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 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 pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  22                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  23                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  24                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  25                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  26                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  28                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  29                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  30                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  31                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  32
  33                 vector<string> myArray;
  34                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  35                 return myArray;
  36         }
  37         catch(exception& e) {
  38                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  39                 exit(1);
  40         }
  41 }
  42 //**********************************************************************************************************************
  43 string ScreenSeqsCommand::getHelpString(){
  44         try {
  45                 string helpString = "";
  46                 helpString += "The screen.seqs command reads a fastafile and creates .....\n";
  47                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, optimize, criteria and processors.\n";
  48                 helpString += "The fasta parameter is required.\n";
  49                 helpString += "The start parameter .... The default is -1.\n";
  50                 helpString += "The end parameter .... The default is -1.\n";
  51                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  52                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  53                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  54                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  55                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  56                 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";
  57                 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";
  58                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  59                 helpString += "The screen.seqs command should be in the following format: \n";
  60                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  61                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  62                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  63                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  64                 return helpString;
  65         }
  66         catch(exception& e) {
  67                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  68                 exit(1);
  69         }
  70 }
  71 //**********************************************************************************************************************
  72 ScreenSeqsCommand::ScreenSeqsCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76                 vector<string> tempOutNames;
  77                 outputTypes["fasta"] = tempOutNames;
  78                 outputTypes["name"] = tempOutNames;
  79                 outputTypes["group"] = tempOutNames;
  80                 outputTypes["alignreport"] = tempOutNames;
  81                 outputTypes["accnos"] = tempOutNames;
  82                 outputTypes["qfile"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
  86                 exit(1);
  87         }
  88 }
  89 //***************************************************************************************************************
  90
  91 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  92         try {
  93                 abort = false; calledHelp = false;
  94
  95                 //allow user to run help
  96                 if(option == "help") { help(); abort = true; calledHelp = true; }
  97                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  98
  99                 else {
 100                         vector<string> myArray = setParameters();
 101
 102                         OptionParser parser(option);
 103                         map<string,string> parameters = parser.getParameters();
 104
 105                         ValidParameters validParameter("screen.seqs");
 106                         map<string,string>::iterator it;
 107
 108                         //check to make sure all parameters are valid for command
 109                         for (it = parameters.begin(); it != parameters.end(); it++) {
 110                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 111                         }
 112
 113                         //initialize outputTypes
 114                         vector<string> tempOutNames;
 115                         outputTypes["fasta"] = tempOutNames;
 116                         outputTypes["name"] = tempOutNames;
 117                         outputTypes["group"] = tempOutNames;
 118                         outputTypes["alignreport"] = tempOutNames;
 119                         outputTypes["accnos"] = tempOutNames;
 120                         outputTypes["qfile"] = tempOutNames;
 121
 122                         //if the user changes the input directory command factory will send this info to us in the output parameter
 123                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 124                         if (inputDir == "not found"){   inputDir = "";          }
 125                         else {
 126                                 string path;
 127                                 it = parameters.find("fasta");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 133                                 }
 134
 135                                 it = parameters.find("group");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 141                                 }
 142
 143                                 it = parameters.find("name");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 149                                 }
 150
 151                                 it = parameters.find("alignreport");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 157                                 }
 158
 159                                 it = parameters.find("qfile");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 165                                 }
 166
 167                         }
 168
 169                         //check for required parameters
 170                         fastafile = validParameter.validFile(parameters, "fasta", true);
 171                         if (fastafile == "not found") {
 172                                 fastafile = m->getFastaFile();
 173                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 174                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 175                         }
 176                         else if (fastafile == "not open") { abort = true; }
 177                         else { m->setFastaFile(fastafile); }
 178
 179                         groupfile = validParameter.validFile(parameters, "group", true);
 180                         if (groupfile == "not open") { abort = true; }
 181                         else if (groupfile == "not found") { groupfile = ""; }
 182                         else { m->setGroupFile(groupfile); }
 183
 184                         qualfile = validParameter.validFile(parameters, "qfile", true);
 185                         if (qualfile == "not open") { abort = true; }
 186                         else if (qualfile == "not found") { qualfile = ""; }
 187                         else { m->setQualFile(qualfile); }
 188
 189                         namefile = validParameter.validFile(parameters, "name", true);
 190                         if (namefile == "not open") { namefile = ""; abort = true; }
 191                         else if (namefile == "not found") { namefile = ""; }
 192                         else { m->setNameFile(namefile); }
 193
 194                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 195                         if (alignreport == "not open") { abort = true; }
 196                         else if (alignreport == "not found") { alignreport = ""; }
 197
 198                         //if the user changes the output directory command factory will send this info to us in the output parameter
 199                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 200                                 outputDir = "";
 201                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 202                         }
 203
 204                         //check for optional parameter and set defaults
 205                         // ...at some point should added some additional type checking...
