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
  98                 else {
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string,string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter("screen.seqs");
 105                         map<string,string>::iterator it;
 106
 107                         //check to make sure all parameters are valid for command
 108                         for (it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112                         //initialize outputTypes
 113                         vector<string> tempOutNames;
 114                         outputTypes["fasta"] = tempOutNames;
 115                         outputTypes["name"] = tempOutNames;
 116                         outputTypes["group"] = tempOutNames;
 117                         outputTypes["alignreport"] = tempOutNames;
 118                         outputTypes["accnos"] = tempOutNames;
 119                         outputTypes["qfile"] = tempOutNames;
 120
 121                         //if the user changes the input directory command factory will send this info to us in the output parameter
 122                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 123                         if (inputDir == "not found"){   inputDir = "";          }
 124                         else {
 125                                 string path;
 126                                 it = parameters.find("fasta");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 132                                 }
 133
 134                                 it = parameters.find("group");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 140                                 }
 141
 142                                 it = parameters.find("name");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 148                                 }
 149
 150                                 it = parameters.find("alignreport");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 156                                 }
 157
 158                                 it = parameters.find("qfile");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 164                                 }
 165
 166                         }
 167
 168                         //check for required parameters
 169                         fastafile = validParameter.validFile(parameters, "fasta", true);
 170                         if (fastafile == "not found") {
 171                                 fastafile = m->getFastaFile();
 172                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 173                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 174                         }
 175                         else if (fastafile == "not open") { abort = true; }
 176
 177                         groupfile = validParameter.validFile(parameters, "group", true);
 178                         if (groupfile == "not open") { abort = true; }
 179                         else if (groupfile == "not found") { groupfile = ""; }
 180
 181                         qualfile = validParameter.validFile(parameters, "qfile", true);
 182                         if (qualfile == "not open") { abort = true; }
 183                         else if (qualfile == "not found") { qualfile = ""; }
 184
 185                         namefile = validParameter.validFile(parameters, "name", true);
 186                         if (namefile == "not open") { namefile = ""; abort = true; }
 187                         else if (namefile == "not found") { namefile = ""; }
 188
 189                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 190                         if (alignreport == "not open") { abort = true; }
 191                         else if (alignreport == "not found") { alignreport = ""; }
 192
 193                         //if the user changes the output directory command factory will send this info to us in the output parameter
 194                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 195                                 outputDir = "";
 196                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 197                         }
 198
 199                         //check for optional parameter and set defaults
 200                         // ...at some point should added some additional type checking...
 201                         string temp;
 202                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 203                         convert(temp, startPos);
 204
 205                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 206                         convert(temp, endPos);
 207
 208                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 209                         convert(temp, maxAmbig);
 210
 211                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 212                         convert(temp, maxHomoP);
 213
 214                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 215                         convert(temp, minLength);
 216
 217                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 218                         convert(temp, maxLength);
 219
 220                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 221                         m->setProcessors(temp);
 222                         convert(temp, processors);
 223
 224                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 225                         if (temp == "not found"){       temp = "none";          }
 226                         m->splitAtDash(temp, optimize);
 227
 228                         //check for invalid optimize options
 229                         set<string> validOptimizers;
 230                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 231                         for (int i = 0; i < optimize.size(); i++) {
 232                                 if (validOptimizers.count(optimize[i]) == 0) {
 233                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 234                                         optimize.erase(optimize.begin()+i);
 235                                         i--;
 236                                 }
 237                         }
 238
 239                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 240
 241                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 242                         convert(temp, criteria);
 243                 }
 244
 245         }
 246         catch(exception& e) {
 247                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 248                 exit(1);
 249         }
 250 }
 251 //***************************************************************************************************************
 252
 253 int ScreenSeqsCommand::execute(){
 254         try{
 255
 256                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 257
 258                 //if the user want to optimize we need to know the 90% mark
 259                 vector<unsigned long int> positions;
 260                 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
 261                         //use the namefile to optimize correctly
