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