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
 178                         groupfile = validParameter.validFile(parameters, "group", true);
 179                         if (groupfile == "not open") { abort = true; }
 180                         else if (groupfile == "not found") { groupfile = ""; }
 181
 182                         qualfile = validParameter.validFile(parameters, "qfile", true);
 183                         if (qualfile == "not open") { abort = true; }
 184                         else if (qualfile == "not found") { qualfile = ""; }
 185
 186                         namefile = validParameter.validFile(parameters, "name", true);
 187                         if (namefile == "not open") { namefile = ""; abort = true; }
 188                         else if (namefile == "not found") { namefile = ""; }
 189
 190                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 191                         if (alignreport == "not open") { abort = true; }
 192                         else if (alignreport == "not found") { alignreport = ""; }
 193
 194                         //if the user changes the output directory command factory will send this info to us in the output parameter
 195                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 196                                 outputDir = "";
 197                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 198                         }
 199
 200                         //check for optional parameter and set defaults
 201                         // ...at some point should added some additional type checking...
 202                         string temp;
 203                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 204                         convert(temp, startPos);
 205
 206                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 207                         convert(temp, endPos);
 208
 209                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 210                         convert(temp, maxAmbig);
 211
 212                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 213                         convert(temp, maxHomoP);
 214
 215                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 216                         convert(temp, minLength);
 217
 218                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 219                         convert(temp, maxLength);
 220
 221                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 222                         m->setProcessors(temp);
 223                         convert(temp, processors);
 224
 225                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 226                         if (temp == "not found"){       temp = "none";          }
 227                         m->splitAtDash(temp, optimize);
 228
 229                         //check for invalid optimize options
 230                         set<string> validOptimizers;
 231                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 232                         for (int i = 0; i < optimize.size(); i++) {
 233                                 if (validOptimizers.count(optimize[i]) == 0) {
 234                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 235                                         optimize.erase(optimize.begin()+i);
 236                                         i--;
 237                                 }
 238                         }
 239
 240                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 241
 242                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 243                         convert(temp, criteria);
 244                 }
 245
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 249                 exit(1);
 250         }
 251 }
 252 //***************************************************************************************************************
 253
 254 int ScreenSeqsCommand::execute(){
 255         try{
 256
 257                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 258
 259                 //if the user want to optimize we need to know the 90% mark
 260                 vector<unsigned long int> positions;
 261                 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
 262                         //use the namefile to optimize correctly
 263                         if (namefile != "") { nameMap = m->readNames(namefile); }
 264                         getSummary(positions);
 265                 }
 266                 else {
 267                         positions = m->divideFile(fastafile, processors);
 268                         for (int i = 0; i < (positions.size()-1); i++) {
 269                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 270                         }
 271                 }
 272
 273                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 274                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 275
 276                 int numFastaSeqs = 0;
 277                 set<string> badSeqNames;
 278                 int start = time(NULL);
 279
 280 #ifdef USE_MPI
 281                         int pid, numSeqsPerProcessor;
 282                         int tag = 2001;
 283                         vector<unsigned long int> MPIPos;
 284
 285                         MPI_Status status;
 286                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 287                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 288
 289                         MPI_File inMPI;
 290                         MPI_File outMPIGood;
 291                         MPI_File outMPIBadAccnos;
 292
 293                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 294                         int inMode=MPI_MODE_RDONLY;
 295
 296                         char outGoodFilename[1024];
 297                         strcpy(outGoodFilename, goodSeqFile.c_str());
 298
 299                         char outBadAccnosFilename[1024];
 300                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 301
 302                         char inFileName[1024];
 303                         strcpy(inFileName, fastafile.c_str());
 304
 305                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 306                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 307                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 308
 309                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 310
 311                         if (pid == 0) { //you are the root process
 312
 313                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 314
 315                                 //send file positions to all processes
 316                                 for(int i = 1; i < processors; i++) {
 317                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 318                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 319                                 }
 320
 321                                 //figure out how many sequences you have to align
 322                                 numSeqsPerProcessor = numFastaSeqs / processors;
 323                                 int startIndex =  pid * numSeqsPerProcessor;
 324                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 325                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 326                                 //align your part
 327                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 328                 //cout << pid << " done" << endl;
 329                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 330
 331                                 for (int i = 1; i < processors; i++) {
 332
 333                                         //get bad lists
 334                                         int badSize;