 262                         if (namefile != "") { nameMap = m->readNames(namefile); }
 263                         getSummary(positions);
 264                 }
 265                 else {
 266                         positions = m->divideFile(fastafile, processors);
 267                         for (int i = 0; i < (positions.size()-1); i++) {
 268                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 269                         }
 270                 }
 271
 272                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 273                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 274
 275                 int numFastaSeqs = 0;
 276                 set<string> badSeqNames;
 277                 int start = time(NULL);
 278
 279 #ifdef USE_MPI
 280                         int pid, numSeqsPerProcessor;
 281                         int tag = 2001;
 282                         vector<unsigned long int> MPIPos;
 283
 284                         MPI_Status status;
 285                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 286                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 287
 288                         MPI_File inMPI;
 289                         MPI_File outMPIGood;
 290                         MPI_File outMPIBadAccnos;
 291
 292                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 293                         int inMode=MPI_MODE_RDONLY;
 294
 295                         char outGoodFilename[1024];
 296                         strcpy(outGoodFilename, goodSeqFile.c_str());
 297
 298                         char outBadAccnosFilename[1024];
 299                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 300
 301                         char inFileName[1024];
 302                         strcpy(inFileName, fastafile.c_str());
 303
 304                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 305                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 306                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 307
 308                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 309
 310                         if (pid == 0) { //you are the root process
 311
 312                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 313
 314                                 //send file positions to all processes
 315                                 for(int i = 1; i < processors; i++) {
 316                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 317                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 318                                 }
 319
 320                                 //figure out how many sequences you have to align
 321                                 numSeqsPerProcessor = numFastaSeqs / processors;
 322                                 int startIndex =  pid * numSeqsPerProcessor;
 323                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 324                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 325                                 //align your part
 326                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 327                 //cout << pid << " done" << endl;
 328                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 329
 330                                 for (int i = 1; i < processors; i++) {
 331
 332                                         //get bad lists
 333                                         int badSize;
 334                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 335                                         /*for (int j = 0; j < badSize; j++) {
 336                                                 int length;
 337                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 338                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 339                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 340
 341                                                 string tempBuf = buf2;
 342                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 343                                                 delete buf2;
 344
 345                                                 badSeqNames.insert(tempBuf);
 346                                         }*/
 347                                 }
 348                         }else{ //you are a child process
 349                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 350                                 MPIPos.resize(numFastaSeqs+1);
 351                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 352
 353                                 //figure out how many sequences you have to align
 354                                 numSeqsPerProcessor = numFastaSeqs / processors;
 355                                 int startIndex =  pid * numSeqsPerProcessor;
 356                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 357                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 358                                 //align your part
 359                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 360 //cout << pid << " done" << endl;
 361                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 362
 363                                 //send bad list
 364                                 int badSize = badSeqNames.size();
 365                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 366
 367                                 /*
 368                                 set<string>::iterator it;
 369                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 370                                         string name = *it;
 371                                         int length = name.length();
 372                                         char* buf2 = new char[length];
 373                                         memcpy(buf2, name.c_str(), length);
 374
 375                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 376                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 377                                 }*/
 378                         }
 379
 380                         //close files
 381                         MPI_File_close(&inMPI);
 382                         MPI_File_close(&outMPIGood);
 383                         MPI_File_close(&outMPIBadAccnos);
 384                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 385
 386 #else
 387
 388         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 389                         if(processors == 1){
 390                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 391
 392                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 393
 394                         }else{
 395                                 processIDS.resize(0);
 396
 397                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 398
 399                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 400                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 401
 402                                 //append alignment and report files