 206                         string temp;
 207                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 208                         convert(temp, startPos);
 209
 210                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 211                         convert(temp, endPos);
 212
 213                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 214                         convert(temp, maxAmbig);
 215
 216                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 217                         convert(temp, maxHomoP);
 218
 219                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 220                         convert(temp, minLength);
 221
 222                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 223                         convert(temp, maxLength);
 224
 225                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 226                         m->setProcessors(temp);
 227                         convert(temp, processors);
 228
 229                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 230                         if (temp == "not found"){       temp = "none";          }
 231                         m->splitAtDash(temp, optimize);
 232
 233                         //check for invalid optimize options
 234                         set<string> validOptimizers;
 235                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 236                         for (int i = 0; i < optimize.size(); i++) {
 237                                 if (validOptimizers.count(optimize[i]) == 0) {
 238                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 239                                         optimize.erase(optimize.begin()+i);
 240                                         i--;
 241                                 }
 242                         }
 243
 244                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 245
 246                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 247                         convert(temp, criteria);
 248                 }
 249
 250         }
 251         catch(exception& e) {
 252                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 253                 exit(1);
 254         }
 255 }
 256 //***************************************************************************************************************
 257
 258 int ScreenSeqsCommand::execute(){
 259         try{
 260
 261                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 262
 263                 //if the user want to optimize we need to know the 90% mark
 264                 vector<unsigned long int> positions;
 265                 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
 266                         //use the namefile to optimize correctly
 267                         if (namefile != "") { nameMap = m->readNames(namefile); }
 268                         getSummary(positions);
 269                 }
 270                 else {
 271                         positions = m->divideFile(fastafile, processors);
 272                         for (int i = 0; i < (positions.size()-1); i++) {
 273                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 274                         }
 275                 }
 276
 277                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 278                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 279
 280                 int numFastaSeqs = 0;
 281                 set<string> badSeqNames;
 282                 int start = time(NULL);
 283
 284 #ifdef USE_MPI
 285                         int pid, numSeqsPerProcessor;
 286                         int tag = 2001;
 287                         vector<unsigned long int> MPIPos;
 288
 289                         MPI_Status status;
 290                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 291                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 292
 293                         MPI_File inMPI;
 294                         MPI_File outMPIGood;
 295                         MPI_File outMPIBadAccnos;
 296
 297                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 298                         int inMode=MPI_MODE_RDONLY;
 299
 300                         char outGoodFilename[1024];
 301                         strcpy(outGoodFilename, goodSeqFile.c_str());
 302
 303                         char outBadAccnosFilename[1024];
 304                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 305
 306                         char inFileName[1024];
 307                         strcpy(inFileName, fastafile.c_str());
 308
 309                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 310                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 311                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 312
 313                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 314
 315                         if (pid == 0) { //you are the root process
 316
 317                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 318
 319                                 //send file positions to all processes
 320                                 for(int i = 1; i < processors; i++) {
 321                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 322                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 323                                 }
 324
 325                                 //figure out how many sequences you have to align
 326                                 numSeqsPerProcessor = numFastaSeqs / processors;
 327                                 int startIndex =  pid * numSeqsPerProcessor;
 328                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 329                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 330                                 //align your part
 331                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 332                 //cout << pid << " done" << endl;
 333                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 334
 335                                 for (int i = 1; i < processors; i++) {
 336
 337                                         //get bad lists
 338                                         int badSize;
 339                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 340                                         /*for (int j = 0; j < badSize; j++) {
 341                                                 int length;
 342                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 343                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 344                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 345
 346                                                 string tempBuf = buf2;
 347                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 348                                                 delete buf2;
 349
 350                                                 badSeqNames.insert(tempBuf);
 351                                         }*/
 352                                 }
 353                         }else{ //you are a child process
 354                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 355                                 MPIPos.resize(numFastaSeqs+1);
 356                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 357
 358                                 //figure out how many sequences you have to align
 359                                 numSeqsPerProcessor = numFastaSeqs / processors;
 360                                 int startIndex =  pid * numSeqsPerProcessor;
 361                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 362                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 363                                 //align your part
 364                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 365 //cout << pid << " done" << endl;
 366                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 367
 368                                 //send bad list
 369                                 int badSize = badSeqNames.size();
