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
  15 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
  25                                                                         "name", "group", "alignreport","processors","outputdir","inputdir"};
  26                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("group");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  58                                 }
  59
  60                                 it = parameters.find("name");
  61                                 //user has given a template file
  62                                 if(it != parameters.end()){
  63                                         path = hasPath(it->second);
  64                                         //if the user has not given a path then, add inputdir. else leave path alone.
  65                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  66                                 }
  67
  68                                 it = parameters.find("alignreport");
  69                                 //user has given a template file
  70                                 if(it != parameters.end()){
  71                                         path = hasPath(it->second);
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.
  73                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
  74                                 }
  75                         }
  76
  77                         //check for required parameters
  78                         fastafile = validParameter.validFile(parameters, "fasta", true);
  79                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
  80                         else if (fastafile == "not open") { abort = true; }
  81
  82                         groupfile = validParameter.validFile(parameters, "group", true);
  83                         if (groupfile == "not open") { abort = true; }
  84                         else if (groupfile == "not found") { groupfile = ""; }
  85
  86                         namefile = validParameter.validFile(parameters, "name", true);
  87                         if (namefile == "not open") { abort = true; }
  88                         else if (namefile == "not found") { namefile = ""; }
  89
  90                         alignreport = validParameter.validFile(parameters, "alignreport", true);
  91                         if (alignreport == "not open") { abort = true; }
  92                         else if (alignreport == "not found") { alignreport = ""; }
  93
  94                         //if the user changes the output directory command factory will send this info to us in the output parameter
  95                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  96                                 outputDir = "";
  97                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  98                         }
  99
 100                         //check for optional parameter and set defaults
 101                         // ...at some point should added some additional type checking...
 102                         string temp;
 103                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 104                         convert(temp, startPos);
 105
 106                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 107                         convert(temp, endPos);
 108
 109                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 110                         convert(temp, maxAmbig);
 111
 112                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 113                         convert(temp, maxHomoP);
 114
 115                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 116                         convert(temp, minLength);
 117
 118                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 119                         convert(temp, maxLength);
 120
 121                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 122                         convert(temp, processors);
 123
 124                 }
 125
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 129                 exit(1);
 130         }
 131 }
 132 //**********************************************************************************************************************
 133
 134 void ScreenSeqsCommand::help(){
 135         try {
 136                 m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
 137                 m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group and processors.\n");
 138                 m->mothurOut("The fasta parameter is required.\n");
 139                 m->mothurOut("The start parameter .... The default is -1.\n");
 140                 m->mothurOut("The end parameter .... The default is -1.\n");
 141                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 142                 m->mothurOut("The maxhomop parameter .... The default is -1.\n");
 143                 m->mothurOut("The minlength parameter .... The default is -1.\n");
 144                 m->mothurOut("The maxlength parameter .... The default is -1.\n");
 145                 m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
 146                 m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
 147                 m->mothurOut("The screen.seqs command should be in the following format: \n");
 148                 m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n");
 149                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 150                 m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 151                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 152
 153         }
 154         catch(exception& e) {
 155                 m->errorOut(e, "ScreenSeqsCommand", "help");
 156                 exit(1);
 157         }
 158 }
 159
 160 //***************************************************************************************************************
 161
 162 ScreenSeqsCommand::~ScreenSeqsCommand(){        /*      do nothing      */      }
 163
 164 //***************************************************************************************************************
 165
 166 int ScreenSeqsCommand::execute(){
 167         try{
 168
 169                 if (abort == true) { return 0; }
 170
 171                 string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
 172                 string badSeqFile =  outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
 173                 string badAccnosFile =  outputDir + getRootName(getSimpleName(fastafile)) + "bad.accnos";
 174
 175                 int numFastaSeqs = 0;
 176                 set<string> badSeqNames;
 177                 int start = time(NULL);
 178
 179 #ifdef USE_MPI
 180                         int pid, end, numSeqsPerProcessor;
 181                         int tag = 2001;
 182                         vector<long> MPIPos;
 183
 184                         MPI_Status status;
 185                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 186                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 187
 188                         MPI_File inMPI;
 189                         MPI_File outMPIGood;
 190                         MPI_File outMPIBad;
 191                         MPI_File outMPIBadAccnos;
 192
 193                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 194                         int inMode=MPI_MODE_RDONLY;
 195
 196                         char outGoodFilename[1024];
 197                         strcpy(outGoodFilename, goodSeqFile.c_str());
 198
 199                         char outBadFilename[1024];
 200                         strcpy(outBadFilename, badSeqFile.c_str());
 201
 202                         char outBadAccnosFilename[1024];
 203                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 204
 205                         char inFileName[1024];