 403                                 for(int i=1;i<processors;i++){
 404                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 405                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 406
 407                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 408                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 409                                 }
 410
 411                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 412
 413                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 414                                 ifstream inBad;
 415                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 416
 417                                 if (ableToOpen == 0) {
 418                                         badSeqNames.clear();
 419                                         string tempName;
 420                                         while (!inBad.eof()) {
 421                                                 inBad >> tempName; m->gobble(inBad);
 422                                                 badSeqNames.insert(tempName);
 423                                         }
 424                                         inBad.close();
 425                                 }
 426                         }
 427         #else
 428                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 429
 430                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 431
 432         #endif
 433
 434 #endif
 435
 436                 #ifdef USE_MPI
 437                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 438
 439                         if (pid == 0) { //only one process should fix files
 440
 441                                 //read accnos file with all names in it, process 0 just has its names
 442                                 MPI_File inMPIAccnos;
 443                                 MPI_Offset size;
 444
 445                                 char inFileName[1024];
 446                                 strcpy(inFileName, badAccnosFile.c_str());
 447
 448                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 449                                 MPI_File_get_size(inMPIAccnos, &size);
 450
 451                                 char* buffer = new char[size];
 452                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 453
 454                                 string tempBuf = buffer;
 455                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 456                                 istringstream iss (tempBuf,istringstream::in);
 457
 458                                 delete buffer;
 459                                 MPI_File_close(&inMPIAccnos);
 460
 461                                 badSeqNames.clear();
 462                                 string tempName;
 463                                 while (!iss.eof()) {
 464                                         iss >> tempName; m->gobble(iss);
 465                                         badSeqNames.insert(tempName);
 466                                 }
 467                 #endif
 468
 469                 if(namefile != "" && groupfile != "")   {
 470                         screenNameGroupFile(badSeqNames);
 471                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 472                 }else if(namefile != "")        {
 473                         screenNameGroupFile(badSeqNames);
 474                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 475                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 476
 477                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 478
 479                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 480                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 481
 482                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 483
 484                 #ifdef USE_MPI
 485                         }
 486                 #endif
 487
 488                 m->mothurOutEndLine();
 489                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 490                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 491                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 492                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 493                 m->mothurOutEndLine();
 494                 m->mothurOutEndLine();
 495
 496                 //set fasta file as new current fastafile
 497                 string current = "";
 498                 itTypes = outputTypes.find("fasta");
 499                 if (itTypes != outputTypes.end()) {
 500                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 501                 }
 502
 503                 itTypes = outputTypes.find("name");
 504                 if (itTypes != outputTypes.end()) {
 505                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 506                 }
 507
 508                 itTypes = outputTypes.find("group");
 509                 if (itTypes != outputTypes.end()) {
 510                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 511                 }
 512
 513                 itTypes = outputTypes.find("qfile");
 514                 if (itTypes != outputTypes.end()) {
 515                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 516                 }
 517
 518                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 519                 m->mothurOutEndLine();
 520
 521                 return 0;
 522         }
 523         catch(exception& e) {
 524                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 525                 exit(1);
 526         }
 527 }
 528
 529 //***************************************************************************************************************
 530
 531 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 532         try {
 533                 ifstream inputNames;
 534                 m->openInputFile(namefile, inputNames);
 535                 set<string> badSeqGroups;
 536                 string seqName, seqList, group;
 537                 set<string>::iterator it;
 538
 539                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 540                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 541
 542                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 543
 544                 while(!inputNames.eof()){
 545                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 546
 547                         inputNames >> seqName >> seqList;
 548                         it = badSeqNames.find(seqName);
 549
 550                         if(it != badSeqNames.end()){
 551                                 badSeqNames.erase(it);
 552
 553                                 if(namefile != ""){
 554                                         int start = 0;
 555                                         for(int i=0;i<seqList.length();i++){
 556                                                 if(seqList[i] == ','){
