exception& e) {
1148                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1149                 exit(1);
1150         }
1151
1152 }
1153 //**********************************************************************************************************************
1154
1155 int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1156         try {
1157                 ofstream goodFile;
1158                 m->openOutputFile(goodFName, goodFile);
1159
1160                 ofstream badAccnosFile;
1161                 m->openOutputFile(badAccnosFName, badAccnosFile);
1162
1163                 ifstream inFASTA;
1164                 m->openInputFile(filename, inFASTA);
1165
1166                 inFASTA.seekg(filePos.start);
1167
1168                 bool done = false;
1169                 int count = 0;
1170
1171                 while (!done) {
1172
1173                         if (m->control_pressed) {  return 0; }
1174
1175                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1176                         if (currSeq.getName() != "") {
1177                                 bool goodSeq = 1;               //      innocent until proven guilty
1178                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1179                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1180                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1181                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1182                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1183                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1184
1185                                 if(goodSeq == 1){
1186                                         currSeq.printSequence(goodFile);
1187                                 }
1188                                 else{
1189                                         badAccnosFile << currSeq.getName() << endl;
1190                                         badSeqNames.insert(currSeq.getName());
1191                                 }
1192                         count++;
1193                         }
1194
1195                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1196                                 unsigned long long pos = inFASTA.tellg();
1197                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
1198                         #else
1199                                 if (inFASTA.eof()) { break; }
1200                         #endif
1201
1202                         //report progress
1203                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1204                 }
1205                 //report progress
1206                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1207
1208
1209                 goodFile.close();
1210                 inFASTA.close();
1211                 badAccnosFile.close();
1212
1213                 return count;
1214         }
1215         catch(exception& e) {
1216                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1217                 exit(1);
1218         }
1219 }
1220 //**********************************************************************************************************************
1221 #ifdef USE_MPI
1222 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
1223         try {
1224                 string outputString = "";
1225                 MPI_Status statusGood;
1226                 MPI_Status statusBadAccnos;
1227                 MPI_Status status;
1228                 int pid;
1229                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1230
1231                 for(int i=0;i<num;i++){
1232
1233                         if (m->control_pressed) {  return 0; }
1234
1235                         //read next sequence
1236                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1237
1238                         char* buf4 = new char[length];
1239                         memcpy(buf4, outputString.c_str(), length);
1240
1241                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1242
1243                         string tempBuf = buf4;  delete buf4;
1244                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1245                         istringstream iss (tempBuf,istringstream::in);
1246
1247                         Sequence currSeq(iss);
1248
1249                         //process seq
1250                         if (currSeq.getName() != "") {
1251                                 bool goodSeq = 1;               //      innocent until proven guilty
1252                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1253                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1254                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1255                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1256                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1257                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1258
1259                                 if(goodSeq == 1){
1260                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1261
1262                                         //print good seq
1263                                         length = outputString.length();
1264                                         char* buf2 = new char[length];
1265                                         memcpy(buf2, outputString.c_str(), length);
1266
1267                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1268                                         delete buf2;
1269                                 }
1270                                 else{
1271
1272                                         badSeqNames.insert(currSeq.getName());
1273
1274                                         //write to bad accnos file
1275                                         outputString = currSeq.getName() + "\n";
1276
1277                                         length = outputString.length();
1278                                         char* buf3 = new char[length];
1279                                         memcpy(buf3, outputString.c_str(), length);
1280
1281                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1282                                         delete buf3;
1283                                 }
1284                         }
1285
1286                         //report progress
1287                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1288                 }
1289
1290                 return 1;
1291         }
1292         catch(exception& e) {
1293                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1294                 exit(1);
1295         }
1296 }
1297 #endif
1298 /**************************************************************************************************/
1299
1300 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1301         try {
1302
1303         vector<int> processIDS;
1304         int process = 1;
1305                 int num = 0;
1306
1307 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1308
1309                 //loop through and create all the processes you want
1310                 while (process != processors) {
1311                         int pid = fork();
1312
1313                         if (pid > 0) {
1314                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1315                                 process++;
1316                         }else if (pid == 0){
1317                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1318
1319                                 //pass numSeqs to parent
1320                                 ofstream out;
1321                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1322                                 m->openOutputFile(tempFile, out);
1323                                 out << num << endl;
1324                                 out.close();
1325
1326                                 exit(0);
1327                         }else {
1328                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1329                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1330                                 exit(0);
1331                         }
1332                 }
1333
1334         num = driver(lines[0], goodFileName, badAccnos, filename, badSeqNames);
1335
1336                 //force parent to wait until all the processes are done
1337                 for (int i=0;i<processIDS.size();i++) {
1338                         int temp = processIDS[i];
1339                         wait(&temp);
1340                 }
1341
1342                 for (int i = 0; i < processIDS.size(); i++) {
1343                         ifstream in;
1344                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1345                         m->openInputFile(tempFile, in);
1346                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1347                         in.close(); m->mothurRemove(tempFile);
1348
1349             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1350             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1351
1352             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1353             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1354                 }
1355
1356         //read badSeqs in because root process doesnt know what other "bad" seqs the children found
1357         ifstream inBad;
1358         int ableToOpen = m->openInputFile(badAccnos, inBad, "no error");
1359
1360         if (ableToOpen == 0) {
1361             badSeqNames.clear();
1362             string tempName;
1363             while (!inBad.eof()) {
1364                 inBad >> tempName; m->gobble(inBad);
1365                 badSeqNames.insert(tempName);
1366             }
1367             inBad.close();
1368         }
1369 #else
1370
1371         //////////////////////////////////////////////////////////////////////////////////////////////////////
1372                 //Windows version shared memory, so be careful when passing variables through the sumScreenData struct.
1373                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1374                 //Taking advantage of shared memory to allow both threads to add info to badSeqNames.
1375                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1376
1377                 vector<sumScreenData*> pDataArray;
1378                 DWORD   dwThreadIdArray[processors-1];
1379                 HANDLE  hThreadArray[processors-1];
1380
1381                 //Create processor worker threads.
1382                 for( int i=0; i<processors-1; i++ ){
1383
1384             string extension = "";
1385             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
1386
1387                         // Allocate memory for thread data.
1388                         sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
1389                         pDataArray.push_back(tempSum);
1390
1391                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1392                         hThreadArray[i] = CreateThread(NULL, 0, MySumScreenThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1393                 }
1394
1395         //do your part
1396         num = driver(lines[processors-1], (goodFileName+toString(processors-1)+".temp"), (badAccnos+toString(processors-1)+".temp"), filename, badSeqNames);
1397         processIDS.push_back(processors-1);
1398
1399                 //Wait until all threads have terminated.
1400                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1401
1402                 //Close all thread handles and free memory allocations.
1403                 for(int i=0; i < pDataArray.size(); i++){
1404                         num += pDataArray[i]->count;
1405             for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it);       }
1406                         CloseHandle(hThreadArray[i]);
1407                         delete pDataArray[i];
1408                 }
1409
1410         for (int i = 0; i < processIDS.size(); i++) {
1411             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1412             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1413
1414             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1415             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1416                 }
1417
1418 #endif
1419
1420         return num;
1421
1422         }
1423         catch(exception& e) {
1424                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1425                 exit(1);
1426         }
1427 }
1428
1429 //***************************************************************************************************************
1430
1431