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 vector<string> ScreenSeqsCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  20                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
  21                 CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
  22                 CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  23                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  24                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  25                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  26                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  27                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  28                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  29                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  30                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string ScreenSeqsCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The screen.seqs command reads a fastafile and creates .....\n";
  48                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
  49                 helpString += "The fasta parameter is required.\n";
  50                 helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
  51                 helpString += "The start parameter .... The default is -1.\n";
  52                 helpString += "The end parameter .... The default is -1.\n";
  53                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  54                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  55                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  56                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  57                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  58                 helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
  59                 helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
  60                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  61                 helpString += "The screen.seqs command should be in the following format: \n";
  62                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  63                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  64                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  65                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  66                 return helpString;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 ScreenSeqsCommand::ScreenSeqsCommand(){
  75         try {
  76                 abort = true; calledHelp = true;
  77                 setParameters();
  78                 vector<string> tempOutNames;
  79                 outputTypes["fasta"] = tempOutNames;
  80                 outputTypes["name"] = tempOutNames;
  81                 outputTypes["group"] = tempOutNames;
  82                 outputTypes["alignreport"] = tempOutNames;
  83                 outputTypes["accnos"] = tempOutNames;
  84                 outputTypes["qfile"] = tempOutNames;
  85                 outputTypes["taxonomy"] = tempOutNames;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
  89                 exit(1);
  90         }
  91 }
  92 //***************************************************************************************************************
  93
  94 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  95         try {
  96                 abort = false; calledHelp = false;
  97
  98                 //allow user to run help
  99                 if(option == "help") { help(); abort = true; calledHelp = true; }
 100                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 101
 102                 else {
 103                         vector<string> myArray = setParameters();
 104
 105                         OptionParser parser(option);
 106                         map<string,string> parameters = parser.getParameters();
 107
 108                         ValidParameters validParameter("screen.seqs");
 109                         map<string,string>::iterator it;
 110
 111                         //check to make sure all parameters are valid for command
 112                         for (it = parameters.begin(); it != parameters.end(); it++) {
 113                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 114                         }
 115
 116                         //initialize outputTypes
 117                         vector<string> tempOutNames;
 118                         outputTypes["fasta"] = tempOutNames;
 119                         outputTypes["name"] = tempOutNames;
 120                         outputTypes["group"] = tempOutNames;
 121                         outputTypes["alignreport"] = tempOutNames;
 122                         outputTypes["accnos"] = tempOutNames;
 123                         outputTypes["qfile"] = tempOutNames;
 124                         outputTypes["taxonomy"] = tempOutNames;
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128                         if (inputDir == "not found"){   inputDir = "";          }
 129                         else {
 130                                 string path;
 131                                 it = parameters.find("fasta");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 137                                 }
 138
 139                                 it = parameters.find("group");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 145                                 }
 146
 147                                 it = parameters.find("name");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 153                                 }
 154
 155                                 it = parameters.find("alignreport");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 161                                 }
 162
 163                                 it = parameters.find("qfile");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 169                                 }
 170
 171                                 it = parameters.find("taxonomy");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 177                                 }
 178                         }
 179
 180                         //check for required parameters
 181                         fastafile = validParameter.validFile(parameters, "fasta", true);
 182                         if (fastafile == "not found") {
 183                                 fastafile = m->getFastaFile();
 184                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 185                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 186                         }
 187                         else if (fastafile == "not open") { abort = true; }
 188                         else { m->setFastaFile(fastafile); }
 189
 190                         groupfile = validParameter.validFile(parameters, "group", true);
 191                         if (groupfile == "not open") { abort = true; }
 192                         else if (groupfile == "not found") { groupfile = ""; }
 193                         else { m->setGroupFile(groupfile); }
 194
 195                         qualfile = validParameter.validFile(parameters, "qfile", true);
 196                         if (qualfile == "not open") { abort = true; }
 197                         else if (qualfile == "not found") { qualfile = ""; }
 198                         else { m->setQualFile(qualfile); }
 199
 200                         namefile = validParameter.validFile(parameters, "name", true);
 201                         if (namefile == "not open") { namefile = ""; abort = true; }
 202                         else if (namefile == "not found") { namefile = ""; }
 203                         else { m->setNameFile(namefile); }
 204
 205                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 206                         if (alignreport == "not open") { abort = true; }
 207                         else if (alignreport == "not found") { alignreport = ""; }
 208
 209                         taxonomy = validParameter.validFile(parameters, "taxonomy", true);
 210                         if (taxonomy == "not open") { abort = true; }
 211                         else if (taxonomy == "not found") { taxonomy = ""; }
 212
 213                         //if the user changes the output directory command factory will send this info to us in the output parameter
 214                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 215                                 outputDir = "";
 216                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 217                         }
 218
 219                         //check for optional parameter and set defaults
 220                         // ...at some point should added some additional type checking...