 335                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 336                                         /*for (int j = 0; j < badSize; j++) {
 337                                                 int length;
 338                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 339                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 340                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 341
 342                                                 string tempBuf = buf2;
 343                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 344                                                 delete buf2;
 345
 346                                                 badSeqNames.insert(tempBuf);
 347                                         }*/
 348                                 }
 349                         }else{ //you are a child process
 350                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 351                                 MPIPos.resize(numFastaSeqs+1);
 352                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 353
 354                                 //figure out how many sequences you have to align
 355                                 numSeqsPerProcessor = numFastaSeqs / processors;
 356                                 int startIndex =  pid * numSeqsPerProcessor;
 357                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 358                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 359                                 //align your part
 360                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 361 //cout << pid << " done" << endl;
 362                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 363
 364                                 //send bad list
 365                                 int badSize = badSeqNames.size();
 366                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 367
 368                                 /*
 369                                 set<string>::iterator it;
 370                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 371                                         string name = *it;
 372                                         int length = name.length();
 373                                         char* buf2 = new char[length];
 374                                         memcpy(buf2, name.c_str(), length);
 375
 376                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 377                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 378                                 }*/
 379                         }
 380
 381                         //close files
 382                         MPI_File_close(&inMPI);
 383                         MPI_File_close(&outMPIGood);
 384                         MPI_File_close(&outMPIBadAccnos);
 385                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 386
 387 #else
 388
 389         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 390                         if(processors == 1){
 391                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 392
 393                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 394
 395                         }else{
 396                                 processIDS.resize(0);
 397
 398                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 399
 400                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 401                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 402
 403                                 //append alignment and report files
 404                                 for(int i=1;i<processors;i++){
 405                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 406                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 407
 408                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 409                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 410                                 }
 411
 412                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 413
 414                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 415                                 ifstream inBad;
 416                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 417
 418                                 if (ableToOpen == 0) {
 419                                         badSeqNames.clear();
 420                                         string tempName;
 421                                         while (!inBad.eof()) {
 422                                                 inBad >> tempName; m->gobble(inBad);
 423                                                 badSeqNames.insert(tempName);
 424                                         }
 425                                         inBad.close();
 426                                 }
 427                         }
 428         #else
 429                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 430
 431                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 432
 433         #endif
 434
 435 #endif
 436
 437                 #ifdef USE_MPI
 438                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 439
 440                         if (pid == 0) { //only one process should fix files
 441
 442                                 //read accnos file with all names in it, process 0 just has its names
 443                                 MPI_File inMPIAccnos;
 444                                 MPI_Offset size;
 445
 446                                 char inFileName[1024];
 447                                 strcpy(inFileName, badAccnosFile.c_str());
 448
 449                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 450                                 MPI_File_get_size(inMPIAccnos, &size);
 451
 452                                 char* buffer = new char[size];
 453                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 454
 455                                 string tempBuf = buffer;
 456                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 457                                 istringstream iss (tempBuf,istringstream::in);
 458
 459                                 delete buffer;
 460                                 MPI_File_close(&inMPIAccnos);
 461
 462                                 badSeqNames.clear();
 463                                 string tempName;
 464                                 while (!iss.eof()) {
 465                                         iss >> tempName; m->gobble(iss);
 466                                         badSeqNames.insert(tempName);
 467                                 }
 468                 #endif
 469
 470                 if(namefile != "" && groupfile != "")   {
 471                         screenNameGroupFile(badSeqNames);
 472                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 473                 }else if(namefile != "")        {
 474                         screenNameGroupFile(badSeqNames);
 475                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 476                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 477
 478                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 479
 480                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 481                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 482
 483                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 484
 485                 #ifdef USE_MPI
 486                         }
 487                 #endif
 488
 489                 m->mothurOutEndLine();
