classifyseqscommand.cpp

   1 /*
   2  *  classifyseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/2/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "classifyseqscommand.h"
  11
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> ClassifySeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
  18                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  20                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  23                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  24                 CommandParameter pmethod("method", "Multiple", "bayesian-knn", "bayesian", "", "", "",false,false); parameters.push_back(pmethod);
  25                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  26                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  27                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  28                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  29                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  30                 //CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  31                 CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
  32                 CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
  33                 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
  34                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  35                 CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "ClassifySeqsCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string ClassifySeqsCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
  53                 helpString += "The classify.seqs command parameters are reference, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
  54                 helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
  55                 helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer, blast and distance. The default is kmer.\n";
  56                 helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n";
  57                 helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
  58                 helpString += "The method parameter allows you to specify classification method to use.  Your options are: bayesian and knn. The default is bayesian.\n";
  59                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n";
  60                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  61 #ifdef USE_MPI
  62                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  63 #endif
  64                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  65                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  66                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  67                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  68                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  69                 helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
  70                 helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
  71                 helpString += "The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n";
  72                 helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method.  The default is 100.\n";
  73                 //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
  74                 helpString += "The classify.seqs command should be in the following format: \n";
  75                 helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
  76                 helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
  77                 helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
  78                 helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
  79                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 string ClassifySeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  89         try {
  90         string outputFileName = "";
  91                 map<string, vector<string> >::iterator it;
  92
  93         //is this a type this command creates
  94         it = outputTypes.find(type);
  95         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  96         else {
  97             if (type == "taxonomy") {  outputFileName =  "taxonomy"; }
  98             else if (type == "accnos") {  outputFileName =  "flip.accnos"; }
  99             else if (type == "taxsummary") {  outputFileName =  "tax.summary"; }
 100             else if (type == "matchdist") {  outputFileName =  "match.dist"; }
 101             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 102         }
 103         return outputFileName;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "ClassifySeqsCommand", "getOutputFileNameTag");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111 ClassifySeqsCommand::ClassifySeqsCommand(){
 112         try {
 113                 abort = true; calledHelp = true;
 114                 setParameters();
 115                 vector<string> tempOutNames;
 116                 outputTypes["taxonomy"] = tempOutNames;
 117                 outputTypes["accnos"] = tempOutNames;
 118                 outputTypes["taxsummary"] = tempOutNames;
 119                 outputTypes["matchdist"] = tempOutNames;
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 128         try {
 129                 abort = false; calledHelp = false;
 130                 rdb = ReferenceDB::getInstance();
 131
 132                 //allow user to run help
 133                 if(option == "help") { help(); abort = true; calledHelp = true; }
 134                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 135
 136                 else {
 137                         vector<string> myArray = setParameters();
 138
 139                         OptionParser parser(option);
 140                         map<string, string> parameters = parser.getParameters();
 141
 142                         ValidParameters validParameter("classify.seqs");
 143                         map<string, string>::iterator it;
 144
 145                         //check to make sure all parameters are valid for command
 146                         for (it = parameters.begin(); it != parameters.end(); it++) {
 147                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 148                         }
 149
 150                         //initialize outputTypes
 151                         vector<string> tempOutNames;
 152                         outputTypes["taxonomy"] = tempOutNames;
 153                         outputTypes["taxsummary"] = tempOutNames;
 154                         outputTypes["matchdist"] = tempOutNames;
 155                         outputTypes["accnos"] = tempOutNames;
 156
 157                         //if the user changes the output directory command factory will send this info to us in the output parameter
 158                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 159
 160                         //if the user changes the input directory command factory will send this info to us in the output parameter
 161                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 162                         if (inputDir == "not found"){   inputDir = "";          }
 163                         else {
 164                                 string path;
 165                                 it = parameters.find("reference");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 171                                 }
 172
 173                                 it = parameters.find("taxonomy");
 174                                 //user has given a template file
 175                                 if(it != parameters.end()){
 176                                         path = m->hasPath(it->second);
 177                                         //if the user has not given a path then, add inputdir. else leave path alone.