 221                         string temp;
 222                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 223                         m->mothurConvert(temp, startPos);
 224
 225                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 226                         m->mothurConvert(temp, endPos);
 227
 228                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 229                         m->mothurConvert(temp, maxAmbig);
 230
 231                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 232                         m->mothurConvert(temp, maxHomoP);
 233
 234                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 235                         m->mothurConvert(temp, minLength);
 236
 237                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 238                         m->mothurConvert(temp, maxLength);
 239
 240                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 241                         m->setProcessors(temp);
 242                         m->mothurConvert(temp, processors);
 243
 244                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 245                         if (temp == "not found"){       temp = "none";          }
 246                         m->splitAtDash(temp, optimize);
 247
 248                         //check for invalid optimize options
 249                         set<string> validOptimizers;
 250                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 251                         for (int i = 0; i < optimize.size(); i++) {
 252                                 if (validOptimizers.count(optimize[i]) == 0) {
 253                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 254                                         optimize.erase(optimize.begin()+i);
 255                                         i--;
 256                                 }
 257                         }
 258
 259                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 260
 261                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 262                         m->mothurConvert(temp, criteria);
 263
 264                         if (namefile == "") {
 265                                 vector<string> files; files.push_back(fastafile);
 266                                 parser.getNameFile(files);
 267                         }
 268                 }
 269
 270         }
 271         catch(exception& e) {
 272                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 273                 exit(1);
 274         }
 275 }
 276 //***************************************************************************************************************
 277
 278 int ScreenSeqsCommand::execute(){
 279         try{
 280
 281                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 282
 283                 //if the user want to optimize we need to know the 90% mark
 284                 vector<unsigned long long> positions;
 285                 if (optimize.size() != 0) {  //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
 286                         //use the namefile to optimize correctly
 287                         if (namefile != "") { nameMap = m->readNames(namefile); }
 288                         getSummary(positions);
 289                 }
 290                 else {
 291                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 292                         positions = m->divideFile(fastafile, processors);
 293                         for (int i = 0; i < (positions.size()-1); i++) {
 294                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 295                         }
 296                         #else
 297                                 positions.push_back(0); positions.push_back(1000);
 298                                 lines.push_back(new linePair(0, 1000));
 299                         #endif
 300                 }
 301
 302                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 303                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 304
 305                 int numFastaSeqs = 0;
 306                 set<string> badSeqNames;
 307                 int start = time(NULL);
 308
 309 #ifdef USE_MPI
 310                         int pid, numSeqsPerProcessor;
 311                         int tag = 2001;
 312                         vector<unsigned long long> MPIPos;
 313
 314                         MPI_Status status;
 315                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 316                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 317
 318                         MPI_File inMPI;
 319                         MPI_File outMPIGood;
 320                         MPI_File outMPIBadAccnos;
 321
 322                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 323                         int inMode=MPI_MODE_RDONLY;
 324
 325                         char outGoodFilename[1024];
 326                         strcpy(outGoodFilename, goodSeqFile.c_str());
 327
 328                         char outBadAccnosFilename[1024];
 329                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 330
 331                         char inFileName[1024];
 332                         strcpy(inFileName, fastafile.c_str());
 333
 334                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 335                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 336                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 337
 338                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 339
 340                         if (pid == 0) { //you are the root process
 341
 342                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 343
 344                                 //send file positions to all processes
 345                                 for(int i = 1; i < processors; i++) {
 346                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 347                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 348                                 }
 349
 350                                 //figure out how many sequences you have to align
 351                                 numSeqsPerProcessor = numFastaSeqs / processors;
 352                                 int startIndex =  pid * numSeqsPerProcessor;
 353                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 354                 //      cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
 355                                 //align your part
 356                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 357                 //cout << pid << " done" << endl;
 358                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 359
 360                                 for (int i = 1; i < processors; i++) {
 361
 362                                         //get bad lists
 363                                         int badSize;
 364                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 365                                         /*for (int j = 0; j < badSize; j++) {
 366                                                 int length;
 367                                                 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);  //recv the length of the name