 206                         strcpy(inFileName, fastafile.c_str());
 207
 208                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 209                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 210                         MPI_File_open(MPI_COMM_WORLD, outBadFilename, outMode, MPI_INFO_NULL, &outMPIBad);
 211                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 212
 213                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
 214
 215                         if (pid == 0) { //you are the root process
 216
 217                                 MPIPos = setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 218
 219                                 //send file positions to all processes
 220                                 for(int i = 1; i < processors; i++) {
 221                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 222                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 223                                 }
 224
 225                                 //figure out how many sequences you have to align
 226                                 numSeqsPerProcessor = numFastaSeqs / processors;
 227                                 int startIndex =  pid * numSeqsPerProcessor;
 228                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 229
 230                                 //align your part
 231                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
 232
 233                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad);  return 0; }
 234
 235                                 for (int i = 1; i < processors; i++) {
 236
 237                                         //get bad lists
 238                                         int badSize;
 239                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 240                                         /*for (int j = 0; j < badSize; j++) {
 241                                                 int length;
 242                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 243                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 244                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 245
 246                                                 string tempBuf = buf2;
 247                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 248                                                 delete buf2;
 249
 250                                                 badSeqNames.insert(tempBuf);
 251                                         }*/
 252                                 }
 253                         }else{ //you are a child process
 254                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 255                                 MPIPos.resize(numFastaSeqs+1);
 256                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 257
 258                                 //figure out how many sequences you have to align
 259                                 numSeqsPerProcessor = numFastaSeqs / processors;
 260                                 int startIndex =  pid * numSeqsPerProcessor;
 261                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 262
 263                                 //align your part
 264                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
 265
 266                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
 267
 268                                 //send bad list
 269                                 int badSize = badSeqNames.size();
 270                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 271
 272                                 /*
 273                                 set<string>::iterator it;
 274                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 275                                         string name = *it;
 276                                         int length = name.length();
 277                                         char* buf2 = new char[length];
 278                                         memcpy(buf2, name.c_str(), length);
 279
 280                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 281                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 282                                 }*/
 283                         }
 284
 285                         //close files
 286                         MPI_File_close(&inMPI);
 287                         MPI_File_close(&outMPIGood);
 288                         MPI_File_close(&outMPIBad);
 289                         MPI_File_close(&outMPIBadAccnos);
 290                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 291
 292 #else
 293
 294         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 295                         if(processors == 1){
 296                                 ifstream inFASTA;
 297                                 openInputFile(fastafile, inFASTA);
 298                                 getNumSeqs(inFASTA, numFastaSeqs);
 299                                 inFASTA.close();
 300
 301                                 lines.push_back(new linePair(0, numFastaSeqs));
 302
 303                                 driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 304
 305                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 306
 307                         }else{
 308                                 vector<int> positions;
 309                                 processIDS.resize(0);
 310
 311                                 ifstream inFASTA;
 312                                 openInputFile(fastafile, inFASTA);
 313
 314                                 string input;
 315                                 while(!inFASTA.eof()){
 316                                         input = getline(inFASTA);
 317                                         if (input.length() != 0) {
 318                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 319                                         }
 320                                 }
 321                                 inFASTA.close();
 322
 323                                 numFastaSeqs = positions.size();
 324
 325                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 326
 327                                 for (int i = 0; i < processors; i++) {
 328                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 329                                         if(i == processors - 1){
 330                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 331                                         }
 332                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 333                                 }
 334
 335                                 createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 336
 337                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 338                                 rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
 339                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 340
 341                                 //append alignment and report files
 342                                 for(int i=1;i<processors;i++){
 343                                         appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 344                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 345
 346                                         appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
 347                                         remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
 348
 349                                         appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 350                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 351                                 }
 352
 353                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 354