 370                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 371
 372                                 /*
 373                                 set<string>::iterator it;
 374                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 375                                         string name = *it;
 376                                         int length = name.length();
 377                                         char* buf2 = new char[length];
 378                                         memcpy(buf2, name.c_str(), length);
 379
 380                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 381                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 382                                 }*/
 383                         }
 384
 385                         //close files
 386                         MPI_File_close(&inMPI);
 387                         MPI_File_close(&outMPIGood);
 388                         MPI_File_close(&outMPIBadAccnos);
 389                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 390
 391 #else
 392
 393         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 394                         if(processors == 1){
 395                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 396
 397                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 398
 399                         }else{
 400                                 processIDS.resize(0);
 401
 402                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 403
 404                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 405                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 406
 407                                 //append alignment and report files
 408                                 for(int i=1;i<processors;i++){
 409                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 410                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 411
 412                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 413                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 414                                 }
 415
 416                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 417
 418                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 419                                 ifstream inBad;
 420                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 421
 422                                 if (ableToOpen == 0) {
 423                                         badSeqNames.clear();
 424                                         string tempName;
 425                                         while (!inBad.eof()) {
 426                                                 inBad >> tempName; m->gobble(inBad);
 427                                                 badSeqNames.insert(tempName);
 428                                         }
 429                                         inBad.close();
 430                                 }
 431                         }
 432         #else
 433                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 434
 435                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 436
 437         #endif
 438
 439 #endif
 440
 441                 #ifdef USE_MPI
 442                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 443
 444                         if (pid == 0) { //only one process should fix files
 445
 446                                 //read accnos file with all names in it, process 0 just has its names
 447                                 MPI_File inMPIAccnos;
 448                                 MPI_Offset size;
 449
 450                                 char inFileName[1024];
 451                                 strcpy(inFileName, badAccnosFile.c_str());
 452
 453                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 454                                 MPI_File_get_size(inMPIAccnos, &size);
 455
 456                                 char* buffer = new char[size];
 457                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 458
 459                                 string tempBuf = buffer;
 460                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 461                                 istringstream iss (tempBuf,istringstream::in);
 462
 463                                 delete buffer;
 464                                 MPI_File_close(&inMPIAccnos);
 465
 466                                 badSeqNames.clear();
 467                                 string tempName;
 468                                 while (!iss.eof()) {
 469                                         iss >> tempName; m->gobble(iss);
 470                                         badSeqNames.insert(tempName);
 471                                 }
 472                 #endif
 473
 474                 if(namefile != "" && groupfile != "")   {
 475                         screenNameGroupFile(badSeqNames);
 476                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 477                 }else if(namefile != "")        {
 478                         screenNameGroupFile(badSeqNames);
 479                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 480                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 481
 482                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 483
 484                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 485                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 486
 487                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 488
 489                 #ifdef USE_MPI
 490                         }
 491                 #endif
 492
 493                 m->mothurOutEndLine();
 494                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 495                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 496                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 497                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 498                 m->mothurOutEndLine();
 499                 m->mothurOutEndLine();
 500
 501                 //set fasta file as new current fastafile
 502                 string current = "";
 503                 itTypes = outputTypes.find("fasta");
 504                 if (itTypes != outputTypes.end()) {
 505                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 506                 }
 507
 508                 itTypes = outputTypes.find("name");
 509                 if (itTypes != outputTypes.end()) {
 510                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 511                 }
 512
 513                 itTypes = outputTypes.find("group");
 514                 if (itTypes != outputTypes.end()) {
 515                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 516                 }
 517
 518                 itTypes = outputTypes.find("qfile");
 519                 if (itTypes != outputTypes.end()) {
 520                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(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)) + "good" + m->getExtension(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(); remove(goodNameFile.c_str());  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)) + "good" + m->getExtension(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(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); 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 int>& 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 int> positions = m->divideFile(fastafile, processors);
 642
 643                 for (int i = 0; i < (positions.size()-1); i++) {
 644                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 645                 }
 646
 647                 int numSeqs = 0;
 648                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 649                         if(processors == 1){
 650                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 651                         }else{
 652                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 653                         }