 490                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 491                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 492                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 493                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 494                 m->mothurOutEndLine();
 495                 m->mothurOutEndLine();
 496
 497                 //set fasta file as new current fastafile
 498                 string current = "";
 499                 itTypes = outputTypes.find("fasta");
 500                 if (itTypes != outputTypes.end()) {
 501                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 502                 }
 503
 504                 itTypes = outputTypes.find("name");
 505                 if (itTypes != outputTypes.end()) {
 506                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 507                 }
 508
 509                 itTypes = outputTypes.find("group");
 510                 if (itTypes != outputTypes.end()) {
 511                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 512                 }
 513
 514                 itTypes = outputTypes.find("qfile");
 515                 if (itTypes != outputTypes.end()) {
 516                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 517                 }
 518
 519                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 520                 m->mothurOutEndLine();
 521
 522                 return 0;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 526                 exit(1);
 527         }
 528 }
 529
 530 //***************************************************************************************************************
 531
 532 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 533         try {
 534                 ifstream inputNames;
 535                 m->openInputFile(namefile, inputNames);
 536                 set<string> badSeqGroups;
 537                 string seqName, seqList, group;
 538                 set<string>::iterator it;
 539
 540                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 541                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 542
 543                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 544
 545                 while(!inputNames.eof()){
 546                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 547
 548                         inputNames >> seqName >> seqList;
 549                         it = badSeqNames.find(seqName);
 550
 551                         if(it != badSeqNames.end()){
 552                                 badSeqNames.erase(it);
 553
 554                                 if(namefile != ""){
 555                                         int start = 0;
 556                                         for(int i=0;i<seqList.length();i++){
 557                                                 if(seqList[i] == ','){
 558                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 559                                                         start = i+1;
 560                                                 }
 561                                         }
 562                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 563                                 }
 564                         }
 565                         else{
 566                                 goodNameOut << seqName << '\t' << seqList << endl;
 567                         }
 568                         m->gobble(inputNames);
 569                 }
 570                 inputNames.close();
 571                 goodNameOut.close();
 572
 573                 //we were unable to remove some of the bad sequences
 574                 if (badSeqNames.size() != 0) {
 575                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 576                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 577                                 m->mothurOutEndLine();
 578                         }
 579                 }
 580
 581                 if(groupfile != ""){
 582
 583                         ifstream inputGroups;
 584                         m->openInputFile(groupfile, inputGroups);
 585
 586                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 587                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 588
 589                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 590
 591                         while(!inputGroups.eof()){
 592                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 593
 594                                 inputGroups >> seqName >> group;
 595
 596                                 it = badSeqGroups.find(seqName);
 597
 598                                 if(it != badSeqGroups.end()){
 599                                         badSeqGroups.erase(it);
 600                                 }
 601                                 else{
 602                                         goodGroupOut << seqName << '\t' << group << endl;
 603                                 }
 604                                 m->gobble(inputGroups);
 605                         }
 606                         inputGroups.close();
 607                         goodGroupOut.close();
 608
 609                         //we were unable to remove some of the bad sequences
 610                         if (badSeqGroups.size() != 0) {
 611                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 612                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 613                                         m->mothurOutEndLine();
 614                                 }
 615                         }
 616                 }
 617
 618
 619                 return 0;
 620
 621         }
 622         catch(exception& e) {
 623                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 624                 exit(1);
 625         }
 626 }
 627 //***************************************************************************************************************
 628 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 629         try {
 630
 631                 vector<int> startPosition;
 632                 vector<int> endPosition;
 633                 vector<int> seqLength;
 634                 vector<int> ambigBases;
 635                 vector<int> longHomoPolymer;
 636
 637                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 638
 639                 for (int i = 0; i < (positions.size()-1); i++) {
 640                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 641                 }
 642
 643                 int numSeqs = 0;
 644                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 645                         if(processors == 1){
 646                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 647                         }else{
 648                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 649                         }
 650
 651                         if (m->control_pressed) {  return 0; }
 652                 #else
 653                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 654                         if (m->control_pressed) {  return 0; }
 655                 #endif
 656
 657                 sort(startPosition.begin(), startPosition.end());
 658                 sort(endPosition.begin(), endPosition.end());
 659                 sort(seqLength.begin(), seqLength.end());
 660                 sort(ambigBases.begin(), ambigBases.end());
 661                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 662
 663                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 664                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 665
 666                 for (int i = 0; i < optimize.size(); i++) {
 667                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 668                         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();}
