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