 178                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 179                                 }
 180
 181                                 it = parameters.find("group");
 182                                 //user has given a template file
 183                                 if(it != parameters.end()){
 184                                         path = m->hasPath(it->second);
 185                                         //if the user has not given a path then, add inputdir. else leave path alone.
 186                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 187                                 }
 188                         }
 189
 190                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 191                         if (fastaFileName == "not found") {
 192                                 //if there is a current fasta file, use it
 193                                 string filename = m->getFastaFile();
 194                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 195                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 196                         }
 197                         else {
 198                                 m->splitAtDash(fastaFileName, fastaFileNames);
 199
 200                                 //go through files and make sure they are good, if not, then disregard them
 201                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 202
 203                                         bool ignore = false;
 204                                         if (fastaFileNames[i] == "current") {
 205                                                 fastaFileNames[i] = m->getFastaFile();
 206                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 207                                                 else {
 208                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 209                                                         //erase from file list
 210                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 211                                                         i--;
 212                                                 }
 213                                         }
 214
 215                                         if (!ignore) {
 216
 217                                                 if (inputDir != "") {
 218                                                         string path = m->hasPath(fastaFileNames[i]);
 219                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 220                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 221                                                 }
 222
 223                                                 int ableToOpen;
 224
 225                                                 ifstream in;
 226                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 227
 228                                                 //if you can't open it, try default location
 229                                                 if (ableToOpen == 1) {
 230                                                         if (m->getDefaultPath() != "") { //default path is set
 231                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 232                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 233                                                                 ifstream in2;
 234                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 235                                                                 in2.close();
 236                                                                 fastaFileNames[i] = tryPath;
 237                                                         }
 238                                                 }
 239
 240                                                 if (ableToOpen == 1) {
 241                                                         if (m->getOutputDir() != "") { //default path is set
 242                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 243                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 244                                                                 ifstream in2;
 245                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 246                                                                 in2.close();
 247                                                                 fastaFileNames[i] = tryPath;
 248                                                         }
 249                                                 }
 250
 251                                                 in.close();
 252
 253                                                 if (ableToOpen == 1) {
 254                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 255                                                         //erase from file list
 256                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 257                                                         i--;
 258                                                 }else {
 259                                                         m->setFastaFile(fastaFileNames[i]);
 260                                                 }
 261                                         }
 262
 263                                 }
 264
 265                                 //make sure there is at least one valid file left
 266                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 267                         }
 268
 269                         namefile = validParameter.validFile(parameters, "name", false);
 270                         if (namefile == "not found") { namefile = "";  }
 271
 272                         else {
 273                                 m->splitAtDash(namefile, namefileNames);
 274
 275                                 //go through files and make sure they are good, if not, then disregard them
 276                                 for (int i = 0; i < namefileNames.size(); i++) {
 277                                         bool ignore = false;
 278                                         if (namefileNames[i] == "current") {
 279                                                 namefileNames[i] = m->getNameFile();
 280                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 281                                                 else {
 282                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 283                                                         //erase from file list
 284                                                         namefileNames.erase(namefileNames.begin()+i);
 285                                                         i--;
 286                                                 }
 287                                         }
 288
 289                                         if (!ignore) {
 290
 291                                                 if (inputDir != "") {