 368                                                 char* buf2 = new char[length];                                                                          //make space to recieve it
 369                                                 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);  //get name
 370
 371                                                 string tempBuf = buf2;
 372                                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 373                                                 delete buf2;
 374
 375                                                 badSeqNames.insert(tempBuf);
 376                                         }*/
 377                                 }
 378                         }else{ //you are a child process
 379                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 380                                 MPIPos.resize(numFastaSeqs+1);
 381                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 382
 383                                 //figure out how many sequences you have to align
 384                                 numSeqsPerProcessor = numFastaSeqs / processors;
 385                                 int startIndex =  pid * numSeqsPerProcessor;
 386                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 387                 //cout << pid << '\t' << numSeqsPerProcessor << '\t' <<         startIndex << endl;
 388                                 //align your part
 389                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 390 //cout << pid << " done" << endl;
 391                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 392
 393                                 //send bad list
 394                                 int badSize = badSeqNames.size();
 395                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 396
 397                                 /*
 398                                 set<string>::iterator it;
 399                                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 400                                         string name = *it;
 401                                         int length = name.length();
 402                                         char* buf2 = new char[length];
 403                                         memcpy(buf2, name.c_str(), length);
 404
 405                                         MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 406                                         MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 407                                 }*/
 408                         }
 409
 410                         //close files
 411                         MPI_File_close(&inMPI);
 412                         MPI_File_close(&outMPIGood);
 413                         MPI_File_close(&outMPIBadAccnos);
 414                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 415
 416 #else
 417
 418         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 419                         if(processors == 1){
 420                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 421
 422                                 if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 423
 424                         }else{
 425                                 processIDS.resize(0);
 426
 427                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 428
 429                                 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
 430                                 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
 431
 432                                 //append alignment and report files
 433                                 for(int i=1;i<processors;i++){
 434                                         m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
 435                                         m->mothurRemove((goodSeqFile + toString(processIDS[i]) + ".temp"));
 436
 437                                         m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
 438                                         m->mothurRemove((badAccnosFile + toString(processIDS[i]) + ".temp"));
 439                                 }
 440
 441                                 if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 442
 443                                 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
 444                                 ifstream inBad;
 445                                 int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
 446
 447                                 if (ableToOpen == 0) {
 448                                         badSeqNames.clear();
 449                                         string tempName;
 450                                         while (!inBad.eof()) {
 451                                                 inBad >> tempName; m->gobble(inBad);
 452                                                 badSeqNames.insert(tempName);
 453                                         }
 454                                         inBad.close();
 455                                 }
 456                         }
 457         #else
 458                         numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 459
 460                         if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 461
 462         #endif
 463
 464 #endif
 465
 466                 #ifdef USE_MPI
 467                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 468
 469                         if (pid == 0) { //only one process should fix files
 470
 471                                 //read accnos file with all names in it, process 0 just has its names
 472                                 MPI_File inMPIAccnos;
 473                                 MPI_Offset size;
 474
 475                                 char inFileName[1024];
 476                                 strcpy(inFileName, badAccnosFile.c_str());
 477
 478                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 479                                 MPI_File_get_size(inMPIAccnos, &size);
 480
 481                                 char* buffer = new char[size];
 482                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 483
 484                                 string tempBuf = buffer;
 485                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 486                                 istringstream iss (tempBuf,istringstream::in);
 487
 488                                 delete buffer;
 489                                 MPI_File_close(&inMPIAccnos);
 490
 491                                 badSeqNames.clear();
 492                                 string tempName;
 493                                 while (!iss.eof()) {
 494                                         iss >> tempName; m->gobble(iss);
 495                                         badSeqNames.insert(tempName);
 496                                 }
 497                 #endif
 498
 499                 if(namefile != "" && groupfile != "")   {
 500                         screenNameGroupFile(badSeqNames);
 501                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile); return 0; }
 502                 }else if(namefile != "")        {
 503                         screenNameGroupFile(badSeqNames);
 504                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile);  return 0; }