 669                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 670                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 671                         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(); }
 672                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 673                 }
 674
 675                 return 0;
 676         }
 677         catch(exception& e) {
 678                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 679                 exit(1);
 680         }
 681 }
 682 /**************************************************************************************/
 683 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 684         try {
 685
 686                 ifstream in;
 687                 m->openInputFile(filename, in);
 688
 689                 in.seekg(filePos->start);
 690
 691                 bool done = false;
 692                 int count = 0;
 693
 694                 while (!done) {
 695
 696                         if (m->control_pressed) { in.close(); return 1; }
 697
 698                         Sequence current(in); m->gobble(in);
 699
 700                         if (current.getName() != "") {
 701                                 int num = 1;
 702                                 if (namefile != "") {
 703                                         //make sure this sequence is in the namefile, else error
 704                                         map<string, int>::iterator it = nameMap.find(current.getName());
 705
 706                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 707                                         else { num = it->second; }
 708                                 }
 709
 710                                 //for each sequence this sequence represents
 711                                 for (int i = 0; i < num; i++) {
 712                                         startPosition.push_back(current.getStartPos());
 713                                         endPosition.push_back(current.getEndPos());
 714                                         seqLength.push_back(current.getNumBases());
 715                                         ambigBases.push_back(current.getAmbigBases());
 716                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 717                                 }
 718
 719                                 count++;
 720                         }
 721
 722                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 723                                 unsigned long int pos = in.tellg();
 724                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 725                         #else
 726                                 if (in.eof()) { break; }
 727                         #endif
 728
 729                 }
 730
 731                 in.close();
 732
 733                 return count;
 734         }
 735         catch(exception& e) {
 736                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 737                 exit(1);
 738         }
 739 }
 740 /**************************************************************************************************/
 741 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 742         try {
 743 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 744                 int process = 1;
 745                 int num = 0;
 746                 processIDS.clear();
 747
 748                 //loop through and create all the processes you want
 749                 while (process != processors) {
 750                         int pid = fork();
 751
 752                         if (pid > 0) {
 753                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 754                                 process++;
 755                         }else if (pid == 0){
 756                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 757
 758                                 //pass numSeqs to parent
 759                                 ofstream out;
 760                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 761                                 m->openOutputFile(tempFile, out);
 762
 763                                 out << num << endl;
 764                                 out << startPosition.size() << endl;
 765                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 766                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 767                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 768                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 769                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 770
 771                                 out.close();
 772
 773                                 exit(0);
 774                         }else {
 775                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 776                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 777                                 exit(0);
 778                         }
 779                 }
 780
 781                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 782
 783                 //force parent to wait until all the processes are done
 784                 for (int i=0;i<processIDS.size();i++) {
 785                         int temp = processIDS[i];
 786                         wait(&temp);
 787                 }
 788
 789                 //parent reads in and combine Filter info
 790                 for (int i = 0; i < processIDS.size(); i++) {
 791                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 792                         ifstream in;
 793                         m->openInputFile(tempFilename, in);
 794
 795                         int temp, tempNum;
 796                         in >> tempNum; m->gobble(in); num += tempNum;
 797                         in >> tempNum; m->gobble(in);
 798                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 799                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 800                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 801                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 802                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 803
 804                         in.close();
 805                         remove(tempFilename.c_str());
 806                 }
 807
 808                 return num;
 809 #endif
 810         }
 811         catch(exception& e) {
 812                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 813                 exit(1);
 814         }
 815 }
 816
 817 //***************************************************************************************************************
 818
 819 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 820         try {
 821                 ifstream inputGroups;
 822                 m->openInputFile(groupfile, inputGroups);
 823                 string seqName, group;
 824                 set<string>::iterator it;
 825
 826                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 827                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 828                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 829
 830                 while(!inputGroups.eof()){
 831                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 832
 833                         inputGroups >> seqName >> group;
 834                         it = badSeqNames.find(seqName);
 835
 836                         if(it != badSeqNames.end()){
 837                                 badSeqNames.erase(it);
 838                         }
 839                         else{
 840                                 goodGroupOut << seqName << '\t' << group << endl;
 841                         }
 842                         m->gobble(inputGroups);
 843                 }
 844