 654
 655                         if (m->control_pressed) {  return 0; }
 656                 #else
 657                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 658                         if (m->control_pressed) {  return 0; }
 659                 #endif
 660
 661                 sort(startPosition.begin(), startPosition.end());
 662                 sort(endPosition.begin(), endPosition.end());
 663                 sort(seqLength.begin(), seqLength.end());
 664                 sort(ambigBases.begin(), ambigBases.end());
 665                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 666
 667                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 668                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 669
 670                 for (int i = 0; i < optimize.size(); i++) {
 671                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 672                         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();}
 673                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 674                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 675                         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(); }
 676                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 677                 }
 678
 679                 return 0;
 680         }
 681         catch(exception& e) {
 682                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 683                 exit(1);
 684         }
 685 }
 686 /**************************************************************************************/
 687 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 688         try {
 689
 690                 ifstream in;
 691                 m->openInputFile(filename, in);
 692
 693                 in.seekg(filePos->start);
 694
 695                 bool done = false;
 696                 int count = 0;
 697
 698                 while (!done) {
 699
 700                         if (m->control_pressed) { in.close(); return 1; }
 701
 702                         Sequence current(in); m->gobble(in);
 703
 704                         if (current.getName() != "") {
 705                                 int num = 1;
 706                                 if (namefile != "") {
 707                                         //make sure this sequence is in the namefile, else error
 708                                         map<string, int>::iterator it = nameMap.find(current.getName());
 709
 710                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 711                                         else { num = it->second; }
 712                                 }
 713
 714                                 //for each sequence this sequence represents
 715                                 for (int i = 0; i < num; i++) {
 716                                         startPosition.push_back(current.getStartPos());
 717                                         endPosition.push_back(current.getEndPos());
 718                                         seqLength.push_back(current.getNumBases());
 719                                         ambigBases.push_back(current.getAmbigBases());
 720                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 721                                 }
 722
 723                                 count++;
 724                         }
 725
 726                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 727                                 unsigned long int pos = in.tellg();
 728                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 729                         #else
 730                                 if (in.eof()) { break; }
 731                         #endif
 732
 733                 }
 734
 735                 in.close();
 736
 737                 return count;
 738         }
 739         catch(exception& e) {
 740                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 741                 exit(1);
 742         }
 743 }
 744 /**************************************************************************************************/
 745 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 746         try {
 747 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 748                 int process = 1;
 749                 int num = 0;
 750                 processIDS.clear();
 751
 752                 //loop through and create all the processes you want
 753                 while (process != processors) {
 754                         int pid = fork();
 755
 756                         if (pid > 0) {
 757                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 758                                 process++;
 759                         }else if (pid == 0){
 760                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 761
 762                                 //pass numSeqs to parent
 763                                 ofstream out;
 764                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 765                                 m->openOutputFile(tempFile, out);
 766
 767                                 out << num << endl;
 768                                 out << startPosition.size() << endl;
 769                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 770                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 771                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 772                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 773                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 774
 775                                 out.close();
 776
 777                                 exit(0);
 778                         }else {
 779                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 780                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 781                                 exit(0);
 782                         }
 783                 }
 784
 785                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 786
 787                 //force parent to wait until all the processes are done
 788                 for (int i=0;i<processIDS.size();i++) {
 789                         int temp = processIDS[i];
 790                         wait(&temp);
 791                 }
 792
 793                 //parent reads in and combine Filter info
 794                 for (int i = 0; i < processIDS.size(); i++) {
 795                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 796                         ifstream in;
 797                         m->openInputFile(tempFilename, in);
 798
 799                         int temp, tempNum;
 800                         in >> tempNum; m->gobble(in); num += tempNum;
 801                         in >> tempNum; m->gobble(in);
 802                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 803                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 804                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 805                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 806                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 807
 808                         in.close();
 809                         remove(tempFilename.c_str());
 810                 }
 811
 812                 return num;
 813 #endif
 814         }
 815         catch(exception& e) {
 816                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 817                 exit(1);
 818         }
 819 }
 820
 821 //***************************************************************************************************************
 822
 823 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 824         try {
 825                 ifstream inputGroups;
 826                 m->openInputFile(groupfile, inputGroups);
 827                 string seqName, group;
 828                 set<string>::iterator it;
 829
 830                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 831                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 832                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 833
