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                                 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 221                                 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 222
 223                                 //figure out how many sequences you have to align
 224                                 numSeqsPerProcessor = numFastaSeqs / processors;
 225                                 int startIndex =  pid * numSeqsPerProcessor;
 226                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 227
 228                                 //align your part
 229                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
 230
 231                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad);  return 0; }
 232
 233                                 for (int i = 1; i < processors; i++) {
 234
 235                                         //get bad lists
 236                                         int badSize;
 237                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 238                                         /*for (int j = 0; j < badSize; j++) {
 239                                                 int length;
 240                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 241                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 242                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 243
 244                                                 string tempBuf = buf2;
 245                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 246                                                 delete buf2;
 247
 248                                                 badSeqNames.insert(tempBuf);
 249                                         }*/
 250                                 }
 251                         }else{ //you are a child process
 252                                 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 253                                 MPIPos.resize(numFastaSeqs+1);
 254                                 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 255
 256                                 //figure out how many sequences you have to align
 257                                 numSeqsPerProcessor = numFastaSeqs / processors;
 258                                 int startIndex =  pid * numSeqsPerProcessor;
 259                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 260
 261                                 //align your part
 262                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
 263
 264                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
 265
 266                                 //send bad list
 267                                 int badSize = badSeqNames.size();
 268                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 269
 270                                 /*
 271                                 set<string>::iterator it;
 272                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 273                                         string name = *it;
 274                                         int length = name.length();
 275                                         char* buf2 = new char[length];
 276                                         memcpy(buf2, name.c_str(), length);
 277
 278                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 279                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 280                                 }*/
 281                         }
 282
 283                         //close files
 284                         MPI_File_close(&inMPI);
 285                         MPI_File_close(&outMPIGood);
 286                         MPI_File_close(&outMPIBad);
 287                         MPI_File_close(&outMPIBadAccnos);
 288
 289 #else
 290
 291         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 292                         if(processors == 1){
 293                                 ifstream inFASTA;
 294                                 openInputFile(fastafile, inFASTA);
 295                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 296                                 inFASTA.close();
 297
 298                                 lines.push_back(new linePair(0, numFastaSeqs));
 299
 300                                 driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 301
 302                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 303
 304                         }else{
 305                                 vector<int> positions;
 306                                 processIDS.resize(0);
 307
 308                                 ifstream inFASTA;
 309                                 openInputFile(fastafile, inFASTA);
 310
 311                                 string input;
 312                                 while(!inFASTA.eof()){
 313                                         input = getline(inFASTA);
 314                                         if (input.length() != 0) {
 315                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 316                                         }
 317                                 }
 318                                 inFASTA.close();
 319
 320                                 numFastaSeqs = positions.size();
 321
 322                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 323
 324                                 for (int i = 0; i < processors; i++) {
 325                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 326                                         if(i == processors - 1){
 327                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 328                                         }
 329                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 330                                 }
 331
 332                                 createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 333
 334                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 335                                 rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
 336                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 337
 338                                 //append alignment and report files
 339                                 for(int i=1;i<processors;i++){
 340                                         appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 341                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 342
 343                                         appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
 344                                         remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
 345
 346                                         appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 347                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 348                                 }
 349
 350                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 351
 352                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 353                                 ifstream inBad;
 354                                 int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
 355
 356                                 if (ableToOpen == 0) {
 357                                         badSeqNames.clear();
 358                                         string tempName;
 359                                         while (!inBad.eof()) {
 360                                                 inBad >> tempName; gobble(inBad);
 361                                                 badSeqNames.insert(tempName);