 505                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 506
 507                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 508
 509                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 510                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 511                 if(taxonomy != "")                                              {       screenTaxonomy(badSeqNames);            }
 512
 513                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 514
 515                 #ifdef USE_MPI
 516                         }
 517                 #endif
 518
 519                 m->mothurOutEndLine();
 520                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 521                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 522                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 523                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 524                 m->mothurOutEndLine();
 525                 m->mothurOutEndLine();
 526
 527                 //set fasta file as new current fastafile
 528                 string current = "";
 529                 itTypes = outputTypes.find("fasta");
 530                 if (itTypes != outputTypes.end()) {
 531                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 532                 }
 533
 534                 itTypes = outputTypes.find("name");
 535                 if (itTypes != outputTypes.end()) {
 536                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 537                 }
 538
 539                 itTypes = outputTypes.find("group");
 540                 if (itTypes != outputTypes.end()) {
 541                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 542                 }
 543
 544                 itTypes = outputTypes.find("qfile");
 545                 if (itTypes != outputTypes.end()) {
 546                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 547                 }
 548
 549                 itTypes = outputTypes.find("taxonomy");
 550                 if (itTypes != outputTypes.end()) {
 551                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 552                 }
 553
 554                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 555                 m->mothurOutEndLine();
 556
 557                 return 0;
 558         }
 559         catch(exception& e) {
 560                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 561                 exit(1);
 562         }
 563 }
 564
 565 //***************************************************************************************************************
 566
 567 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 568         try {
 569                 ifstream inputNames;
 570                 m->openInputFile(namefile, inputNames);
 571                 set<string> badSeqGroups;
 572                 string seqName, seqList, group;
 573                 set<string>::iterator it;
 574
 575                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 576                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 577
 578                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 579
 580                 while(!inputNames.eof()){
 581                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 582
 583                         inputNames >> seqName >> seqList;
 584                         it = badSeqNames.find(seqName);
 585
 586                         if(it != badSeqNames.end()){
 587                                 badSeqNames.erase(it);
 588
 589                                 if(namefile != ""){
 590                                         int start = 0;
 591                                         for(int i=0;i<seqList.length();i++){
 592                                                 if(seqList[i] == ','){
 593                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 594                                                         start = i+1;
 595                                                 }
 596                                         }
 597                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 598                                 }
 599                         }
 600                         else{
 601                                 goodNameOut << seqName << '\t' << seqList << endl;
 602                         }
 603                         m->gobble(inputNames);
 604                 }
 605                 inputNames.close();
 606                 goodNameOut.close();
 607
 608                 //we were unable to remove some of the bad sequences
 609                 if (badSeqNames.size() != 0) {
 610                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 611                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 612                                 m->mothurOutEndLine();
 613                         }
 614                 }
 615
 616                 if(groupfile != ""){
 617
 618                         ifstream inputGroups;
 619                         m->openInputFile(groupfile, inputGroups);
 620
 621                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 622                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 623
 624                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 625
 626                         while(!inputGroups.eof()){
 627                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 628
 629                                 inputGroups >> seqName >> group;
 630
 631                                 it = badSeqGroups.find(seqName);
 632
 633                                 if(it != badSeqGroups.end()){
 634                                         badSeqGroups.erase(it);
 635                                 }
 636                                 else{
 637                                         goodGroupOut << seqName << '\t' << group << endl;
 638                                 }
 639                                 m->gobble(inputGroups);
 640                         }
 641                         inputGroups.close();
 642                         goodGroupOut.close();
 643
 644                         //we were unable to remove some of the bad sequences
 645                         if (badSeqGroups.size() != 0) {
 646                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 647                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 648                                         m->mothurOutEndLine();
 649                                 }
 650                         }
 651                 }
 652
 653
 654                 return 0;
 655
 656         }
 657         catch(exception& e) {
 658                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 659                 exit(1);
 660         }
 661 }
 662 //***************************************************************************************************************
 663 int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 664         try {
 665
 666                 vector<int> startPosition;
 667                 vector<int> endPosition;
 668                 vector<int> seqLength;
 669                 vector<int> ambigBases;
 670                 vector<int> longHomoPolymer;
 671