 292                                                         string path = m->hasPath(namefileNames[i]);
 293                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 294                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 295                                                 }
 296                                                 int ableToOpen;
 297
 298                                                 ifstream in;
 299                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 300
 301                                                 //if you can't open it, try default location
 302                                                 if (ableToOpen == 1) {
 303                                                         if (m->getDefaultPath() != "") { //default path is set
 304                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 305                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 306                                                                 ifstream in2;
 307                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 308                                                                 in2.close();
 309                                                                 namefileNames[i] = tryPath;
 310                                                         }
 311                                                 }
 312
 313                                                 if (ableToOpen == 1) {
 314                                                         if (m->getOutputDir() != "") { //default path is set
 315                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 316                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 317                                                                 ifstream in2;
 318                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 319                                                                 in2.close();
 320                                                                 namefileNames[i] = tryPath;
 321                                                         }
 322                                                 }
 323                                                 in.close();
 324
 325                                                 if (ableToOpen == 1) {
 326                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 327                                                         //erase from file list
 328                                                         namefileNames.erase(namefileNames.begin()+i);
 329                                                         i--;
 330                                                 }else {
 331                                                         m->setNameFile(namefileNames[i]);
 332                                                 }
 333                                         }
 334                                 }
 335                         }
 336
 337                         if (namefile != "") {
 338                                 if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
 339                         }
 340
 341                         groupfile = validParameter.validFile(parameters, "group", false);
 342                         if (groupfile == "not found") { groupfile = "";  }
 343                         else {
 344                                 m->splitAtDash(groupfile, groupfileNames);
 345
 346                                 //go through files and make sure they are good, if not, then disregard them
 347                                 for (int i = 0; i < groupfileNames.size(); i++) {
 348                                         if (inputDir != "") {
 349                                                 string path = m->hasPath(groupfileNames[i]);
 350                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 351                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 352                                         }
 353                                         int ableToOpen;
 354
 355                                         ifstream in;
 356                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 357
 358                                         //if you can't open it, try default location
 359                                         if (ableToOpen == 1) {
 360                                                 if (m->getDefaultPath() != "") { //default path is set
 361                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 362                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 363                                                         ifstream in2;
 364                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 365                                                         in2.close();
 366                                                         groupfileNames[i] = tryPath;
 367                                                 }
 368                                         }
 369
 370                                         if (ableToOpen == 1) {
 371                                                 if (m->getOutputDir() != "") { //default path is set
 372                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 373                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 374                                                         ifstream in2;
 375                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 376                                                         in2.close();
 377                                                         groupfileNames[i] = tryPath;
 378                                                 }
 379                                         }
 380
 381                                         in.close();
 382
 383                                         if (ableToOpen == 1) {
 384                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 385                                                 //erase from file list
 386                                                 groupfileNames.erase(groupfileNames.begin()+i);
 387                                                 i--;
 388                                         }else {
 389                                                 m->setGroupFile(groupfileNames[i]);
 390                                         }
 391                                 }
 392                         }
 393
 394                         if (groupfile != "") {
 395                                 if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
 396                         }else {
 397                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 398                         }
 399
 400                         //check for optional parameter and set defaults
 401                         // ...at some point should added some additional type checking...