 557                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 558                                                         start = i+1;
 559                                                 }
 560                                         }
 561                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 562                                 }
 563                         }
 564                         else{
 565                                 goodNameOut << seqName << '\t' << seqList << endl;
 566                         }
 567                         m->gobble(inputNames);
 568                 }
 569                 inputNames.close();
 570                 goodNameOut.close();
 571
 572                 //we were unable to remove some of the bad sequences
 573                 if (badSeqNames.size() != 0) {
 574                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 575                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 576                                 m->mothurOutEndLine();
 577                         }
 578                 }
 579
 580                 if(groupfile != ""){
 581
 582                         ifstream inputGroups;
 583                         m->openInputFile(groupfile, inputGroups);
 584
 585                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 586                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 587
 588                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 589
 590                         while(!inputGroups.eof()){
 591                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 592
 593                                 inputGroups >> seqName >> group;
 594
 595                                 it = badSeqGroups.find(seqName);
 596
 597                                 if(it != badSeqGroups.end()){
 598                                         badSeqGroups.erase(it);
 599                                 }
 600                                 else{
 601                                         goodGroupOut << seqName << '\t' << group << endl;
 602                                 }
 603                                 m->gobble(inputGroups);
 604                         }
 605                         inputGroups.close();
 606                         goodGroupOut.close();
 607
 608                         //we were unable to remove some of the bad sequences
 609                         if (badSeqGroups.size() != 0) {
 610                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 611                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 612                                         m->mothurOutEndLine();
 613                                 }
 614                         }
 615                 }
 616
 617
 618                 return 0;
 619
 620         }
 621         catch(exception& e) {
 622                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 623                 exit(1);
 624         }
 625 }
 626 //***************************************************************************************************************
 627 int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
 628         try {
 629
 630                 vector<int> startPosition;
 631                 vector<int> endPosition;
 632                 vector<int> seqLength;
 633                 vector<int> ambigBases;
 634                 vector<int> longHomoPolymer;
 635
 636                 vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 637
 638                 for (int i = 0; i < (positions.size()-1); i++) {
 639                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 640                 }
 641
 642                 int numSeqs = 0;
 643                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 644                         if(processors == 1){
 645                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 646                         }else{
 647                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 648                         }
 649
 650                         if (m->control_pressed) {  return 0; }
 651                 #else
 652                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 653                         if (m->control_pressed) {  return 0; }
 654                 #endif
 655
 656                 sort(startPosition.begin(), startPosition.end());
 657                 sort(endPosition.begin(), endPosition.end());
 658                 sort(seqLength.begin(), seqLength.end());
 659                 sort(ambigBases.begin(), ambigBases.end());
 660                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 661
 662                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 663                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 664
 665                 for (int i = 0; i < optimize.size(); i++) {
 666                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 667                         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();}
 668                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 669                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 670                         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(); }
 671                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 672                 }
 673
 674                 return 0;
 675         }
 676         catch(exception& e) {
 677                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 678                 exit(1);
 679         }
 680 }
 681 /**************************************************************************************/
 682 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 683         try {
 684
 685                 ifstream in;
 686                 m->openInputFile(filename, in);
 687
 688                 in.seekg(filePos->start);
 689
 690                 bool done = false;
 691                 int count = 0;
 692
 693                 while (!done) {
 694
 695                         if (m->control_pressed) { in.close(); return 1; }
 696
 697                         Sequence current(in); m->gobble(in);
 698
 699                         if (current.getName() != "") {
 700                                 int num = 1;
 701                                 if (namefile != "") {
 702                                         //make sure this sequence is in the namefile, else error
 703                                         map<string, int>::iterator it = nameMap.find(current.getName());
 704
 705                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 706                                         else { num = it->second; }
 707                                 }
 708
 709                                 //for each sequence this sequence represents
 710                                 for (int i = 0; i < num; i++) {
 711                                         startPosition.push_back(current.getStartPos());
 712                                         endPosition.push_back(current.getEndPos());
 713                                         seqLength.push_back(current.getNumBases());