 672 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 673                 vector<unsigned long long> positions = m->divideFile(fastafile, processors);
 674
 675                 for (int i = 0; i < (positions.size()-1); i++) {
 676                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 677                 }
 678 #else
 679                 lines.push_back(new linePair(0, 1000));
 680 #endif
 681
 682 #ifdef USE_MPI
 683                 int pid;
 684                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 685
 686                 if (pid == 0) {
 687                         driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 688 #else
 689                 int numSeqs = 0;
 690                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 691                         if(processors == 1){
 692                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 693                         }else{
 694                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 695                         }
 696
 697                         if (m->control_pressed) {  return 0; }
 698                 #else
 699                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 700                         if (m->control_pressed) {  return 0; }
 701                 #endif
 702 #endif
 703                 sort(startPosition.begin(), startPosition.end());
 704                 sort(endPosition.begin(), endPosition.end());
 705                 sort(seqLength.begin(), seqLength.end());
 706                 sort(ambigBases.begin(), ambigBases.end());
 707                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 708
 709                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 710                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 711
 712                 for (int i = 0; i < optimize.size(); i++) {
 713                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 714                         else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
 715                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 716                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 717                         else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
 718                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 719                 }
 720
 721 #ifdef USE_MPI
 722                 }
 723
 724                 MPI_Status status;
 725                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 726                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 727
 728                 if (pid == 0) {
 729                         //send file positions to all processes
 730                         for(int i = 1; i < processors; i++) {
 731                                 MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 732                                 MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 733                                 MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 734                                 MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 735                                 MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 736                                 MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 737                         }
 738                 }else {
 739                         MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 740                         MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 741                         MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 742                         MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 743                         MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 744                         MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 745                 }
 746                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 747 #endif
 748                 return 0;
 749         }
 750         catch(exception& e) {
 751                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 752                 exit(1);
 753         }
 754 }
 755 /**************************************************************************************/
 756 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
 757         try {
 758
 759                 ifstream in;
 760                 m->openInputFile(filename, in);
 761
 762                 in.seekg(filePos->start);
 763
 764                 bool done = false;
 765                 int count = 0;
 766
 767                 while (!done) {
 768
 769                         if (m->control_pressed) { in.close(); return 1; }
 770
 771                         Sequence current(in); m->gobble(in);
 772
 773                         if (current.getName() != "") {
 774                                 int num = 1;
 775                                 if (namefile != "") {
 776                                         //make sure this sequence is in the namefile, else error
 777                                         map<string, int>::iterator it = nameMap.find(current.getName());
 778
 779                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 780                                         else { num = it->second; }
 781                                 }
 782
 783                                 //for each sequence this sequence represents
 784                                 for (int i = 0; i < num; i++) {
 785                                         startPosition.push_back(current.getStartPos());
 786                                         endPosition.push_back(current.getEndPos());
 787                                         seqLength.push_back(current.getNumBases());
 788                                         ambigBases.push_back(current.getAmbigBases());
 789                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 790                                 }
 791
 792                                 count++;
 793                         }
 794                         //if((count) % 100 == 0){       m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();         }
 795                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 796                                 unsigned long long pos = in.tellg();
 797                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 798                         #else
 799                                 if (in.eof()) { break; }
 800                         #endif
 801
 802                 }
 803
 804                 in.close();
 805
 806                 return count;
 807         }
 808         catch(exception& e) {
 809                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 810                 exit(1);
 811         }
 812 }
 813 /**************************************************************************************************/
 814 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 815         try {
 816 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 817                 int process = 1;
 818                 int num = 0;
 819                 processIDS.clear();
 820
 821                 //loop through and create all the processes you want
 822                 while (process != processors) {
 823                         int pid = fork();
 824
 825                         if (pid > 0) {
