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