 355                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 356                                 ifstream inBad;
 357                                 int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
 358
 359                                 if (ableToOpen == 0) {
 360                                         badSeqNames.clear();
 361                                         string tempName;
 362                                         while (!inBad.eof()) {
 363                                                 inBad >> tempName; gobble(inBad);
 364                                                 badSeqNames.insert(tempName);
 365                                         }
 366                                         inBad.close();
 367                                 }
 368                         }
 369         #else
 370                         ifstream inFASTA;
 371                         openInputFile(fastafile, inFASTA);
 372                         getNumSeqs(inFASTA, numFastaSeqs);
 373                         inFASTA.close();
 374
 375                         lines.push_back(new linePair(0, numFastaSeqs));
 376
 377                         driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 378
 379                         if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 380
 381         #endif
 382
 383 #endif
 384
 385                 #ifdef USE_MPI
 386                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 387
 388                         if (pid == 0) { //only one process should fix files
 389
 390                                 //read accnos file with all names in it, process 0 just has its names
 391                                 MPI_File inMPIAccnos;
 392                                 MPI_Offset size;
 393
 394                                 char inFileName[1024];
 395                                 strcpy(inFileName, badAccnosFile.c_str());
 396
 397                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 398                                 MPI_File_get_size(inMPIAccnos, &size);
 399
 400                                 char* buffer = new char[size];
 401                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 402
 403                                 string tempBuf = buffer;
 404                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 405                                 istringstream iss (tempBuf,istringstream::in);
 406
 407                                 delete buffer;
 408                                 MPI_File_close(&inMPIAccnos);
 409
 410                                 badSeqNames.clear();
 411                                 string tempName;
 412                                 while (!iss.eof()) {
 413                                         iss >> tempName; gobble(iss);
 414                                         badSeqNames.insert(tempName);
 415                                 }
 416                 #endif
 417
 418                 if(namefile != "" && groupfile != "")   {
 419                         screenNameGroupFile(badSeqNames);
 420                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 421                 }else if(namefile != "")        {
 422                         screenNameGroupFile(badSeqNames);
 423                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 424                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 425
 426                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 427
 428                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 429
 430                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 431
 432                 #ifdef USE_MPI
 433                         }
 434                 #endif
 435
 436                 m->mothurOutEndLine();
 437                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 438                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
 439                 m->mothurOut(badSeqFile); m->mothurOutEndLine();
 440                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();
 441                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 442                 m->mothurOutEndLine();
 443                 m->mothurOutEndLine();
 444
 445                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 446                 m->mothurOutEndLine();
 447
 448                 return 0;
 449         }
 450         catch(exception& e) {
 451                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 452                 exit(1);
 453         }
 454 }
 455
 456 //***************************************************************************************************************
 457
 458 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 459         try {
 460                 ifstream inputNames;
 461                 openInputFile(namefile, inputNames);
 462                 set<string> badSeqGroups;
 463                 string seqName, seqList, group;
 464                 set<string>::iterator it;
 465
 466                 string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
 467                 string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
 468
 469                 outputNames.push_back(goodNameFile);  outputNames.push_back(badNameFile);
 470
 471                 ofstream goodNameOut;   openOutputFile(goodNameFile, goodNameOut);
 472                 ofstream badNameOut;    openOutputFile(badNameFile, badNameOut);
 473
 474                 while(!inputNames.eof()){
 475                         if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
 476
 477                         inputNames >> seqName >> seqList;
 478                         it = badSeqNames.find(seqName);
 479
 480                         if(it != badSeqNames.end()){
 481                                 badSeqNames.erase(it);
 482                                 badNameOut << seqName << '\t' << seqList << endl;
 483                                 if(namefile != ""){
 484                                         int start = 0;
 485                                         for(int i=0;i<seqList.length();i++){
 486                                                 if(seqList[i] == ','){
 487                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 488                                                         start = i+1;
 489                                                 }
 490                                         }
 491                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 492                                 }
 493                         }
 494                         else{
 495                                 goodNameOut << seqName << '\t' << seqList << endl;
 496                         }
 497                         gobble(inputNames);
 498                 }
 499                 inputNames.close();
 500                 goodNameOut.close();
 501                 badNameOut.close();
 502
 503                 //we were unable to remove some of the bad sequences
 504                 if (badSeqNames.size() != 0) {
 505                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 506                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 507                                 m->mothurOutEndLine();
 508                         }
 509                 }
 510
 511                 if(groupfile != ""){
 512
 513                         ifstream inputGroups;
 514                         openInputFile(groupfile, inputGroups);
 515
 516                         string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 517                         string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 518
 519                         outputNames.push_back(goodGroupFile);  outputNames.push_back(badGroupFile);
 520
 521                         ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 522                         ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 523