 826                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 827                                 process++;
 828                         }else if (pid == 0){
 829                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 830
 831                                 //pass numSeqs to parent
 832                                 ofstream out;
 833                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 834                                 m->openOutputFile(tempFile, out);
 835
 836                                 out << num << endl;
 837                                 out << startPosition.size() << endl;
 838                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 839                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 840                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 841                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 842                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 843
 844                                 out.close();
 845
 846                                 exit(0);
 847                         }else {
 848                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 849                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 850                                 exit(0);
 851                         }
 852                 }
 853
 854                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 855
 856                 //force parent to wait until all the processes are done
 857                 for (int i=0;i<processIDS.size();i++) {
 858                         int temp = processIDS[i];
 859                         wait(&temp);
 860                 }
 861
 862                 //parent reads in and combine Filter info
 863                 for (int i = 0; i < processIDS.size(); i++) {
 864                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 865                         ifstream in;
 866                         m->openInputFile(tempFilename, in);
 867
 868                         int temp, tempNum;
 869                         in >> tempNum; m->gobble(in); num += tempNum;
 870                         in >> tempNum; m->gobble(in);
 871                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 872                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 873                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 874                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 875                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 876
 877                         in.close();
 878                         m->mothurRemove(tempFilename);
 879                 }
 880
 881                 return num;
 882 #endif
 883         }
 884         catch(exception& e) {
 885                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 886                 exit(1);
 887         }
 888 }
 889
 890 //***************************************************************************************************************
 891
 892 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 893         try {
 894                 ifstream inputGroups;
 895                 m->openInputFile(groupfile, inputGroups);
 896                 string seqName, group;
 897                 set<string>::iterator it;
 898
 899                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 900                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 901                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 902
 903                 while(!inputGroups.eof()){
 904                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 905
 906                         inputGroups >> seqName >> group;
 907                         it = badSeqNames.find(seqName);
 908
 909                         if(it != badSeqNames.end()){
 910                                 badSeqNames.erase(it);
 911                         }
 912                         else{
 913                                 goodGroupOut << seqName << '\t' << group << endl;
 914                         }
 915                         m->gobble(inputGroups);
 916                 }
 917
 918                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
 919
 920                 //we were unable to remove some of the bad sequences
 921                 if (badSeqNames.size() != 0) {
 922                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 923                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 924                                 m->mothurOutEndLine();
 925                         }
 926                 }
 927
 928                 inputGroups.close();
 929                 goodGroupOut.close();
 930
 931                 if (m->control_pressed) { m->mothurRemove(goodGroupFile);   }
 932
 933                 return 0;
 934
 935         }
 936         catch(exception& e) {
 937                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 938                 exit(1);
 939         }
 940 }
 941
 942 //***************************************************************************************************************
 943
 944 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 945         try {
 946                 ifstream inputAlignReport;
 947                 m->openInputFile(alignreport, inputAlignReport);
 948                 string seqName, group;
 949                 set<string>::iterator it;
 950
 951                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 952                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 953                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 954
 955                 while (!inputAlignReport.eof()) {               //      need to copy header
 956                         char c = inputAlignReport.get();
 957                         goodAlignReportOut << c;
 958                         if (c == 10 || c == 13){        break;  }
 959                 }
 960
 961                 while(!inputAlignReport.eof()){
 962                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
 963
 964                         inputAlignReport >> seqName;
 965                         it = badSeqNames.find(seqName);
 966                         string line;
 967                         while (!inputAlignReport.eof()) {               //      need to copy header
 968                                 char c = inputAlignReport.get();
 969                                 line += c;
 970                                 if (c == 10 || c == 13){        break;  }
 971                         }
 972
 973                         if(it != badSeqNames.end()){
 974                                 badSeqNames.erase(it);
 975                         }
 976                         else{
 977                                 goodAlignReportOut << seqName << '\t' << line;
 978                         }
 979                         m->gobble(inputAlignReport);
 980                 }
 981
 982                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); m->mothurRemove(goodAlignReportFile);  return 0; }
 983
 984                 //we were unable to remove some of the bad sequences
 985                 if (badSeqNames.size() != 0) {
