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("screen.seqs");
  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 = m->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 = m->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 = m->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 = m->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 += m->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 + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 172                 string badAccnosFile =  outputDir + m->getRootName(m->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<unsigned long int> 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 outMPIBadAccnos;
 190
 191                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 192                         int inMode=MPI_MODE_RDONLY;
 193
 194                         char outGoodFilename[1024];
 195                         strcpy(outGoodFilename, goodSeqFile.c_str());
 196
 197                         char outBadAccnosFilename[1024];
 198                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 199
 200                         char inFileName[1024];
 201                         strcpy(inFileName, fastafile.c_str());
 202
 203                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 204                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 205                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 206
 207                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 208
 209                         if (pid == 0) { //you are the root process
 210
 211                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 212
 213                                 //send file positions to all processes
 214                                 for(int i = 1; i < processors; i++) {
 215                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 216                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 217                                 }
 218
 219                                 //figure out how many sequences you have to align
 220                                 numSeqsPerProcessor = numFastaSeqs / processors;
 221                                 int startIndex =  pid * numSeqsPerProcessor;
 222                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 223
 224                                 //align your part
 225                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 226
 227                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 228
 229                                 for (int i = 1; i < processors; i++) {
 230
 231                                         //get bad lists
 232                                         int badSize;
 233                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 234                                         /*for (int j = 0; j < badSize; j++) {
 235                                                 int length;
 236                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 237                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 238                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 239
 240                                                 string tempBuf = buf2;
 241                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 242                                                 delete buf2;
 243
 244                                                 badSeqNames.insert(tempBuf);
 245                                         }*/
 246                                 }
 247                         }else{ //you are a child process
 248                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 249                                 MPIPos.resize(numFastaSeqs+1);
 250                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 251
 252                                 //figure out how many sequences you have to align
 253                                 numSeqsPerProcessor = numFastaSeqs / processors;
 254                                 int startIndex =  pid * numSeqsPerProcessor;
 255                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 256
 257                                 //align your part
 258                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 259
 260                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 261
 262                                 //send bad list
 263                                 int badSize = badSeqNames.size();
 264                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 265
 266                                 /*
 267                                 set<string>::iterator it;
 268                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 269                                         string name = *it;
 270                                         int length = name.length();
 271                                         char* buf2 = new char[length];
 272                                         memcpy(buf2, name.c_str(), length);
 273
 274                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 275                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 276                                 }*/
 277                         }
 278
 279                         //close files
 280                         MPI_File_close(&inMPI);
 281                         MPI_File_close(&outMPIGood);
 282                         MPI_File_close(&outMPIBadAccnos);
 283                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 284
 285 #else
 286                         vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 287
 288                         for (int i = 0; i < (positions.size()-1); i++) {
 289                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 290                         }
 291
 292         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 293                         if(processors == 1){
 294                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 295
 296                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 297
 298                         }else{
 299                                 processIDS.resize(0);
 300
 301                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 302
 303                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 304                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 305
 306                                 //append alignment and report files
 307                                 for(int i=1;i<processors;i++){
 308                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 309                                         remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
 310
 311                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 312                                         remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
 313                                 }
 314
 315                                 if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 316
 317                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 318                                 ifstream inBad;
 319                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 320