 714                                         ambigBases.push_back(current.getAmbigBases());
 715                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 716                                 }
 717
 718                                 count++;
 719                         }
 720
 721                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 722                                 unsigned long int pos = in.tellg();
 723                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 724                         #else
 725                                 if (in.eof()) { break; }
 726                         #endif
 727
 728                 }
 729
 730                 in.close();
 731
 732                 return count;
 733         }
 734         catch(exception& e) {
 735                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 736                 exit(1);
 737         }
 738 }
 739 /**************************************************************************************************/
 740 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 741         try {
 742 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 743                 int process = 1;
 744                 int num = 0;
 745                 processIDS.clear();
 746
 747                 //loop through and create all the processes you want
 748                 while (process != processors) {
 749                         int pid = fork();
 750
 751                         if (pid > 0) {
 752                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 753                                 process++;
 754                         }else if (pid == 0){
 755                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 756
 757                                 //pass numSeqs to parent
 758                                 ofstream out;
 759                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 760                                 m->openOutputFile(tempFile, out);
 761
 762                                 out << num << endl;
 763                                 out << startPosition.size() << endl;
 764                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 765                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 766                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 767                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 768                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 769
 770                                 out.close();
 771
 772                                 exit(0);
 773                         }else {
 774                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 775                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 776                                 exit(0);
 777                         }
 778                 }
 779
 780                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 781
 782                 //force parent to wait until all the processes are done
 783                 for (int i=0;i<processIDS.size();i++) {
 784                         int temp = processIDS[i];
 785                         wait(&temp);
 786                 }
 787
 788                 //parent reads in and combine Filter info
 789                 for (int i = 0; i < processIDS.size(); i++) {
 790                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 791                         ifstream in;
 792                         m->openInputFile(tempFilename, in);
 793
 794                         int temp, tempNum;
 795                         in >> tempNum; m->gobble(in); num += tempNum;
 796                         in >> tempNum; m->gobble(in);
 797                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 798                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 799                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 800                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 801                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 802
 803                         in.close();
 804                         remove(tempFilename.c_str());
 805                 }
 806
 807                 return num;
 808 #endif
 809         }
 810         catch(exception& e) {
 811                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 812                 exit(1);
 813         }
 814 }
 815
 816 //***************************************************************************************************************
 817
 818 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 819         try {
 820                 ifstream inputGroups;
 821                 m->openInputFile(groupfile, inputGroups);
 822                 string seqName, group;
 823                 set<string>::iterator it;
 824
 825                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 826                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 827                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 828
 829                 while(!inputGroups.eof()){
 830                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 831
 832                         inputGroups >> seqName >> group;
 833                         it = badSeqNames.find(seqName);
 834
 835                         if(it != badSeqNames.end()){
 836                                 badSeqNames.erase(it);
 837                         }
 838                         else{
 839                                 goodGroupOut << seqName << '\t' << group << endl;
 840                         }
 841                         m->gobble(inputGroups);
 842                 }
 843
 844                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 845
 846                 //we were unable to remove some of the bad sequences
 847                 if (badSeqNames.size() != 0) {
 848                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 849                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 850                                 m->mothurOutEndLine();
 851                         }
 852                 }
 853
 854                 inputGroups.close();
 855                 goodGroupOut.close();
 856
 857                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 858
 859                 return 0;
 860
 861         }
 862         catch(exception& e) {
 863                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 864                 exit(1);
 865         }
 866 }
 867
 868 //***************************************************************************************************************
 869
 870 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 871         try {
 872                 ifstream inputAlignReport;
 873                 m->openInputFile(alignreport, inputAlignReport);
 874                 string seqName, group;
 875                 set<string>::iterator it;
 876
 877                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 878                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 879                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 880