 986                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 987                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 988                                 m->mothurOutEndLine();
 989                         }
 990                 }
 991
 992                 inputAlignReport.close();
 993                 goodAlignReportOut.close();
 994
 995                 if (m->control_pressed) {  m->mothurRemove(goodAlignReportFile);  return 0; }
 996
 997                 return 0;
 998
 999         }
1000         catch(exception& e) {
1001                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
1002                 exit(1);
1003         }
1004
1005 }
1006 //***************************************************************************************************************
1007
1008 int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
1009         try {
1010                 ifstream input;
1011                 m->openInputFile(taxonomy, input);
1012                 string seqName, tax;
1013                 set<string>::iterator it;
1014
1015                 string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy);
1016                 outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
1017                 ofstream goodTaxOut;    m->openOutputFile(goodTaxFile, goodTaxOut);
1018
1019                 while(!input.eof()){
1020                         if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1021
1022                         input >> seqName >> tax;
1023                         it = badSeqNames.find(seqName);
1024
1025                         if(it != badSeqNames.end()){ badSeqNames.erase(it); }
1026                         else{
1027                                 goodTaxOut << seqName << '\t' << tax << endl;
1028                         }
1029                         m->gobble(input);
1030                 }
1031
1032                 if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1033
1034                 //we were unable to remove some of the bad sequences
1035                 if (badSeqNames.size() != 0) {
1036                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1037                                 m->mothurOut("Your taxonomy file does not include the sequence " + *it + " please correct.");
1038                                 m->mothurOutEndLine();
1039                         }
1040                 }
1041
1042                 input.close();
1043                 goodTaxOut.close();
1044
1045                 if (m->control_pressed) {  m->mothurRemove(goodTaxFile);  return 0; }
1046
1047                 return 0;
1048
1049         }
1050         catch(exception& e) {
1051                 m->errorOut(e, "ScreenSeqsCommand", "screenTaxonomy");
1052                 exit(1);
1053         }
1054
1055 }
1056 //***************************************************************************************************************
1057
1058 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
1059         try {
1060                 ifstream in;
1061                 m->openInputFile(qualfile, in);
1062                 set<string>::iterator it;
1063
1064                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
1065                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
1066                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
1067
1068                 while(!in.eof()){
1069
1070                         if (m->control_pressed) { goodQual.close(); in.close(); m->mothurRemove(goodQualFile); return 0; }
1071
1072                         string saveName = "";
1073                         string name = "";
1074                         string scores = "";
1075
1076                         in >> name;
1077
1078                         if (name.length() != 0) {
1079                                 saveName = name.substr(1);
1080                                 while (!in.eof())       {
1081                                         char c = in.get();
1082                                         if (c == 10 || c == 13){        break;  }
1083                                         else { name += c; }
1084                                 }
1085                                 m->gobble(in);
1086                         }
1087
1088                         while(in){
1089                                 char letter= in.get();
1090                                 if(letter == '>'){      in.putback(letter);     break;  }
1091                                 else{ scores += letter; }
1092                         }
1093
1094                         m->gobble(in);
1095
1096                         it = badSeqNames.find(saveName);
1097
1098                         if(it != badSeqNames.end()){
1099                                 badSeqNames.erase(it);
1100                         }else{
1101                                 goodQual << name << endl << scores;
1102                         }
1103
1104                         m->gobble(in);
1105                 }
1106
1107                 in.close();
1108                 goodQual.close();
1109
1110                 //we were unable to remove some of the bad sequences
1111                 if (badSeqNames.size() != 0) {
1112                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1113                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
1114                                 m->mothurOutEndLine();
1115                         }
1116                 }
1117
1118                 if (m->control_pressed) {  m->mothurRemove(goodQualFile);  return 0; }
1119
1120                 return 0;
1121
1122         }
1123         catch(exception& e) {
1124                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1125                 exit(1);
1126         }
1127
1128 }
1129 //**********************************************************************************************************************
1130
1131 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1132         try {
1133                 ofstream goodFile;
1134                 m->openOutputFile(goodFName, goodFile);
1135
1136                 ofstream badAccnosFile;
1137                 m->openOutputFile(badAccnosFName, badAccnosFile);
1138
1139                 ifstream inFASTA;
1140                 m->openInputFile(filename, inFASTA);
1141
1142                 inFASTA.seekg(filePos->start);
1143
1144                 bool done = false;
1145                 int count = 0;
1146
1147                 while (!done) {
1148
1149                         if (m->control_pressed) {  return 0; }
1150
1151                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1152                         if (currSeq.getName() != "") {
1153                                 bool goodSeq = 1;               //      innocent until proven guilty
1154                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1155                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1156                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1157                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1158                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1159                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1160
1161                                 if(goodSeq == 1){
1162                                         currSeq.printSequence(goodFile);
1163                                 }
1164                                 else{