 845                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 846
 847                 //we were unable to remove some of the bad sequences
 848                 if (badSeqNames.size() != 0) {
 849                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 850                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 851                                 m->mothurOutEndLine();
 852                         }
 853                 }
 854
 855                 inputGroups.close();
 856                 goodGroupOut.close();
 857
 858                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 859
 860                 return 0;
 861
 862         }
 863         catch(exception& e) {
 864                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 865                 exit(1);
 866         }
 867 }
 868
 869 //***************************************************************************************************************
 870
 871 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 872         try {
 873                 ifstream inputAlignReport;
 874                 m->openInputFile(alignreport, inputAlignReport);
 875                 string seqName, group;
 876                 set<string>::iterator it;
 877
 878                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 879                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 880                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 881
 882                 while (!inputAlignReport.eof()) {               //      need to copy header
 883                         char c = inputAlignReport.get();
 884                         goodAlignReportOut << c;
 885                         if (c == 10 || c == 13){        break;  }
 886                 }
 887
 888                 while(!inputAlignReport.eof()){
 889                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 890
 891                         inputAlignReport >> seqName;
 892                         it = badSeqNames.find(seqName);
 893                         string line;
 894                         while (!inputAlignReport.eof()) {               //      need to copy header
 895                                 char c = inputAlignReport.get();
 896                                 line += c;
 897                                 if (c == 10 || c == 13){        break;  }
 898                         }
 899
 900                         if(it != badSeqNames.end()){
 901                                 badSeqNames.erase(it);
 902                         }
 903                         else{
 904                                 goodAlignReportOut << seqName << '\t' << line;
 905                         }
 906                         m->gobble(inputAlignReport);
 907                 }
 908
 909                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 910
 911                 //we were unable to remove some of the bad sequences
 912                 if (badSeqNames.size() != 0) {
 913                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 914                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 915                                 m->mothurOutEndLine();
 916                         }
 917                 }
 918
 919                 inputAlignReport.close();
 920                 goodAlignReportOut.close();
 921
 922                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 923
 924                 return 0;
 925
 926         }
 927         catch(exception& e) {
 928                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 929                 exit(1);
 930         }
 931
 932 }
 933 //***************************************************************************************************************
 934
 935 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
 936         try {
 937                 ifstream in;
 938                 m->openInputFile(qualfile, in);
 939                 set<string>::iterator it;
 940
 941                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
 942                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
 943                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
 944
 945                 while(!in.eof()){
 946
 947                         if (m->control_pressed) { goodQual.close(); in.close(); remove(goodQualFile.c_str()); return 0; }
 948
 949                         string saveName = "";
 950                         string name = "";
 951                         string scores = "";
 952
 953                         in >> name;
 954
 955                         if (name.length() != 0) {
 956                                 saveName = name.substr(1);
 957                                 while (!in.eof())       {
 958                                         char c = in.get();
 959                                         if (c == 10 || c == 13){        break;  }
 960                                         else { name += c; }
 961                                 }
 962                                 m->gobble(in);
 963                         }
 964
 965                         while(in){
 966                                 char letter= in.get();
 967                                 if(letter == '>'){      in.putback(letter);     break;  }
 968                                 else{ scores += letter; }
 969                         }
 970
 971                         m->gobble(in);
 972
 973                         it = badSeqNames.find(saveName);
 974
 975                         if(it != badSeqNames.end()){
 976                                 badSeqNames.erase(it);
 977                         }else{
 978                                 goodQual << name << endl << scores;
 979                         }
 980
 981                         m->gobble(in);
 982                 }
 983
 984                 in.close();
 985                 goodQual.close();
 986
 987                 //we were unable to remove some of the bad sequences
 988                 if (badSeqNames.size() != 0) {
 989                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 990                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
 991                                 m->mothurOutEndLine();
 992                         }
 993                 }
 994
 995                 if (m->control_pressed) {  remove(goodQualFile.c_str());  return 0; }
 996
 997                 return 0;
 998
 999         }
1000         catch(exception& e) {
1001                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1002                 exit(1);
1003         }
1004
1005 }
1006 //**********************************************************************************************************************
1007
1008 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1009         try {
1010                 ofstream goodFile;
1011                 m->openOutputFile(goodFName, goodFile);
1012
1013                 ofstream badAccnosFile;
1014                 m->openOutputFile(badAccnosFName, badAccnosFile);
1015
1016                 ifstream inFASTA;
1017                 m->openInputFile(filename, inFASTA);
1018
1019                 inFASTA.seekg(filePos->start);
1020
1021                 bool done = false;
1022                 int count = 0;
1023
1024                 while (!done) {
1025
1026                         if (m->control_pressed) {  return 0; }
1027
1028                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1029                         if (currSeq.getName() != "") {
1030                                 bool goodSeq = 1;               //      innocent until proven guilty