 321                                 if (ableToOpen == 0) {
 322                                         badSeqNames.clear();
 323                                         string tempName;
 324                                         while (!inBad.eof()) {
 325                                                 inBad >> tempName; m->gobble(inBad);
 326                                                 badSeqNames.insert(tempName);
 327                                         }
 328                                         inBad.close();
 329                                 }
 330                         }
 331         #else
 332                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 333
 334                         if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
 335
 336         #endif
 337
 338 #endif
 339
 340                 #ifdef USE_MPI
 341                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 342
 343                         if (pid == 0) { //only one process should fix files
 344
 345                                 //read accnos file with all names in it, process 0 just has its names
 346                                 MPI_File inMPIAccnos;
 347                                 MPI_Offset size;
 348
 349                                 char inFileName[1024];
 350                                 strcpy(inFileName, badAccnosFile.c_str());
 351
 352                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 353                                 MPI_File_get_size(inMPIAccnos, &size);
 354
 355                                 char* buffer = new char[size];
 356                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 357
 358                                 string tempBuf = buffer;
 359                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 360                                 istringstream iss (tempBuf,istringstream::in);
 361
 362                                 delete buffer;
 363                                 MPI_File_close(&inMPIAccnos);
 364
 365                                 badSeqNames.clear();
 366                                 string tempName;
 367                                 while (!iss.eof()) {
 368                                         iss >> tempName; m->gobble(iss);
 369                                         badSeqNames.insert(tempName);
 370                                 }
 371                 #endif
 372
 373                 if(namefile != "" && groupfile != "")   {
 374                         screenNameGroupFile(badSeqNames);
 375                         if (m->control_pressed) {  remove(goodSeqFile.c_str()); return 0; }
 376                 }else if(namefile != "")        {
 377                         screenNameGroupFile(badSeqNames);
 378                         if (m->control_pressed) {  remove(goodSeqFile.c_str());  return 0; }
 379                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 380
 381                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 382
 383                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 384
 385                 if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 386
 387                 #ifdef USE_MPI
 388                         }
 389                 #endif
 390
 391                 m->mothurOutEndLine();
 392                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 393                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
 394                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();
 395                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 396                 m->mothurOutEndLine();
 397                 m->mothurOutEndLine();
 398
 399                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 400                 m->mothurOutEndLine();
 401
 402                 return 0;
 403         }
 404         catch(exception& e) {
 405                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 406                 exit(1);
 407         }
 408 }
 409
 410 //***************************************************************************************************************
 411
 412 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 413         try {
 414                 ifstream inputNames;
 415                 m->openInputFile(namefile, inputNames);
 416                 set<string> badSeqGroups;
 417                 string seqName, seqList, group;
 418                 set<string>::iterator it;
 419
 420                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 421                 outputNames.push_back(goodNameFile);
 422
 423                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 424
 425                 while(!inputNames.eof()){
 426                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 427
 428                         inputNames >> seqName >> seqList;
 429                         it = badSeqNames.find(seqName);
 430
 431                         if(it != badSeqNames.end()){
 432                                 badSeqNames.erase(it);
 433
 434                                 if(namefile != ""){
 435                                         int start = 0;
 436                                         for(int i=0;i<seqList.length();i++){
 437                                                 if(seqList[i] == ','){
 438                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 439                                                         start = i+1;
 440                                                 }
 441                                         }
 442                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 443                                 }
 444                         }
 445                         else{
 446                                 goodNameOut << seqName << '\t' << seqList << endl;
 447                         }
 448                         m->gobble(inputNames);
 449                 }
 450                 inputNames.close();
 451                 goodNameOut.close();
 452
 453                 //we were unable to remove some of the bad sequences
 454                 if (badSeqNames.size() != 0) {
 455                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 456                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 457                                 m->mothurOutEndLine();
 458                         }
 459                 }
 460
 461                 if(groupfile != ""){
 462
 463                         ifstream inputGroups;
 464                         m->openInputFile(groupfile, inputGroups);
 465
 466                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 467                         outputNames.push_back(goodGroupFile);
 468
 469                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 470
 471                         while(!inputGroups.eof()){
 472                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 473
 474                                 inputGroups >> seqName >> group;
 475
 476                                 it = badSeqGroups.find(seqName);
 477
 478                                 if(it != badSeqGroups.end()){
 479                                         badSeqGroups.erase(it);