 402                         string temp;
 403                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 404                         m->mothurConvert(temp, kmerSize);
 405
 406                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 407                         m->setProcessors(temp);
 408                         m->mothurConvert(temp, processors);
 409
 410                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 411                         save = m->isTrue(temp);
 412                         rdb->save = save;
 413                         if (save) { //clear out old references
 414                                 rdb->clearMemory();
 415                         }
 416
 417                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 418                         templateFileName = validParameter.validFile(parameters, "reference", true);
 419                         if (templateFileName == "not found") {
 420                                 //check for saved reference sequences
 421                                 if (rdb->referenceSeqs.size() != 0) {
 422                                         templateFileName = "saved";
 423                                 }else {
 424                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
 425                                         m->mothurOutEndLine();
 426                                         abort = true;
 427                                 }
 428                         }else if (templateFileName == "not open") { abort = true; }
 429                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 430
 431                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 432                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 433                         if (taxonomyFileName == "not found") {
 434                                 //check for saved reference sequences
 435                                 if (rdb->wordGenusProb.size() != 0) {
 436                                         taxonomyFileName = "saved";
 437                                 }else {
 438                                         m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
 439                                         m->mothurOutEndLine();
 440                                         abort = true;
 441                                 }
 442                         }else if (taxonomyFileName == "not open") { abort = true; }
 443                         else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
 444
 445                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 446
 447                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 448
 449                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 450                         m->mothurConvert(temp, match);
 451
 452                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 453                         m->mothurConvert(temp, misMatch);
 454
 455                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 456                         m->mothurConvert(temp, gapOpen);
 457
 458                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 459                         m->mothurConvert(temp, gapExtend);
 460
 461                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 462                         m->mothurConvert(temp, numWanted);
 463
 464                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 465                         m->mothurConvert(temp, cutoff);
 466
 467                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 468                         probs = m->isTrue(temp);
 469
 470                         //temp = validParameter.validFile(parameters, "flip", false);                   if (temp == "not found"){       temp = "T";                             }
 471                         //flip = m->isTrue(temp);
 472                         flip = true;
 473
 474                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 475                         m->mothurConvert(temp, iters);
 476
 477
 478                         if ((method == "bayesian") && (search != "kmer"))  {
 479                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 480                                 search = "kmer";
 481                         }
 482
 483             if (!abort) {
 484                 if (namefileNames.size() == 0){
 485                     if (fastaFileNames.size() != 0) {
 486                         vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
 487                         parser.getNameFile(files);
 488                     }
 489                 }
 490             }
 491         }
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 495                 exit(1);
 496         }
 497 }
 498
 499 //**********************************************************************************************************************
 500 ClassifySeqsCommand::~ClassifySeqsCommand(){
 501         if (abort == false) {
 502                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 503         }
 504 }
 505 //**********************************************************************************************************************
 506
 507 int ClassifySeqsCommand::execute(){
 508         try {
 509                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 510
 511                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);             }
 512                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
 513                 else {
 514                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 515                         m->mothurOutEndLine();
 516                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);
 517                 }
 518
 519                 if (m->control_pressed) { delete classify; return 0; }
 520
 521                 for (int s = 0; s < fastaFileNames.size(); s++) {
 522
 523                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 524
 525                         string baseTName = taxonomyFileName;
 526                         if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy();  }
 527
 528             //set rippedTaxName to
 529                         string RippedTaxName = "";
 530             bool foundDot = false;
 531             for (int i = baseTName.length()-1; i >= 0; i--) {
 532                 if (foundDot && (baseTName[i] != '.')) {  RippedTaxName = baseTName[i] + RippedTaxName; }
 533                 else if (foundDot && (baseTName[i] == '.')) {  break; }
 534                 else if (!foundDot && (baseTName[i] == '.')) {  foundDot = true; }
 535             }
 536             if (RippedTaxName != "") { RippedTaxName +=  "."; }
 537
 538                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 539                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxonomy");
 540                         string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("accnos");
 541                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 542                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxsummary");
 543
 544                         if ((method == "knn") && (search == "distance")) {
 545                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("matchdist");
 546                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 547                         }
 548
 549                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 550                         outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
 551                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 552
 553                         int start = time(NULL);
 554                         int numFastaSeqs = 0;
 555                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 556
 557 #ifdef USE_MPI
 558                                 int pid, numSeqsPerProcessor;