 834                 while(!inputGroups.eof()){
 835                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 836
 837                         inputGroups >> seqName >> group;
 838                         it = badSeqNames.find(seqName);
 839
 840                         if(it != badSeqNames.end()){
 841                                 badSeqNames.erase(it);
 842                         }
 843                         else{
 844                                 goodGroupOut << seqName << '\t' << group << endl;
 845                         }
 846                         m->gobble(inputGroups);
 847                 }
 848
 849                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 850
 851                 //we were unable to remove some of the bad sequences
 852                 if (badSeqNames.size() != 0) {
 853                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 854                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 855                                 m->mothurOutEndLine();
 856                         }
 857                 }
 858
 859                 inputGroups.close();
 860                 goodGroupOut.close();
 861
 862                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 863
 864                 return 0;
 865
 866         }
 867         catch(exception& e) {
 868                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 869                 exit(1);
 870         }
 871 }
 872
 873 //***************************************************************************************************************
 874
 875 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 876         try {
 877                 ifstream inputAlignReport;
 878                 m->openInputFile(alignreport, inputAlignReport);
 879                 string seqName, group;
 880                 set<string>::iterator it;
 881
 882                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 883                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 884                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 885
 886                 while (!inputAlignReport.eof()) {               //      need to copy header
 887                         char c = inputAlignReport.get();
 888                         goodAlignReportOut << c;
 889                         if (c == 10 || c == 13){        break;  }
 890                 }
 891
 892                 while(!inputAlignReport.eof()){
 893                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 894
 895                         inputAlignReport >> seqName;
 896                         it = badSeqNames.find(seqName);
 897                         string line;
 898                         while (!inputAlignReport.eof()) {               //      need to copy header
 899                                 char c = inputAlignReport.get();
 900                                 line += c;
 901                                 if (c == 10 || c == 13){        break;  }
 902                         }
 903
 904                         if(it != badSeqNames.end()){
 905                                 badSeqNames.erase(it);
 906                         }
 907                         else{
 908                                 goodAlignReportOut << seqName << '\t' << line;
 909                         }
 910                         m->gobble(inputAlignReport);
 911                 }
 912
 913                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 914
 915                 //we were unable to remove some of the bad sequences
 916                 if (badSeqNames.size() != 0) {
 917                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 918                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 919                                 m->mothurOutEndLine();
 920                         }
 921                 }
 922
 923                 inputAlignReport.close();
 924                 goodAlignReportOut.close();
 925
 926                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 927
 928                 return 0;
 929
 930         }
 931         catch(exception& e) {
 932                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 933                 exit(1);
 934         }
 935
 936 }
 937 //***************************************************************************************************************
 938
 939 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
 940         try {
 941                 ifstream in;
 942                 m->openInputFile(qualfile, in);
 943                 set<string>::iterator it;
 944
 945                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
 946                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
 947                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
 948
 949                 while(!in.eof()){
 950
 951                         if (m->control_pressed) { goodQual.close(); in.close(); remove(goodQualFile.c_str()); return 0; }
 952
 953                         string saveName = "";
 954                         string name = "";
 955                         string scores = "";
 956
 957                         in >> name;
 958
 959                         if (name.length() != 0) {
 960                                 saveName = name.substr(1);
 961                                 while (!in.eof())       {
 962                                         char c = in.get();
 963                                         if (c == 10 || c == 13){        break;  }
 964                                         else { name += c; }
 965                                 }
 966                                 m->gobble(in);
 967                         }
 968
 969                         while(in){
 970                                 char letter= in.get();
 971                                 if(letter == '>'){      in.putback(letter);     break;  }
 972                                 else{ scores += letter; }
 973                         }
 974
 975                         m->gobble(in);
 976
 977                         it = badSeqNames.find(saveName);
 978
 979                         if(it != badSeqNames.end()){
 980                                 badSeqNames.erase(it);
 981                         }else{
 982                                 goodQual << name << endl << scores;
 983                         }
 984
 985                         m->gobble(in);
 986                 }
 987
 988                 in.close();
 989                 goodQual.close();
 990
 991                 //we were unable to remove some of the bad sequences
 992                 if (badSeqNames.size() != 0) {
 993                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 994                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
 995                                 m->mothurOutEndLine();
 996                         }
 997                 }
 998
 999                 if (m->control_pressed) {  remove(goodQualFile.c_str());  return 0; }
1000
1001                 return 0;
1002
1003         }
1004         catch(exception& e) {
1005                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1006                 exit(1);
1007         }
1008
1009 }
1010 //**********************************************************************************************************************
1011
1012 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1013         try {
1014                 ofstream goodFile;
1015                 m->openOutputFile(goodFName, goodFile);
1016
1017                 ofstream badAccnosFile;
1018                 m->openOutputFile(badAccnosFName, badAccnosFile);
1019
1020                 ifstream inFASTA;
1021                 m->openInputFile(filename, inFASTA);
1022
1023                 inFASTA.seekg(filePos->start);
1024
1025                 bool done = false;
1026                 int count = 0;
1027
1028                 while (!done) {
1029
1030                         if (m->control_pressed) {  return 0; }
1031
1032                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1033                         if (currSeq.getName() != "") {