 524                         while(!inputGroups.eof()){
 525                                 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
 526
 527                                 inputGroups >> seqName >> group;
 528
 529                                 it = badSeqGroups.find(seqName);
 530
 531                                 if(it != badSeqGroups.end()){
 532                                         badSeqGroups.erase(it);
 533                                         badGroupOut << seqName << '\t' << group << endl;
 534                                 }
 535                                 else{
 536                                         goodGroupOut << seqName << '\t' << group << endl;
 537                                 }
 538                                 gobble(inputGroups);
 539                         }
 540                         inputGroups.close();
 541                         goodGroupOut.close();
 542                         badGroupOut.close();
 543
 544                         //we were unable to remove some of the bad sequences
 545                         if (badSeqGroups.size() != 0) {
 546                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 547                                         m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 548                                         m->mothurOutEndLine();
 549                                 }
 550                         }
 551                 }
 552
 553                 return 0;
 554
 555         }
 556         catch(exception& e) {
 557                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 558                 exit(1);
 559         }
 560 }
 561
 562 //***************************************************************************************************************
 563
 564 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 565         try {
 566                 ifstream inputGroups;
 567                 openInputFile(groupfile, inputGroups);
 568                 string seqName, group;
 569                 set<string>::iterator it;
 570
 571                 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 572                 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 573
 574                 outputNames.push_back(goodGroupFile);  outputNames.push_back(badGroupFile);
 575
 576                 ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 577                 ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 578
 579                 while(!inputGroups.eof()){
 580                         if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
 581
 582                         inputGroups >> seqName >> group;
 583                         it = badSeqNames.find(seqName);
 584
 585                         if(it != badSeqNames.end()){
 586                                 badSeqNames.erase(it);
 587                                 badGroupOut << seqName << '\t' << group << endl;
 588                         }
 589                         else{
 590                                 goodGroupOut << seqName << '\t' << group << endl;
 591                         }
 592                         gobble(inputGroups);
 593                 }
 594
 595                 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
 596
 597                 //we were unable to remove some of the bad sequences
 598                 if (badSeqNames.size() != 0) {
 599                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 600                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 601                                 m->mothurOutEndLine();
 602                         }
 603                 }
 604
 605                 inputGroups.close();
 606                 goodGroupOut.close();
 607                 badGroupOut.close();
 608
 609                 if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str());  }
 610
 611
 612                 return 0;
 613
 614         }
 615         catch(exception& e) {
 616                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 617                 exit(1);
 618         }
 619 }
 620
 621 //***************************************************************************************************************
 622
 623 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 624         try {
 625                 ifstream inputAlignReport;
 626                 openInputFile(alignreport, inputAlignReport);
 627                 string seqName, group;
 628                 set<string>::iterator it;
 629
 630                 string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
 631                 string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
 632
 633                 outputNames.push_back(goodAlignReportFile);  outputNames.push_back(badAlignReportFile);
 634
 635                 ofstream goodAlignReportOut;    openOutputFile(goodAlignReportFile, goodAlignReportOut);
 636                 ofstream badAlignReportOut;             openOutputFile(badAlignReportFile, badAlignReportOut);
 637
 638                 while (!inputAlignReport.eof()) {               //      need to copy header
 639                         char c = inputAlignReport.get();
 640                         goodAlignReportOut << c;
 641                         badAlignReportOut << c;
 642                         if (c == 10 || c == 13){        break;  }
 643                 }
 644
 645                 while(!inputAlignReport.eof()){
 646                         if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 647
 648                         inputAlignReport >> seqName;
 649                         it = badSeqNames.find(seqName);
 650                         string line;
 651                         while (!inputAlignReport.eof()) {               //      need to copy header
 652                                 char c = inputAlignReport.get();
 653                                 line += c;
 654                                 if (c == 10 || c == 13){        break;  }
 655                         }
 656
 657                         if(it != badSeqNames.end()){
 658                                 badSeqNames.erase(it);
 659                                 badAlignReportOut << seqName << '\t' << line;
 660                         }
 661                         else{
 662                                 goodAlignReportOut << seqName << '\t' << line;
 663                         }
 664                         gobble(inputAlignReport);
 665                 }
 666
 667                 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 668
 669                 //we were unable to remove some of the bad sequences
 670                 if (badSeqNames.size() != 0) {
 671                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 672                                 m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
 673                                 m->mothurOutEndLine();
 674                         }
 675                 }
 676
 677                 inputAlignReport.close();
 678                 goodAlignReportOut.close();
 679                 badAlignReportOut.close();
 680
 681                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 682
 683                 return 0;
 684
 685         }
 686         catch(exception& e) {
 687                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 688                 exit(1);
 689         }
 690
 691 }
 692 //**********************************************************************************************************************
 693
 694 int ScreenSeqsCommand::driver(linePair* line, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 695         try {
 696                 ofstream goodFile;
 697                 openOutputFile(goodFName, goodFile);
 698