 559                                 int tag = 2001;
 560                                 vector<unsigned long long> MPIPos;
 561
 562                                 MPI_Status status;
 563                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 564                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 565
 566                                 MPI_File inMPI;
 567                                 MPI_File outMPINewTax;
 568                                 MPI_File outMPITempTax;
 569                                 MPI_File outMPIAcc;
 570
 571                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 572                                 int inMode=MPI_MODE_RDONLY;
 573
 574                                 char outNewTax[1024];
 575                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 576
 577                                 char outTempTax[1024];
 578                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 579
 580                                 char outAcc[1024];
 581                                 strcpy(outAcc, newaccnosFile.c_str());
 582
 583                                 char inFileName[1024];
 584                                 strcpy(inFileName, fastaFileNames[s].c_str());
 585
 586                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 587                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 588                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 589                                 MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
 590
 591                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  delete classify;  return 0;  }
 592
 593                                 if (pid == 0) { //you are the root process
 594
 595                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 596
 597                                         //send file positions to all processes
 598                                         for(int i = 1; i < processors; i++) {
 599                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 600                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 601                                         }
 602
 603                                         //figure out how many sequences you have to align
 604                                         numSeqsPerProcessor = numFastaSeqs / processors;
 605                                         int startIndex =  pid * numSeqsPerProcessor;
 606                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 607
 608
 609                                         //align your part
 610                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 611
 612                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } delete classify; return 0;  }
 613
 614                                         for (int i = 1; i < processors; i++) {
 615                                                 int done;
 616                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 617                                         }
 618                                 }else{ //you are a child process
 619                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 620                                         MPIPos.resize(numFastaSeqs+1);
 621                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 622
 623                                         //figure out how many sequences you have to align
 624                                         numSeqsPerProcessor = numFastaSeqs / processors;
 625                                         int startIndex =  pid * numSeqsPerProcessor;
 626                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 627
 628
 629                                         //align your part
 630                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 631
 632                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);  MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 633
 634                                         int done = 0;
 635                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 636                                 }
 637
 638                                 //close files
 639                                 MPI_File_close(&inMPI);
 640                                 MPI_File_close(&outMPINewTax);
 641                                 MPI_File_close(&outMPITempTax);
 642                                 MPI_File_close(&outMPIAcc);
 643                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 644
 645 #else
 646
 647                         vector<unsigned long long> positions;
 648 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 649                         positions = m->divideFile(fastaFileNames[s], processors);
 650                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 651 #else
 652                         if (processors == 1) {
 653                                 lines.push_back(new linePair(0, 1000));
 654                         }else {
 655                                 positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
 656                 if (positions.size() < processors) { processors = positions.size(); }
 657
 658                                 //figure out how many sequences you have to process
 659                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 660                                 for (int i = 0; i < processors; i++) {
 661                                         int startIndex =  i * numSeqsPerProcessor;
 662                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 663                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 664                                 }
 665                         }
 666 #endif
 667                         if(processors == 1){
 668                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 669                         }else{
 670                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 671                         }
 672 #endif
 673
 674                         if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
 675
 676                 m->mothurOutEndLine();
 677                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 678                 start = time(NULL);
 679
 680
 681
 682                 #ifdef USE_MPI
 683                         if (pid == 0) {  //this part does not need to be paralellized
 684
 685                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 686                 #else
 687                         //read namefile
 688                         if(namefile != "") {
 689
 690                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 691                                 nameMap.clear(); //remove old names
 692                                 m->readNames(namefileNames[s], nameMap);
 693                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 694                         }
 695                 #endif
 696
 697                         string group = "";
 698                         if (groupfile != "") {  group = groupfileNames[s]; }
 699
 700                         PhyloSummary taxaSum(baseTName, group);
 701
 702                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 703
 704                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 705                         else {
 706                                 ifstream in;
 707                                 m->openInputFile(tempTaxonomyFile, in);
 708
 709                                 //read in users taxonomy file and add sequences to tree
 710                                 string name, taxon;
 711
 712                                 while(!in.eof()){
 713                                         in >> name >> taxon; m->gobble(in);
 714
 715                                         itNames = nameMap.find(name);
 716