 480                                 }
 481                                 else{
 482                                         goodGroupOut << seqName << '\t' << group << endl;
 483                                 }
 484                                 m->gobble(inputGroups);
 485                         }
 486                         inputGroups.close();
 487                         goodGroupOut.close();
 488
 489                         //we were unable to remove some of the bad sequences
 490                         if (badSeqGroups.size() != 0) {
 491                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 492                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 493                                         m->mothurOutEndLine();
 494                                 }
 495                         }
 496                 }
 497
 498                 return 0;
 499
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 503                 exit(1);
 504         }
 505 }
 506
 507 //***************************************************************************************************************
 508
 509 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 510         try {
 511                 ifstream inputGroups;
 512                 m->openInputFile(groupfile, inputGroups);
 513                 string seqName, group;
 514                 set<string>::iterator it;
 515
 516                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 517                 outputNames.push_back(goodGroupFile);
 518                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 519
 520                 while(!inputGroups.eof()){
 521                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
 522
 523                         inputGroups >> seqName >> group;
 524                         it = badSeqNames.find(seqName);
 525
 526                         if(it != badSeqNames.end()){
 527                                 badSeqNames.erase(it);
 528                         }
 529                         else{
 530                                 goodGroupOut << seqName << '\t' << group << endl;
 531                         }
 532                         m->gobble(inputGroups);
 533                 }
 534
 535                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); remove(goodGroupFile.c_str());  return 0; }
 536
 537                 //we were unable to remove some of the bad sequences
 538                 if (badSeqNames.size() != 0) {
 539                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 540                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 541                                 m->mothurOutEndLine();
 542                         }
 543                 }
 544
 545                 inputGroups.close();
 546                 goodGroupOut.close();
 547
 548                 if (m->control_pressed) { remove(goodGroupFile.c_str());   }
 549
 550                 return 0;
 551
 552         }
 553         catch(exception& e) {
 554                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 555                 exit(1);
 556         }
 557 }
 558
 559 //***************************************************************************************************************
 560
 561 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 562         try {
 563                 ifstream inputAlignReport;
 564                 m->openInputFile(alignreport, inputAlignReport);
 565                 string seqName, group;
 566                 set<string>::iterator it;
 567
 568                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 569                 outputNames.push_back(goodAlignReportFile);
 570                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 571
 572                 while (!inputAlignReport.eof()) {               //      need to copy header
 573                         char c = inputAlignReport.get();
 574                         goodAlignReportOut << c;
 575                         if (c == 10 || c == 13){        break;  }
 576                 }
 577
 578                 while(!inputAlignReport.eof()){
 579                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
 580
 581                         inputAlignReport >> seqName;
 582                         it = badSeqNames.find(seqName);
 583                         string line;
 584                         while (!inputAlignReport.eof()) {               //      need to copy header
 585                                 char c = inputAlignReport.get();
 586                                 line += c;
 587                                 if (c == 10 || c == 13){        break;  }
 588                         }
 589
 590                         if(it != badSeqNames.end()){
 591                                 badSeqNames.erase(it);
 592                         }
 593                         else{
 594                                 goodAlignReportOut << seqName << '\t' << line;
 595                         }
 596                         m->gobble(inputAlignReport);
 597                 }
 598
 599                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); remove(goodAlignReportFile.c_str());  return 0; }
 600
 601                 //we were unable to remove some of the bad sequences
 602                 if (badSeqNames.size() != 0) {
 603                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 604                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 605                                 m->mothurOutEndLine();
 606                         }
 607                 }
 608
 609                 inputAlignReport.close();
 610                 goodAlignReportOut.close();
 611
 612                 if (m->control_pressed) {  remove(goodAlignReportFile.c_str());  return 0; }
 613
 614                 return 0;
 615
 616         }
 617         catch(exception& e) {
 618                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
 619                 exit(1);
 620         }
 621
 622 }
 623 //**********************************************************************************************************************
 624
 625 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
 626         try {
 627                 ofstream goodFile;
 628                 m->openOutputFile(goodFName, goodFile);
 629
 630                 ofstream badAccnosFile;
 631                 m->openOutputFile(badAccnosFName, badAccnosFile);
 632
 633                 ifstream inFASTA;
 634                 m->openInputFile(filename, inFASTA);
 635
 636                 inFASTA.seekg(filePos->start);
 637
 638                 bool done = false;
 639                 int count = 0;
 640
 641                 while (!done) {
 642
 643                         if (m->control_pressed) {  return 0; }
 644
 645                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 646                         if (currSeq.getName() != "") {
 647                                 bool goodSeq = 1;               //      innocent until proven guilty