 699                 ofstream badFile;
 700                 openOutputFile(badFName, badFile);
 701
 702                 ofstream badAccnosFile;
 703                 openOutputFile(badAccnosFName, badAccnosFile);
 704
 705                 ifstream inFASTA;
 706                 openInputFile(filename, inFASTA);
 707
 708                 inFASTA.seekg(line->start);
 709
 710                 for(int i=0;i<line->numSeqs;i++){
 711
 712                         if (m->control_pressed) {  return 0; }
 713
 714                         Sequence currSeq(inFASTA);
 715                         if (currSeq.getName() != "") {
 716                                 bool goodSeq = 1;               //      innocent until proven guilty
 717                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 718                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 719                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 720                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 721                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 722                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 723
 724                                 if(goodSeq == 1){
 725                                         currSeq.printSequence(goodFile);
 726                                 }
 727                                 else{
 728                                         currSeq.printSequence(badFile);
 729                                         badAccnosFile << currSeq.getName() << endl;
 730                                         badSeqNames.insert(currSeq.getName());
 731                                 }
 732                         }
 733                         gobble(inFASTA);
 734                 }
 735
 736
 737                 goodFile.close();
 738                 inFASTA.close();
 739                 badFile.close();
 740                 badAccnosFile.close();
 741
 742                 return 1;
 743         }
 744         catch(exception& e) {
 745                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 746                 exit(1);
 747         }
 748 }
 749 //**********************************************************************************************************************
 750 #ifdef USE_MPI
 751 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badFile, MPI_File& badAccnosFile, vector<long>& MPIPos, set<string>& badSeqNames){
 752         try {
 753                 string outputString = "";
 754                 MPI_Status statusGood;
 755                 MPI_Status statusBad;
 756                 MPI_Status statusBadAccnos;
 757                 MPI_Status status;
 758                 int pid;
 759                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 760
 761                 for(int i=0;i<num;i++){
 762
 763                         if (m->control_pressed) {  return 0; }
 764
 765                         //read next sequence
 766                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 767
 768                         char* buf4 = new char[length];
 769                         memcpy(buf4, outputString.c_str(), length);
 770
 771                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 772
 773                         string tempBuf = buf4;  delete buf4;
 774                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 775                         istringstream iss (tempBuf,istringstream::in);
 776
 777                         Sequence currSeq(iss);
 778
 779                         //process seq
 780                         if (currSeq.getName() != "") {
 781                                 bool goodSeq = 1;               //      innocent until proven guilty
 782                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 783                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 784                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 785                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 786                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 787                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 788
 789                                 if(goodSeq == 1){
 790                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 791
 792                                         //print good seq
 793                                         length = outputString.length();
 794                                         char* buf2 = new char[length];
 795                                         memcpy(buf2, outputString.c_str(), length);
 796
 797                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
 798                                         delete buf2;
 799                                 }
 800                                 else{
 801                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 802
 803                                         //print bad seq to fasta
 804                                         length = outputString.length();
 805                                         char* buf2 = new char[length];
 806                                         memcpy(buf2, outputString.c_str(), length);
 807
 808                                         MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
 809                                         delete buf2;
 810
 811                                         badSeqNames.insert(currSeq.getName());
 812
 813                                         //write to bad accnos file
 814                                         outputString = currSeq.getName() + "\n";
 815
 816                                         length = outputString.length();
 817                                         char* buf3 = new char[length];
 818                                         memcpy(buf3, outputString.c_str(), length);
 819
 820                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
 821                                         delete buf3;
 822                                 }
 823                         }
 824                 }
 825
 826                 return 1;
 827         }
 828         catch(exception& e) {
 829                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
 830                 exit(1);
 831         }
 832 }
 833 #endif
 834 /**************************************************************************************************/
 835
 836 int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
 837         try {
 838 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 839                 int process = 0;
 840                 int exitCommand = 1;
 841
 842                 //loop through and create all the processes you want
 843                 while (process != processors) {
 844                         int pid = fork();
 845
 846                         if (pid > 0) {
 847                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 848                                 process++;
 849                         }else if (pid == 0){
 850                                 exitCommand = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
 851                                 exit(0);
 852                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 853                 }
 854
 855                 //force parent to wait until all the processes are done
 856                 for (int i=0;i<processors;i++) {
 857                         int temp = processIDS[i];
 858                         wait(&temp);
 859                 }
 860
 861                 return exitCommand;
 862 #endif
 863         }
 864         catch(exception& e) {
 865                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
 866                 exit(1);
 867         }
 868 }
 869
 870 //***************************************************************************************************************
 871
 872