 717                                         if (itNames == nameMap.end()) {
 718                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 719                                         }else{
 720                                                 for (int i = 0; i < itNames->second.size(); i++) {
 721                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 722                                                 }
 723                                                 itNames->second.clear();
 724                                                 nameMap.erase(itNames->first);
 725                                         }
 726                                 }
 727                                 in.close();
 728                         }
 729                         m->mothurRemove(tempTaxonomyFile);
 730
 731                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 732
 733                         //print summary file
 734                         ofstream outTaxTree;
 735                         m->openOutputFile(taxSummary, outTaxTree);
 736                         taxaSum.print(outTaxTree);
 737                         outTaxTree.close();
 738
 739                         //output taxonomy with the unclassified bins added
 740                         ifstream inTax;
 741                         m->openInputFile(newTaxonomyFile, inTax);
 742
 743                         ofstream outTax;
 744                         string unclass = newTaxonomyFile + ".unclass.temp";
 745                         m->openOutputFile(unclass, outTax);
 746
 747                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 748                         int maxLevel = taxaSum.getMaxLevel();
 749
 750                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 751                         string name, taxon;
 752                         while (!inTax.eof()) {
 753                                 if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } m->mothurRemove(unclass); delete classify; return 0; }
 754
 755                                 inTax >> name >> taxon; m->gobble(inTax);
 756
 757                                 string newTax = addUnclassifieds(taxon, maxLevel);
 758
 759                                 outTax << name << '\t' << newTax << endl;
 760                         }
 761                         inTax.close();
 762                         outTax.close();
 763
 764                         m->mothurRemove(newTaxonomyFile);
 765                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 766
 767                         m->mothurOutEndLine();
 768                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 769
 770                         #ifdef USE_MPI
 771                                 }
 772                         #endif
 773
 774                         m->mothurOutEndLine();
 775                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 776                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 777                         m->mothurOutEndLine();
 778                 }
 779
 780                 //set taxonomy file as new current taxonomyfile
 781                 string current = "";
 782                 itTypes = outputTypes.find("taxonomy");
 783                 if (itTypes != outputTypes.end()) {
 784                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 785                 }
 786
 787                 current = "";
 788                 itTypes = outputTypes.find("accnos");
 789                 if (itTypes != outputTypes.end()) {
 790                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 791                 }
 792
 793                 delete classify;
 794
 795                 return 0;
 796         }
 797         catch(exception& e) {
 798                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 799                 exit(1);
 800         }
 801 }
 802
 803 /**************************************************************************************************/
 804 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 805         try{
 806                 string newTax, taxon;
 807                 int level = 0;
 808
 809                 //keep what you have counting the levels
 810                 while (tax.find_first_of(';') != -1) {
 811                         //get taxon
 812                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 813                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 814                         newTax += taxon;
 815                         level++;
 816                 }
 817
 818                 //add "unclassified" until you reach maxLevel
 819                 while (level < maxlevel) {
 820                         newTax += "unclassified;";
 821                         level++;
 822                 }
 823
 824                 return newTax;
 825         }
 826         catch(exception& e) {
 827                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 828                 exit(1);
 829         }
 830 }
 831
 832 /**************************************************************************************************/
 833
 834 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
 835         try {
 836
 837                 int num = 0;
 838                 processIDS.clear();
 839
 840 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 841                 int process = 1;
 842
 843                 //loop through and create all the processes you want
 844                 while (process != processors) {
 845                         int pid = fork();
 846
 847                         if (pid > 0) {
 848                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 849                                 process++;
 850                         }else if (pid == 0){
 851                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
 852
 853                                 //pass numSeqs to parent
 854                                 ofstream out;
 855                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 856                                 m->openOutputFile(tempFile, out);
 857                                 out << num << endl;
 858                                 out.close();
 859
 860                                 exit(0);
 861                         }else {
 862                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 863                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 864                                 exit(0);
 865                         }
 866                 }
 867
 868                 //parent does its part
 869                 num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
 870
 871                 //force parent to wait until all the processes are done
 872                 for (int i=0;i<processIDS.size();i++) {
 873                         int temp = processIDS[i];
 874                         wait(&temp);
 875                 }
 876
 877                 for (int i = 0; i < processIDS.size(); i++) {
 878                         ifstream in;
 879                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 880                         m->openInputFile(tempFile, in);
 881                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 882                         in.close(); m->mothurRemove(m->getFullPathName(tempFile));
 883                 }
 884 #else
 885                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 886                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 887                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 888                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 889
 890                 vector<classifyData*> pDataArray;
 891                 DWORD   dwThreadIdArray[processors-1];
 892                 HANDLE  hThreadArray[processors-1];
 893
 894                 //Create processor worker threads.