 648                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 649                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 650                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 651                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 652                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 653                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 654
 655                                 if(goodSeq == 1){
 656                                         currSeq.printSequence(goodFile);
 657                                 }
 658                                 else{
 659                                         badAccnosFile << currSeq.getName() << endl;
 660                                         badSeqNames.insert(currSeq.getName());
 661                                 }
 662                         count++;
 663                         }
 664
 665                         unsigned long int pos = inFASTA.tellg();
 666                         if ((pos == -1) || (pos >= filePos->end)) { break; }
 667
 668                         //report progress
 669                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 670                 }
 671                 //report progress
 672                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 673
 674
 675                 goodFile.close();
 676                 inFASTA.close();
 677                 badAccnosFile.close();
 678
 679                 return count;
 680         }
 681         catch(exception& e) {
 682                 m->errorOut(e, "ScreenSeqsCommand", "driver");
 683                 exit(1);
 684         }
 685 }
 686 //**********************************************************************************************************************
 687 #ifdef USE_MPI
 688 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
 689         try {
 690                 string outputString = "";
 691                 MPI_Status statusGood;
 692                 MPI_Status statusBadAccnos;
 693                 MPI_Status status;
 694                 int pid;
 695                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 696
 697                 for(int i=0;i<num;i++){
 698
 699                         if (m->control_pressed) {  return 0; }
 700
 701                         //read next sequence
 702                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 703
 704                         char* buf4 = new char[length];
 705                         memcpy(buf4, outputString.c_str(), length);
 706
 707                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 708
 709                         string tempBuf = buf4;  delete buf4;
 710                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 711                         istringstream iss (tempBuf,istringstream::in);
 712
 713                         Sequence currSeq(iss);
 714
 715                         //process seq
 716                         if (currSeq.getName() != "") {
 717                                 bool goodSeq = 1;               //      innocent until proven guilty
 718                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 719                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 720                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 721                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 722                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 723                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 724
 725                                 if(goodSeq == 1){
 726                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
 727
 728                                         //print good seq
 729                                         length = outputString.length();
 730                                         char* buf2 = new char[length];
 731                                         memcpy(buf2, outputString.c_str(), length);
 732
 733                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
 734                                         delete buf2;
 735                                 }
 736                                 else{
 737
 738                                         badSeqNames.insert(currSeq.getName());
 739
 740                                         //write to bad accnos file
 741                                         outputString = currSeq.getName() + "\n";
 742
 743                                         length = outputString.length();
 744                                         char* buf3 = new char[length];
 745                                         memcpy(buf3, outputString.c_str(), length);
 746
 747                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
 748                                         delete buf3;
 749                                 }
 750                         }
 751                 }
 752
 753                 return 1;
 754         }
 755         catch(exception& e) {
 756                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
 757                 exit(1);
 758         }
 759 }
 760 #endif
 761 /**************************************************************************************************/
 762
 763 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
 764         try {
 765 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 766                 int process = 0;
 767                 int num = 0;
 768
 769                 //loop through and create all the processes you want
 770                 while (process != processors) {
 771                         int pid = fork();
 772
 773                         if (pid > 0) {
 774                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 775                                 process++;
 776                         }else if (pid == 0){
 777                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
 778
 779                                 //pass numSeqs to parent
 780                                 ofstream out;
 781                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 782                                 m->openOutputFile(tempFile, out);
 783                                 out << num << endl;
 784                                 out.close();
 785
 786                                 exit(0);
 787                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 788                 }
 789
 790                 //force parent to wait until all the processes are done
 791                 for (int i=0;i<processors;i++) {
 792                         int temp = processIDS[i];
 793                         wait(&temp);
 794                 }
 795
 796                 for (int i = 0; i < processIDS.size(); i++) {
 797                         ifstream in;
 798                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 799                         m->openInputFile(tempFile, in);
 800                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 801                         in.close(); remove(tempFile.c_str());
 802                 }
 803
 804                 return num;
 805 #endif
 806         }
 807         catch(exception& e) {
 808                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
 809                 exit(1);
 810         }
 811 }
 812
 813 //***************************************************************************************************************
 814
 815