1165                                         badAccnosFile << currSeq.getName() << endl;
1166                                         badSeqNames.insert(currSeq.getName());
1167                                 }
1168                         count++;
1169                         }
1170
1171                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1172                                 unsigned long long pos = inFASTA.tellg();
1173                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1174                         #else
1175                                 if (inFASTA.eof()) { break; }
1176                         #endif
1177
1178                         //report progress
1179                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1180                 }
1181                 //report progress
1182                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1183
1184
1185                 goodFile.close();
1186                 inFASTA.close();
1187                 badAccnosFile.close();
1188
1189                 return count;
1190         }
1191         catch(exception& e) {
1192                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1193                 exit(1);
1194         }
1195 }
1196 //**********************************************************************************************************************
1197 #ifdef USE_MPI
1198 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
1199         try {
1200                 string outputString = "";
1201                 MPI_Status statusGood;
1202                 MPI_Status statusBadAccnos;
1203                 MPI_Status status;
1204                 int pid;
1205                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1206
1207                 for(int i=0;i<num;i++){
1208
1209                         if (m->control_pressed) {  return 0; }
1210
1211                         //read next sequence
1212                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1213
1214                         char* buf4 = new char[length];
1215                         memcpy(buf4, outputString.c_str(), length);
1216
1217                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1218
1219                         string tempBuf = buf4;  delete buf4;
1220                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1221                         istringstream iss (tempBuf,istringstream::in);
1222
1223                         Sequence currSeq(iss);
1224
1225                         //process seq
1226                         if (currSeq.getName() != "") {
1227                                 bool goodSeq = 1;               //      innocent until proven guilty
1228                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1229                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1230                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1231                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1232                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1233                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1234
1235                                 if(goodSeq == 1){
1236                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1237
1238                                         //print good seq
1239                                         length = outputString.length();
1240                                         char* buf2 = new char[length];
1241                                         memcpy(buf2, outputString.c_str(), length);
1242
1243                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1244                                         delete buf2;
1245                                 }
1246                                 else{
1247
1248                                         badSeqNames.insert(currSeq.getName());
1249
1250                                         //write to bad accnos file
1251                                         outputString = currSeq.getName() + "\n";
1252
1253                                         length = outputString.length();
1254                                         char* buf3 = new char[length];
1255                                         memcpy(buf3, outputString.c_str(), length);
1256
1257                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1258                                         delete buf3;
1259                                 }
1260                         }
1261
1262                         //report progress
1263                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1264                 }
1265
1266                 return 1;
1267         }
1268         catch(exception& e) {
1269                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1270                 exit(1);
1271         }
1272 }
1273 #endif
1274 /**************************************************************************************************/
1275
1276 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1277         try {
1278 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1279                 int process = 0;
1280                 int num = 0;
1281
1282                 //loop through and create all the processes you want
1283                 while (process != processors) {
1284                         int pid = fork();
1285
1286                         if (pid > 0) {
1287                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1288                                 process++;
1289                         }else if (pid == 0){
1290                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1291
1292                                 //pass numSeqs to parent
1293                                 ofstream out;
1294                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1295                                 m->openOutputFile(tempFile, out);
1296                                 out << num << endl;
1297                                 out.close();
1298
1299                                 exit(0);
1300                         }else {
1301                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1302                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1303                                 exit(0);
1304                         }
1305                 }
1306
1307                 //force parent to wait until all the processes are done
1308                 for (int i=0;i<processors;i++) {
1309                         int temp = processIDS[i];
1310                         wait(&temp);
1311                 }
1312
1313                 for (int i = 0; i < processIDS.size(); i++) {
1314                         ifstream in;
1315                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1316                         m->openInputFile(tempFile, in);
1317                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1318                         in.close(); m->mothurRemove(tempFile);
1319                 }
1320
1321                 return num;
1322 #endif
1323         }
1324         catch(exception& e) {
1325                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1326                 exit(1);
1327         }
1328 }
1329
1330 //***************************************************************************************************************
1331
1332