 895                 for( int i=0; i<processors-1; i++ ){
 896                         // Allocate memory for thread data.
 897                         string extension = "";
 898                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 899
 900                         classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip);
 901                         pDataArray.push_back(tempclass);
 902
 903                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 904                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 905                         hThreadArray[i] = CreateThread(NULL, 0, MyClassThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 906
 907                 }
 908
 909                 //parent does its part
 910                 num = driver(lines[processors-1], taxFileName + toString(processors-1) + ".temp", tempTaxFile + toString(processors-1) + ".temp", accnos + toString(processors-1) + ".temp", filename);
 911                 processIDS.push_back((processors-1));
 912
 913                 //Wait until all threads have terminated.
 914                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 915
 916                 //Close all thread handles and free memory allocations.
 917                 for(int i=0; i < pDataArray.size(); i++){
 918                         num += pDataArray[i]->count;
 919                         CloseHandle(hThreadArray[i]);
 920                         delete pDataArray[i];
 921                 }
 922
 923         #endif
 924         vector<string> nonBlankAccnosFiles;
 925                 if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
 926                 else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
 927
 928                 for(int i=0;i<processIDS.size();i++){
 929                         m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 930                         m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 931             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
 932                                 nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
 933                         }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
 934
 935                         m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
 936                         m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
 937                 }
 938
 939         //append accnos files
 940                 if (nonBlankAccnosFiles.size() != 0) {
 941                         rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
 942
 943                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 944                                 m->appendFiles(nonBlankAccnosFiles[h], accnos);
 945                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 946                         }
 947                 }else { //recreate the accnosfile if needed
 948                         ofstream out;
 949                         m->openOutputFile(accnos, out);
 950                         out.close();
 951                 }
 952
 953                 return num;
 954
 955         }
 956         catch(exception& e) {
 957                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 958                 exit(1);
 959         }
 960 }
 961 //**********************************************************************************************************************
 962
 963 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
 964         try {
 965                 ofstream outTax;
 966                 m->openOutputFile(taxFName, outTax);
 967
 968                 ofstream outTaxSimple;
 969                 m->openOutputFile(tempTFName, outTaxSimple);
 970
 971                 ofstream outAcc;
 972                 m->openOutputFile(accnos, outAcc);
 973
 974                 ifstream inFASTA;
 975                 m->openInputFile(filename, inFASTA);
 976
 977                 string taxonomy;
 978
 979                 inFASTA.seekg(filePos->start);
 980
 981                 bool done = false;
 982                 int count = 0;
 983
 984                 while (!done) {
 985                         if (m->control_pressed) {
 986                                 inFASTA.close();
 987                                 outTax.close();
 988                                 outTaxSimple.close();
 989                                 outAcc.close(); return 0; }
 990
 991                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
 992
 993                         if (candidateSeq->getName() != "") {
 994
 995                                 taxonomy = classify->getTaxonomy(candidateSeq);
 996
 997                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 998
 999                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1000
1001                                 //output confidence scores or not
1002                                 if (probs) {
1003                                         outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
1004                                 }else{
1005                                         outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1006                                 }
1007
1008                                 if (classify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
1009
1010                                 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1011
1012                                 count++;
1013                         }
1014                         delete candidateSeq;
1015
1016                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1017                                 unsigned long long pos = inFASTA.tellg();
1018                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1019                         #else
1020                                 if (inFASTA.eof()) { break; }
1021                         #endif
1022
1023                         //report progress
1024                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1025
1026                 }
1027                 //report progress
1028                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1029