 362                                         }
 363                                         inBad.close();
 364                                 }
 365                         }
 366         #else
 367                         ifstream inFASTA;
 368                         openInputFile(fastafile, inFASTA);
 369                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 370                         inFASTA.close();
 371
 372                         lines.push_back(new linePair(0, numFastaSeqs));
 373
 374                         driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
 375
 376                         if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 377
 378         #endif
 379
 380 #endif
 381
 382                 #ifdef USE_MPI
 383                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 384
 385                         if (pid == 0) { //only one process should fix files
 386
 387                                 //read accnos file with all names in it, process 0 just has its names
 388                                 MPI_File inMPIAccnos;
 389                                 MPI_Offset size;
 390
 391                                 char inFileName[1024];
 392                                 strcpy(inFileName, badAccnosFile.c_str());
 393
 394                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 395                                 MPI_File_get_size(inMPIAccnos, &size);
 396
 397                                 char* buffer = new char[size];
 398                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 399
 400                                 string tempBuf = buffer;
 401                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 402                                 istringstream iss (tempBuf,istringstream::in);
 403
 404                                 delete buffer;
 405                                 MPI_File_close(&inMPIAccnos);
 406
 407                                 badSeqNames.clear();
 408                                 string tempName;
 409                                 while (!iss.eof()) {
 410                                         iss >> tempName; gobble(iss);
 411                                         badSeqNames.insert(tempName);
 412                                 }
 413                 #endif
 414
 415                 if(namefile != "" && groupfile != "")   {
 416                         screenNameGroupFile(badSeqNames);
 417                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 418                 }else if(namefile != "")        {
 419                         screenNameGroupFile(badSeqNames);
 420                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 421                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 422
 423                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 424
 425                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 426
 427                 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
 428
 429                 #ifdef USE_MPI
 430                         }
 431                 #endif
 432
 433                 m->mothurOutEndLine();
 434                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 435                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
 436                 m->mothurOut(badSeqFile); m->mothurOutEndLine();
 437                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();
 438                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 439                 m->mothurOutEndLine();
 440                 m->mothurOutEndLine();
 441
 442                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 443                 m->mothurOutEndLine();
 444
 445                 return 0;
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 449                 exit(1);
 450         }
 451 }
 452
 453 //***************************************************************************************************************
 454
 455 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 456         try {
 457                 ifstream inputNames;
 458                 openInputFile(namefile, inputNames);
 459                 set<string> badSeqGroups;
 460                 string seqName, seqList, group;
 461                 set<string>::iterator it;
 462
 463                 string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
 464                 string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
 465
 466                 outputNames.push_back(goodNameFile);  outputNames.push_back(badNameFile);
 467
 468                 ofstream goodNameOut;   openOutputFile(goodNameFile, goodNameOut);
 469                 ofstream badNameOut;    openOutputFile(badNameFile, badNameOut);
 470
 471                 while(!inputNames.eof()){
 472                         if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
 473
 474                         inputNames >> seqName >> seqList;
 475                         it = badSeqNames.find(seqName);
 476
 477                         if(it != badSeqNames.end()){
 478                                 badSeqNames.erase(it);
 479                                 badNameOut << seqName << '\t' << seqList << endl;
 480                                 if(namefile != ""){
 481                                         int start = 0;
 482                                         for(int i=0;i<seqList.length();i++){
 483                                                 if(seqList[i] == ','){
 484                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 485                                                         start = i+1;
 486                                                 }
 487                                         }
 488                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 489                                 }
 490                         }
 491                         else{
 492                                 goodNameOut << seqName << '\t' << seqList << endl;
 493                         }
 494                         gobble(inputNames);
 495                 }
 496                 inputNames.close();
 497                 goodNameOut.close();
 498                 badNameOut.close();
 499
 500                 //we were unable to remove some of the bad sequences
 501                 if (badSeqNames.size() != 0) {
 502                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 503                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 504                                 m->mothurOutEndLine();
 505                         }
 506                 }
 507
 508                 if(groupfile != ""){
 509
 510                         ifstream inputGroups;
 511                         openInputFile(groupfile, inputGroups);
 512
 513                         string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 514                         string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 515
 516                         outputNames.push_back(goodGroupFile);  outputNames.push_back(badGroupFile);
 517
 518                         ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 519                         ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 520
 521                         while(!inputGroups.eof()){
 522                                 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; }
 523
 524                                 inputGroups >> seqName >> group;
 525
 526                                 it = badSeqGroups.find(seqName);
 527