 881                 while (!inputAlignReport.eof()) {               //      need to copy header
 882                         char c = inputAlignReport.get();
 883                         goodAlignReportOut << c;
 884                         if (c == 10 || c == 13){        break;  }
 885                 }
 886
 887                 while(!inputAlignReport.eof()){
 888                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 889
 890                         inputAlignReport >> seqName;
 891                         it = badSeqNames.find(seqName);
 892                         string line;
 893                         while (!inputAlignReport.eof()) {               //      need to copy header
 894                                 char c = inputAlignReport.get();
 895                                 line += c;
 896                                 if (c == 10 || c == 13){        break;  }
 897                         }
 898
 899                         if(it != badSeqNames.end()){
 900                                 badSeqNames.erase(it);
 901                         }
 902                         else{
 903                                 goodAlignReportOut << seqName << '\t' << line;
 904                         }
 905                         m->gobble(inputAlignReport);
 906                 }
 907
 908                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 909
 910                 //we were unable to remove some of the bad sequences
 911                 if (badSeqNames.size() != 0) {
 912                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 913                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 914                                 m->mothurOutEndLine();
 915                         }
 916                 }
 917
 918                 inputAlignReport.close();
 919                 goodAlignReportOut.close();
 920
 921                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 922
 923                 return 0;
 924
 925         }
 926         catch(exception& e) {
 927                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 928                 exit(1);
 929         }
 930
 931 }
 932 //***************************************************************************************************************
 933
 934 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
 935         try {
 936                 ifstream in;
 937                 m->openInputFile(qualfile, in);
 938                 set<string>::iterator it;
 939
 940                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
 941                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
 942                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
 943
 944                 while(!in.eof()){
 945
 946                         if (m->control_pressed) { goodQual.close(); in.close(); remove(goodQualFile.c_str()); return 0; }
 947
 948                         string saveName = "";
 949                         string name = "";
 950                         string scores = "";
 951
 952                         in >> name;
 953
 954                         if (name.length() != 0) {
 955                                 saveName = name.substr(1);
 956                                 while (!in.eof())       {
 957                                         char c = in.get();
 958                                         if (c == 10 || c == 13){        break;  }
 959                                         else { name += c; }
 960                                 }
 961                                 m->gobble(in);
 962                         }
 963
 964                         while(in){
 965                                 char letter= in.get();
 966                                 if(letter == '>'){      in.putback(letter);     break;  }
 967                                 else{ scores += letter; }
 968                         }
 969
 970                         m->gobble(in);
 971
 972                         it = badSeqNames.find(saveName);
 973
 974                         if(it != badSeqNames.end()){
 975                                 badSeqNames.erase(it);
 976                         }else{
 977                                 goodQual << name << endl << scores;
 978                         }
 979
 980                         m->gobble(in);
 981                 }
 982
 983                 in.close();
 984                 goodQual.close();
 985
 986                 //we were unable to remove some of the bad sequences
 987                 if (badSeqNames.size() != 0) {
 988                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 989                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
 990                                 m->mothurOutEndLine();
 991                         }
 992                 }
 993
 994                 if (m->control_pressed) {  remove(goodQualFile.c_str());  return 0; }
 995
 996                 return 0;
 997
 998         }
 999         catch(exception& e) {
1000                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1001                 exit(1);
1002         }
1003
1004 }
1005 //**********************************************************************************************************************
1006
1007 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1008         try {
1009                 ofstream goodFile;
1010                 m->openOutputFile(goodFName, goodFile);
1011
1012                 ofstream badAccnosFile;
1013                 m->openOutputFile(badAccnosFName, badAccnosFile);
1014
1015                 ifstream inFASTA;
1016                 m->openInputFile(filename, inFASTA);
1017
1018                 inFASTA.seekg(filePos->start);
1019
1020                 bool done = false;
1021                 int count = 0;
1022
1023                 while (!done) {
1024
1025                         if (m->control_pressed) {  return 0; }
1026
1027                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1028                         if (currSeq.getName() != "") {
1029                                 bool goodSeq = 1;               //      innocent until proven guilty
1030                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1031                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1032                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1033                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1034                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1035                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1036
1037                                 if(goodSeq == 1){
1038                                         currSeq.printSequence(goodFile);
1039                                 }
1040                                 else{
1041                                         badAccnosFile << currSeq.getName() << endl;
1042                                         badSeqNames.insert(currSeq.getName());
1043                                 }
1044                         count++;