1030                 inFASTA.close();
1031                 outTax.close();
1032                 outTaxSimple.close();
1033                 outAcc.close();
1034
1035                 return count;
1036         }
1037         catch(exception& e) {
1038                 m->errorOut(e, "ClassifySeqsCommand", "driver");
1039                 exit(1);
1040         }
1041 }
1042 //**********************************************************************************************************************
1043 #ifdef USE_MPI
1044 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, MPI_File& accFile, vector<unsigned long long>& MPIPos){
1045         try {
1046                 MPI_Status statusNew;
1047                 MPI_Status statusTemp;
1048                 MPI_Status statusAcc;
1049                 MPI_Status status;
1050
1051                 int pid;
1052                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1053
1054                 string taxonomy;
1055                 string outputString;
1056
1057                 for(int i=0;i<num;i++){
1058
1059                         if (m->control_pressed) { return 0; }
1060
1061                         //read next sequence
1062                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1063                         char* buf4 = new char[length];
1064                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1065
1066                         string tempBuf = buf4;
1067                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1068                         istringstream iss (tempBuf,istringstream::in);
1069                         delete buf4;
1070
1071                         Sequence* candidateSeq = new Sequence(iss);
1072
1073                         if (candidateSeq->getName() != "") {
1074                                 taxonomy = classify->getTaxonomy(candidateSeq);
1075
1076                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1077
1078                                 //output confidence scores or not
1079                                 if (probs) {
1080                                         outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
1081                                 }else{
1082                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1083                                 }
1084
1085                                 int length = outputString.length();
1086                                 char* buf2 = new char[length];
1087                                 memcpy(buf2, outputString.c_str(), length);
1088
1089                                 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
1090                                 delete buf2;
1091
1092                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1093                                 length = outputString.length();
1094                                 char* buf = new char[length];
1095                                 memcpy(buf, outputString.c_str(), length);
1096
1097                                 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
1098                                 delete buf;
1099
1100                                 if (classify->getFlipped()) {
1101                                         outputString =  candidateSeq->getName() + "\n";
1102                                         length = outputString.length();
1103                                         char* buf3 = new char[length];
1104                                         memcpy(buf3, outputString.c_str(), length);
1105
1106                                         MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
1107                                         delete buf3;
1108                                 }
1109
1110                         }
1111                         delete candidateSeq;
1112
1113                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
1114                 }
1115
1116                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
1117
1118
1119                 return 1;
1120         }
1121         catch(exception& e) {
1122                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
1123                 exit(1);
1124         }
1125 }
1126
1127 //**********************************************************************************************************************
1128 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
1129         try {
1130
1131                 nameMap.clear(); //remove old names
1132
1133                 MPI_File inMPI;
1134                 MPI_Offset size;
1135                 MPI_Status status;
1136
1137                 //char* inFileName = new char[nameFilename.length()];
1138                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1139
1140                 char inFileName[1024];
1141                 strcpy(inFileName, nameFilename.c_str());
1142
1143                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1144                 MPI_File_get_size(inMPI, &size);
1145                 //delete inFileName;
1146
1147                 char* buffer = new char[size];
1148                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1149
1150                 string tempBuf = buffer;
1151                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1152                 istringstream iss (tempBuf,istringstream::in);
1153                 delete buffer;
1154
1155                 string firstCol, secondCol;
1156                 while(!iss.eof()) {
1157                         iss >> firstCol >> secondCol; m->gobble(iss);
1158
1159                         vector<string> temp;
1160                         m->splitAtComma(secondCol, temp);
1161
1162                         nameMap[firstCol] = temp;
1163                 }
1164
1165                 MPI_File_close(&inMPI);
1166
1167                 return 1;
1168         }
1169         catch(exception& e) {
1170                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1171                 exit(1);
1172         }
1173 }
1174 #endif
1175 /**************************************************************************************************/