 528                                 if(it != badSeqGroups.end()){
 529                                         badSeqGroups.erase(it);
 530                                         badGroupOut << seqName << '\t' << group << endl;
 531                                 }
 532                                 else{
 533                                         goodGroupOut << seqName << '\t' << group << endl;
 534                                 }
 535                                 gobble(inputGroups);
 536                         }
 537                         inputGroups.close();
 538                         goodGroupOut.close();
 539                         badGroupOut.close();
 540
 541                         //we were unable to remove some of the bad sequences
 542                         if (badSeqGroups.size() != 0) {
 543                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 544                                         m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 545                                         m->mothurOutEndLine();
 546                                 }
 547                         }
 548                 }
 549
 550                 return 0;
 551
 552         }
 553         catch(exception& e) {
 554                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 555                 exit(1);
 556         }
 557 }
 558
 559 //***************************************************************************************************************
 560
 561 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 562         try {
 563                 ifstream inputGroups;
 564                 openInputFile(groupfile, inputGroups);
 565                 string seqName, group;
 566                 set<string>::iterator it;
 567
 568                 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 569                 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 570
 571                 outputNames.push_back(goodGroupFile);  outputNames.push_back(badGroupFile);
 572
 573                 ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 574                 ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 575
 576                 while(!inputGroups.eof()){
 577                         if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
 578
 579                         inputGroups >> seqName >> group;
 580                         it = badSeqNames.find(seqName);
 581
 582                         if(it != badSeqNames.end()){
 583                                 badSeqNames.erase(it);
 584                                 badGroupOut << seqName << '\t' << group << endl;
 585                         }
 586                         else{
 587                                 goodGroupOut << seqName << '\t' << group << endl;
 588                         }
 589                         gobble(inputGroups);
 590                 }
 591
 592                 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
 593
 594                 //we were unable to remove some of the bad sequences
 595                 if (badSeqNames.size() != 0) {
 596                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 597                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 598                                 m->mothurOutEndLine();
 599                         }
 600                 }
 601
 602                 inputGroups.close();
 603                 goodGroupOut.close();
 604                 badGroupOut.close();
 605
 606                 if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str());  }
 607
 608
 609                 return 0;
 610
 611         }
 612         catch(exception& e) {
 613                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 614                 exit(1);
 615         }
 616 }
 617
 618 //***************************************************************************************************************
 619
 620 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 621         try {
 622                 ifstream inputAlignReport;
 623                 openInputFile(alignreport, inputAlignReport);
 624                 string seqName, group;
 625                 set<string>::iterator it;
 626
 627                 string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
 628                 string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
 629
 630                 outputNames.push_back(goodAlignReportFile);  outputNames.push_back(badAlignReportFile);
 631
 632                 ofstream goodAlignReportOut;    openOutputFile(goodAlignReportFile, goodAlignReportOut);
 633                 ofstream badAlignReportOut;             openOutputFile(badAlignReportFile, badAlignReportOut);
 634
 635                 while (!inputAlignReport.eof()) {               //      need to copy header
 636                         char c = inputAlignReport.get();
 637                         goodAlignReportOut << c;
 638                         badAlignReportOut << c;
 639                         if (c == 10 || c == 13){        break;  }
 640                 }
 641
 642                 while(!inputAlignReport.eof()){
 643                         if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 644
 645                         inputAlignReport >> seqName;
 646                         it = badSeqNames.find(seqName);
 647                         string line;
 648                         while (!inputAlignReport.eof()) {               //      need to copy header
 649                                 char c = inputAlignReport.get();
 650                                 line += c;
 651                                 if (c == 10 || c == 13){        break;  }
 652                         }
 653
 654                         if(it != badSeqNames.end()){
 655                                 badSeqNames.erase(it);
 656                                 badAlignReportOut << seqName << '\t' << line;
 657                         }
 658                         else{
 659                                 goodAlignReportOut << seqName << '\t' << line;
 660                         }
 661                         gobble(inputAlignReport);
 662                 }
 663
 664                 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 665
 666                 //we were unable to remove some of the bad sequences
 667                 if (badSeqNames.size() != 0) {
 668                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 669                                 m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
 670                                 m->mothurOutEndLine();
 671                         }
 672                 }
 673
 674                 inputAlignReport.close();
 675                 goodAlignReportOut.close();
 676                 badAlignReportOut.close();
 677
 678                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
 679
 680                 return 0;
 681
 682         }
 683         catch(exception& e) {
 684                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 685                 exit(1);
 686         }
 687
 688 }
 689 //**********************************************************************************************************************
 690
 691 int ScreenSeqsCommand::driver(linePair* line, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 692         try {
 693                 ofstream goodFile;
 694                 openOutputFile(goodFName, goodFile);
 695
 696                 ofstream badFile;
 697                 openOutputFile(badFName, badFile);
 698
 699                 ofstream badAccnosFile;