1034                                 bool goodSeq = 1;               //      innocent until proven guilty
1035                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1036                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1037                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1038                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1039                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1040                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1041
1042                                 if(goodSeq == 1){
1043                                         currSeq.printSequence(goodFile);
1044                                 }
1045                                 else{
1046                                         badAccnosFile << currSeq.getName() << endl;
1047                                         badSeqNames.insert(currSeq.getName());
1048                                 }
1049                         count++;
1050                         }
1051
1052                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1053                                 unsigned long int pos = inFASTA.tellg();
1054                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1055                         #else
1056                                 if (inFASTA.eof()) { break; }
1057                         #endif
1058
1059                         //report progress
1060                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1061                 }
1062                 //report progress
1063                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1064
1065
1066                 goodFile.close();
1067                 inFASTA.close();
1068                 badAccnosFile.close();
1069
1070                 return count;
1071         }
1072         catch(exception& e) {
1073                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1074                 exit(1);
1075         }
1076 }
1077 //**********************************************************************************************************************
1078 #ifdef USE_MPI
1079 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
1080         try {
1081                 string outputString = "";
1082                 MPI_Status statusGood;
1083                 MPI_Status statusBadAccnos;
1084                 MPI_Status status;
1085                 int pid;
1086                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1087
1088                 for(int i=0;i<num;i++){
1089
1090                         if (m->control_pressed) {  return 0; }
1091
1092                         //read next sequence
1093                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1094
1095                         char* buf4 = new char[length];
1096                         memcpy(buf4, outputString.c_str(), length);
1097
1098                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1099
1100                         string tempBuf = buf4;  delete buf4;
1101                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1102                         istringstream iss (tempBuf,istringstream::in);
1103
1104                         Sequence currSeq(iss);
1105
1106                         //process seq
1107                         if (currSeq.getName() != "") {
1108                                 bool goodSeq = 1;               //      innocent until proven guilty
1109                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1110                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1111                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1112                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1113                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1114                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1115
1116                                 if(goodSeq == 1){
1117                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1118
1119                                         //print good seq
1120                                         length = outputString.length();
1121                                         char* buf2 = new char[length];
1122                                         memcpy(buf2, outputString.c_str(), length);
1123
1124                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1125                                         delete buf2;
1126                                 }
1127                                 else{
1128
1129                                         badSeqNames.insert(currSeq.getName());
1130
1131                                         //write to bad accnos file
1132                                         outputString = currSeq.getName() + "\n";
1133
1134                                         length = outputString.length();
1135                                         char* buf3 = new char[length];
1136                                         memcpy(buf3, outputString.c_str(), length);
1137
1138                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1139                                         delete buf3;
1140                                 }
1141                         }
1142
1143                         //report progress
1144                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1145                 }
1146
1147                 return 1;
1148         }
1149         catch(exception& e) {
1150                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1151                 exit(1);
1152         }
1153 }
1154 #endif
1155 /**************************************************************************************************/
1156
1157 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1158         try {
1159 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1160                 int process = 0;
1161                 int num = 0;
1162
1163                 //loop through and create all the processes you want
1164                 while (process != processors) {
1165                         int pid = fork();
1166
1167                         if (pid > 0) {
1168                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1169                                 process++;
1170                         }else if (pid == 0){
1171                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1172
1173                                 //pass numSeqs to parent
1174                                 ofstream out;
1175                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1176                                 m->openOutputFile(tempFile, out);
1177                                 out << num << endl;
1178                                 out.close();
1179
1180                                 exit(0);
1181                         }else {
1182                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1183                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1184                                 exit(0);
1185                         }
1186                 }
1187
1188                 //force parent to wait until all the processes are done
1189                 for (int i=0;i<processors;i++) {
1190                         int temp = processIDS[i];
1191                         wait(&temp);
1192                 }
1193
1194                 for (int i = 0; i < processIDS.size(); i++) {
1195                         ifstream in;
1196                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1197                         m->openInputFile(tempFile, in);
1198                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1199                         in.close(); remove(tempFile.c_str());
1200                 }
1201
1202                 return num;
1203 #endif
1204         }
1205         catch(exception& e) {
1206                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1207                 exit(1);
1208         }
1209 }
1210
1211 //***************************************************************************************************************
1212
1213