1045                         }
1046
1047                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1048                                 unsigned long int pos = inFASTA.tellg();
1049                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1050                         #else
1051                                 if (inFASTA.eof()) { break; }
1052                         #endif
1053
1054                         //report progress
1055                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1056                 }
1057                 //report progress
1058                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1059
1060
1061                 goodFile.close();
1062                 inFASTA.close();
1063                 badAccnosFile.close();
1064
1065                 return count;
1066         }
1067         catch(exception& e) {
1068                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1069                 exit(1);
1070         }
1071 }
1072 //**********************************************************************************************************************
1073 #ifdef USE_MPI
1074 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
1075         try {
1076                 string outputString = "";
1077                 MPI_Status statusGood;
1078                 MPI_Status statusBadAccnos;
1079                 MPI_Status status;
1080                 int pid;
1081                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1082
1083                 for(int i=0;i<num;i++){
1084
1085                         if (m->control_pressed) {  return 0; }
1086
1087                         //read next sequence
1088                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1089
1090                         char* buf4 = new char[length];
1091                         memcpy(buf4, outputString.c_str(), length);
1092
1093                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1094
1095                         string tempBuf = buf4;  delete buf4;
1096                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1097                         istringstream iss (tempBuf,istringstream::in);
1098
1099                         Sequence currSeq(iss);
1100
1101                         //process seq
1102                         if (currSeq.getName() != "") {
1103                                 bool goodSeq = 1;               //      innocent until proven guilty
1104                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1105                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1106                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1107                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1108                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1109                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1110
1111                                 if(goodSeq == 1){
1112                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1113
1114                                         //print good seq
1115                                         length = outputString.length();
1116                                         char* buf2 = new char[length];
1117                                         memcpy(buf2, outputString.c_str(), length);
1118
1119                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1120                                         delete buf2;
1121                                 }
1122                                 else{
1123
1124                                         badSeqNames.insert(currSeq.getName());
1125
1126                                         //write to bad accnos file
1127                                         outputString = currSeq.getName() + "\n";
1128
1129                                         length = outputString.length();
1130                                         char* buf3 = new char[length];
1131                                         memcpy(buf3, outputString.c_str(), length);
1132
1133                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1134                                         delete buf3;
1135                                 }
1136                         }
1137
1138                         //report progress
1139                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1140                 }
1141
1142                 return 1;
1143         }
1144         catch(exception& e) {
1145                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1146                 exit(1);
1147         }
1148 }
1149 #endif
1150 /**************************************************************************************************/
1151
1152 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1153         try {
1154 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1155                 int process = 0;
1156                 int num = 0;
1157
1158                 //loop through and create all the processes you want
1159                 while (process != processors) {
1160                         int pid = fork();
1161
1162                         if (pid > 0) {
1163                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1164                                 process++;
1165                         }else if (pid == 0){
1166                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1167
1168                                 //pass numSeqs to parent
1169                                 ofstream out;
1170                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1171                                 m->openOutputFile(tempFile, out);
1172                                 out << num << endl;
1173                                 out.close();
1174
1175                                 exit(0);
1176                         }else {
1177                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1178                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1179                                 exit(0);
1180                         }
1181                 }
1182
1183                 //force parent to wait until all the processes are done
1184                 for (int i=0;i<processors;i++) {
1185                         int temp = processIDS[i];
1186                         wait(&temp);
1187                 }
1188
1189                 for (int i = 0; i < processIDS.size(); i++) {
1190                         ifstream in;
1191                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1192                         m->openInputFile(tempFile, in);
1193                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1194                         in.close(); remove(tempFile.c_str());
1195                 }
1196
1197                 return num;
1198 #endif
1199         }
1200         catch(exception& e) {
1201                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1202                 exit(1);
1203         }
1204 }
1205
1206 //***************************************************************************************************************
1207
1208