 700                 openOutputFile(badAccnosFName, badAccnosFile);
 701
 702                 ifstream inFASTA;
 703                 openInputFile(filename, inFASTA);
 704
 705                 inFASTA.seekg(line->start);
 706
 707                 for(int i=0;i<line->numSeqs;i++){
 708
 709                         if (m->control_pressed) {  return 0; }
 710
 711                         Sequence currSeq(inFASTA);
 712                         if (currSeq.getName() != "") {
 713                                 bool goodSeq = 1;               //      innocent until proven guilty
 714                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 715                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 716                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 717                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 718                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 719                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 720
 721                                 if(goodSeq == 1){
 722                                         currSeq.printSequence(goodFile);
 723                                 }
 724                                 else{
 725                                         currSeq.printSequence(badFile);
 726                                         badAccnosFile << currSeq.getName() << endl;
 727                                         badSeqNames.insert(currSeq.getName());
 728                                 }
 729                         }
 730                         gobble(inFASTA);
 731                 }
 732
 733
 734                 goodFile.close();
 735                 inFASTA.close();
 736                 badFile.close();
 737                 badAccnosFile.close();
 738
 739                 return 1;
 740         }
 741         catch(exception& e) {
 742                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 743                 exit(1);
 744         }
 745 }
 746 //**********************************************************************************************************************
 747 #ifdef USE_MPI
 748 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){
 749         try {
 750                 string outputString = "";
 751                 MPI_Status statusGood;
 752                 MPI_Status statusBad;
 753                 MPI_Status statusBadAccnos;
 754                 MPI_Status status;
 755                 int pid;
 756                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 757
 758                 for(int i=0;i<num;i++){
 759
 760                         if (m->control_pressed) {  return 0; }
 761
 762                         //read next sequence
 763                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 764
 765                         char* buf4 = new char[length];
 766                         memcpy(buf4, outputString.c_str(), length);
 767
 768                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 769
 770                         string tempBuf = buf4;  delete buf4;
 771                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 772                         istringstream iss (tempBuf,istringstream::in);
 773
 774                         Sequence currSeq(iss);
 775
 776                         //process seq
 777                         if (currSeq.getName() != "") {
 778                                 bool goodSeq = 1;               //      innocent until proven guilty
 779                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 780                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 781                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 782                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 783                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 784                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 785
 786                                 if(goodSeq == 1){
 787                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 788
 789                                         //print good seq
 790                                         length = outputString.length();
 791                                         char* buf2 = new char[length];
 792                                         memcpy(buf2, outputString.c_str(), length);
 793
 794                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
 795                                         delete buf2;
 796                                 }
 797                                 else{
 798                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 799
 800                                         //print bad seq to fasta
 801                                         length = outputString.length();
 802                                         char* buf2 = new char[length];
 803                                         memcpy(buf2, outputString.c_str(), length);
 804
 805                                         MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
 806                                         delete buf2;
 807
 808                                         badSeqNames.insert(currSeq.getName());
 809
 810                                         //write to bad accnos file
 811                                         outputString = currSeq.getName() + "\n";
 812
 813                                         length = outputString.length();
 814                                         char* buf3 = new char[length];
 815                                         memcpy(buf3, outputString.c_str(), length);
 816
 817                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
 818                                         delete buf3;
 819                                 }
 820                         }
 821                 }
 822
 823                 return 1;
 824         }
 825         catch(exception& e) {
 826                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
 827                 exit(1);
 828         }
 829 }
 830 #endif
 831 /**************************************************************************************************/
 832
 833 int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
 834         try {
 835 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 836                 int process = 0;
 837                 int exitCommand = 1;
 838
 839                 //loop through and create all the processes you want
 840                 while (process != processors) {
 841                         int pid = fork();
 842
 843                         if (pid > 0) {
 844                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 845                                 process++;
 846                         }else if (pid == 0){
 847                                 exitCommand = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
 848                                 exit(0);
 849                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 850                 }
 851
 852                 //force parent to wait until all the processes are done
 853                 for (int i=0;i<processors;i++) {
 854                         int temp = processIDS[i];
 855                         wait(&temp);
 856                 }
 857
 858                 return exitCommand;
 859 #endif
 860         }
 861         catch(exception& e) {
 862                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
 863                 exit(1);
 864         }
 865 }
 866
 867 //***************************************************************************************************************
 868
 869