1031                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1032                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1033                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1034                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1035                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1036                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1037
1038                                 if(goodSeq == 1){
1039                                         currSeq.printSequence(goodFile);
1040                                 }
1041                                 else{
1042                                         badAccnosFile << currSeq.getName() << endl;
1043                                         badSeqNames.insert(currSeq.getName());
1044                                 }
1045                         count++;
1046                         }
1047
1048                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1049                                 unsigned long int pos = inFASTA.tellg();
1050                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1051                         #else
1052                                 if (inFASTA.eof()) { break; }
1053                         #endif
1054
1055                         //report progress
1056                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1057                 }
1058                 //report progress
1059                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1060
1061
1062                 goodFile.close();
1063                 inFASTA.close();
1064                 badAccnosFile.close();
1065
1066                 return count;
1067         }
1068         catch(exception& e) {
1069                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1070                 exit(1);
1071         }
1072 }
1073 //**********************************************************************************************************************
1074 #ifdef USE_MPI
1075 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
1076         try {
1077                 string outputString = "";
1078                 MPI_Status statusGood;
1079                 MPI_Status statusBadAccnos;
1080                 MPI_Status status;
1081                 int pid;
1082                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1083
1084                 for(int i=0;i<num;i++){
1085
1086                         if (m->control_pressed) {  return 0; }
1087
1088                         //read next sequence
1089                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1090
1091                         char* buf4 = new char[length];
1092                         memcpy(buf4, outputString.c_str(), length);
1093
1094                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1095
1096                         string tempBuf = buf4;  delete buf4;
1097                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1098                         istringstream iss (tempBuf,istringstream::in);
1099
1100                         Sequence currSeq(iss);
1101
1102                         //process seq
1103                         if (currSeq.getName() != "") {
1104                                 bool goodSeq = 1;               //      innocent until proven guilty
1105                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1106                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1107                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1108                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1109                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1110                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1111
1112                                 if(goodSeq == 1){
1113                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1114
1115                                         //print good seq
1116                                         length = outputString.length();
1117                                         char* buf2 = new char[length];
1118                                         memcpy(buf2, outputString.c_str(), length);
1119
1120                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1121                                         delete buf2;
1122                                 }
1123                                 else{
1124
1125                                         badSeqNames.insert(currSeq.getName());
1126
1127                                         //write to bad accnos file
1128                                         outputString = currSeq.getName() + "\n";
1129
1130                                         length = outputString.length();
1131                                         char* buf3 = new char[length];
1132                                         memcpy(buf3, outputString.c_str(), length);
1133
1134                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1135                                         delete buf3;
1136                                 }
1137                         }
1138
1139                         //report progress
1140                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1141                 }
1142
1143                 return 1;
1144         }
1145         catch(exception& e) {
1146                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1147                 exit(1);
1148         }
1149 }
1150 #endif
1151 /**************************************************************************************************/
1152
1153 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1154         try {
1155 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1156                 int process = 0;
1157                 int num = 0;
1158
1159                 //loop through and create all the processes you want
1160                 while (process != processors) {
1161                         int pid = fork();
1162
1163                         if (pid > 0) {
1164                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1165                                 process++;
1166                         }else if (pid == 0){
1167                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1168
1169                                 //pass numSeqs to parent
1170                                 ofstream out;
1171                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1172                                 m->openOutputFile(tempFile, out);
1173                                 out << num << endl;
1174                                 out.close();
1175
1176                                 exit(0);
1177                         }else {
1178                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1179                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1180                                 exit(0);
1181                         }
1182                 }
1183
1184                 //force parent to wait until all the processes are done
1185                 for (int i=0;i<processors;i++) {
1186                         int temp = processIDS[i];
1187                         wait(&temp);
1188                 }
1189
1190                 for (int i = 0; i < processIDS.size(); i++) {
1191                         ifstream in;
1192                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1193                         m->openInputFile(tempFile, in);
1194                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1195                         in.close(); remove(tempFile.c_str());
1196                 }
1197
1198                 return num;
1199 #endif
1200         }
1201         catch(exception& e) {
1202                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1203                 exit(1);
1204         }
1205 }
1206
1207 //***************************************************************************************************************
1208
1209